NGS in Clinical Research: Meet the NGS Experts Series Part 1

63
Qiagen Webinar – January 19, 2016 Birgit Funke, PhD, FACMG Associate Professor of Pathology, Harvard Medical School Director Clinical R&D; Laboratory for Molecular Medicine http://www.nature.com/nrg/journal/v11/n1/images/nrg2626-f2.jpg 1 NGS IN THE CLINIC A review of its impact on test development, operations and result reporting

Transcript of NGS in Clinical Research: Meet the NGS Experts Series Part 1

Slide 1

Qiagen Webinar January 19, 2016Birgit Funke, PhD, FACMGAssociate Professor of Pathology, Harvard Medical SchoolDirector Clinical R&D; Laboratory for Molecular Medicine

http://www.nature.com/nrg/journal/v11/n1/images/nrg2626-f2.jpg1NGS IN THE CLINICA review of its impact on test development, operations and result reporting

WHAT WILL BE COVEREDHow is NGS used in the clinic today Focus on inherited disorders

Bringing NGS in house: Clinical development and validationThe role of bioinformatics

What NGS does not do wellTechnical limitations

Time permitting: Real world challenges (case example)

Clinical NGS is being implemented in an increasing number of labsMajority focus on gene panelsImplementation of exome/genome sequencing quickly increasingNGS(research)THE DISRUPTIVE NATURE OF NGS

NGS(clinical)

Start with a couple of slides to set the stageMost of you have likely seen this slide already showing the rapid decline of NGs cost (here shown per genome)This started in 2005 NGS made its first appearance in the research realmOnly 4 years later the first clinical labs began implementing it5

DETECTION RATE OVER TIMEDCM

2007: ~10%2011: ~37%NGS

Here is what makes NGS to attractive describe FigureIncrease # genes detection rate goes upScale makes this difficult to se DCM: quadrupled our diagnostic detection rat (ie # patients that get a positive report)6

WHICH DISORDERS BENEFIT FROM NGS TESTING?

This seems like a good thing (though Ill get into some caveats later)Question becomes: Is this type of test useful for all disorders and if not which ones is it useful for and why7

Collective incidence: > 1/500

Can lead to SCD

Substantial genetic component

Incentive for predictive testing

ARVCDCMLVNCHCMRCMOTHER (RARE)1:500> 1:2,5001:1,000 - 1:5,000EXAMPLE: INHERITED CARDIOMYOPATHIES

Best discussed using a prominent example my personal clinical focus

Locus heterogeneity - 1 disease / many genes

Allelic heterogeneity - many disease causing variants/gene

Spectrum of pathogenic variation - not yet well understood

Phenotypic overlap - can complicate testing process

DISEASE CHARACTERISTICS

And here are some challenges that get us to why NGS panels are helpful9

DCM

TTNLMNAMYH7DSPTNNT2

MYH734%

MYBPC350%Ahmed AlfaresMelissa KellyHCM

LOCUS HETEROGENEITY

R502WW792fsR663H927-9G>AMYBPC3MYBPC3MYH7# of Variants

MYBPC3E258K

63% of variants have been seen only once

Courtesy of Ahmed Alfares and Heidi RehmNeed to sequence entire coding sequence of many genes for maximum clinical sensitivity# of ProbandsHypertrophic Cardiomyopathy: 10 years 11 genes testedALLELIC HETEROGENEITY

After a decade of testing most variants are still novel..11

CLINICAL HETEROGENEITY

3

+

3

+++

Proband with clinical Dx + family history of DCM

DCM gene panel detects a variant of uncertain significance

Variant did not segregateTraditional genetic testing : 1 gene panel for each diagnosis

Moving on to clinical heterogeneityTraditional testing algorithm: order a test that is configured for the disease the physician diagnosed clinically12

3

+

3

+++

++++_

Patient was seen again , diagnosis was revised to ARVC

ARVC panel identified a likely pathogenic variant

PREVENTING DIAGNOSTIC ODYSSEYSTraditional testing (disease centric) does not make sense for disorders with clinical and genetic overlap

HCMDCMARVC

MULTI-CARDIOMYOPATHY TESTHCM testDCM testARVC test~3% of DCM patients carry a pathogenic variant in an ARVC geneMULTI-DISEASE GENE PANELS

GeneReviews (2012): 80-90% of patients with Costello syndrome carry a mutation in HRAS.MULTI DISEASE GENE PANELS IMPROVE CLINCAL DIAGNOSIS

(n=23)LMM broad referral population data:

Most patients would have received a NEGATIVE report if only HRAS had been tested

15

Phenotypic expansionOriginal clinical definition based on most severe casesOften too narrow, full range of clinical variability emerges over time

Phenotypic overlapDisorders present the same -> diagnostic errorHappens more often as genetic testing is moving out of specialty clinics to more general (genetics) care

Now widely recognizedMany physicians are beginning to change workflow

MULTI DISEASE GENE PANELS IMPROVE CLINCAL DIAGNOSIS

ClinicalDiagnosissequence first

Patient

ClinicalDiagnosis

Hypothesis

GeneticTest

negative

InterpretationResult

Sequence VariantsFill in failed Confirm variantsTHE CHANGING GENOMIC TESTING WORKFLOWSEQUENCE FIRST

I have a unique combination of responsibilitiesDirect clinical test development (brought on NGS in 2011)Also Board certified and oversee clinical testing for inherited cardiovascular disordersI am deeply involved in all aspects of NGS testingTrying to accomplish 2 thingsGive an overview of the entire NGS testing process including result interpretation and reportingDiscuss what our community needs to improve and develop to improve this testing process and promote standardization17

THE CURRENT DEBATE: PANELS OR EXOME?

Complex phenotypes / diagnostic odysseys

Clinically well defined cases

GENE PANELS10s 100s of genesHigh coverageCompleteness

EXOME22,000 genes

GENOMEExome +IntergenicMed-Low coverageCompleteness 50%)Growing appreciation of phenotypic expansion argument for hypothesis fee testingAdditional tests often end up being more expensive than WESAlways up to date (accelerating pace of gene discovery)Easier to maintain for labs than growing # of gene panelsINCENTIVES

BARRIERSCost (though gap is closing)Incomplete coverage (suboptimal design)RISK Loss of intimate /a priori knowledge on tested genesBARRIERS

20

COMMUNITY EFFORTS TO DEVELOP STANDARDS

ClinGenUnite medical genetics community by developing approaches to curate, centralize and share genetic data

ACMG + AMP (2015)New guideline for clinical grade variant classification (Mendelian disorders)

Traditionally not needed because old tests contained only well established disease genesMany published claims for a gene-disease relationship do not withstand the rigor of clinical grade curationMost novel variants in genes that are not strongly linked with disease cannot be interpretedNEW! ASSESSMENT OF GENE-DISEASE RELATIONSHIPS

Definitive evidence

Strong evidence

Moderate evidence

Limited evidence

Disputed / no evidenceExome/GenomePredictive Tests, Incidental Findings

Diagnostic Panels

Research

Courtesy of ClinGen (Heidi Rehm)USING CLINICAL VALIDITY TO CONFIGURE TESTS

Using this clinical validity framework we can then adequately configure the appropriate contents for different testsFor example predictive genetic tests should only contain genes with definitive or strong evidence for an association with diseaseWhereas exome or genome testing will include genes with limited evidence23

CLINICAL TEST DEVELOPMENT AND VALIDATION

(NGS)

DEVELOPMENT AND VALIDATION OF AN (NGS) TEST

DESIGNTEST DESIGN

http://www.cdc.gov/genomics/gtesting/ACCE/

LIBRARY PREPCAPTURESEQANALYSIS

OPTIMIZATIONTest each stepString togetherOptimizeLock down protocol

VALIDATIONTest analytical performance using locked down protocol

2525Shown here are the 3 main stages of NGS test development (actually any test development)design, optimization, validationIve included a very high level description of what that entails

The most important step in my mind is test designdont have to explain to this audience that there are a ton of things that need to be consideredWell summarized in the ACCE wheel

Optimization, validation

Content

Technology

DESIGN - A THREE DIMENSIONAL EXERCISEGene selectionClinical validity

Gene characteristicsHomology, High GC/AT?Pathogenic variant typesMosaicism?Sequencercapacity/lnRead lengthBioinformatics pipelineSNVIndelCNVSVOperationalTarget size# samples/laneSample volume received Test cost, TATDiagnostic% gene unsequenceableDifficult variants prevalentAbility to detect low AFSupplemental assay/s when:NGS suboptimal but gene or variant type essentialValidation (reference) samplesSpecimen typesVariant TypesReference material sourcesFill-in + confirmation strategy (Sanger)X=Techn. Reality CheckClinical Reality Check Development + validation plan

Consult domain expertsDifficult gene critical?Alternate assays offered elsewhereRequired analytical sensitivity*?Required completeness* TP/TP+FN

Going one level deeper it turns into somewhat of a 3-dimensional exerciseWhat Id like to get across is how technical and clinical considerations are inter-twined

26

THERE IS NO ONE SIZE FITS ALLRenal Panel(PKD1)Hearing Loss Panel(STRC)Essential gene (detection rate)YES (85%)YES (10%)Sequenceable via NGSHighly homologous (partial)Highly homologous (entire gene)Pathogenic variant spectrumSNVs, indels >>CNVsCNVs >>SNVs, indelsWell sequenced geneYESNOClinical specificityHIGHLOWKeep on panelNO - alternate test for ADPKDYESSupplemental assayN/ALR-PCR x 2Operational factorsN/AHigh failure LR-PCR #1 DROPImpact on performance metricN/AReduced analytical sensitivity - OK

Two difficult to sequence genes two solutions* (Laboratory for Molecular Medicine)

Two very different solutions

Both present similar challenge

So we were asked to discuss what types of standards one should apply In my opinion there is no one size fits allAnd here is an example that hopefully illustrates thatI am using 2 difficult to sequence genes (STRC which causes hearing loss and PKD1, which causes ADPKD)for which we ended up developing 2 very different solutionsAt the surface the problem is the sameBoth are essential genesBoth have homology issuesBoth have a diverse variant spectrumThough the details vary a bitButSTRC is poorly sequenced (because of the homology issuesThe clinical specificity is rather low so you

Double check- In line with White Paper?STRC: no clinical CNV assay offered?PKD1: http://www.sciencedirect.com/science/article/pii/S0925443911000512: large deletions only 3%

27

TEST DEVELOPMENT/OPTIMIZATION

DESIGNSelect test contentsCharacterize contentsClinical needsTechnical limitationsSupplemental assays?Fill-in and variant confirmation ?Establish development + validation plan

LIBRARY PREPCAPTURESEQANALYSIS

OPTIMIZATIONTest each stepString togetherOptimize if need beLock down protocolDevelop Q/C stops

VALIDATIONTest analytical performance using locked down protocol

Moving on to optimization- At a high level we28

SECONDARYANALYSISTERTIARYANALYSIS

ANNOTATIONPRIORITIZATIONFILTRATIONCLASSIFICATIONCLINICAL REPORT

FASTQNGS RUNBASE CALLINGALIGNMENTVARIANT CALLINGBAMVCFDEMULTIPLEXING

PRIMARY ANALYSISoutput filesSometimes on the Sequencer (newer machines, e.g. MiSeq)

Trend is to add more functionality to the sequencerbioinformatics pipeline

THE ROLE OF BIOINFORMATICS (not just for NGS)

ResearchClinicalDevClinical Ops

Bioinformatics

IT

3030

BIOINFORMATICS STAFF (Partners Personalized Medicine)20082009201020112013

Bioinformatics FTEsNGS work started201420121st NGSpanelMolecular Dx Lab + Translational Genomics Core

COMMONLY USED DATA ANALYSIS FILTERSSecondary AnalysisCoverage (read depth)Strand biasMapping quality (confidence in location of read)Allelic fraction (% reads containing variant)Quality by depthTertiary AnalysisVariant frequency in control cohorts

Courtesy of Karl VoelkerdingIn theory, a heterozygous variant is present in 50% of the readsIn reality, this is not always the case (range can be broad)To be confident to identify variants with a range of allelic fractions (e.g. >20%): Need ~20x coverage to be 99% confident to detect variant alleleFor details see: Schrijver 2012, J. Mol. Diagn. 14COVERAGE : HOW MUCH IS ENOUGH?Red = reads containing a variant call

Example LMM (germline) 46 genes (~250 kb)Very high average coverage (300-400x)>97% of bases >20x

Need to sequence at high coverage to maximize completeness

3% C[SB= -10.01]TTN_EX45Ac.15318T>C[SB= -146.03]TTN_EX157c.31861A>G[SB= -855.52]LMNA_EX10c.*4C>T[SB= -106.6]TAZ_EX10c.718G>C[SB= -3536.45]TTN_EX37c.8887A>C[SB= 8.04]TTN_EX37c.8887A>C[SB= 14.07]TTN_EX37c.8887A>C[SB= 17.08]HOMHET

203 samples; n=1455 variants: NGS + Sanger

TRUE POSFALSE POSANALYSIS THRESHOLDS ALLELIC FRACTIONNeed large truth setsUntil recently there was none labs could obtain pre-test developmentData shown here generated from launching NGS pipeline w/o any threshold (2011) very high overhead for confirmatory testing till truth set established via Sanger confirmationNow have some community resources: NISTs NA12878 high confidence regions

Determining the assays accuracy is a big part of clinical validation (will talk about next), but one typically does some of it already during the development phaseDont have this early data to show. This the result of 203 samples processed after we had launched our first NGS test Since we do confirm variant calls via Sanger we know whether they were TP or FPY axis = allelic fraction, coverage to the rightHomHet around 50%You will notice that the FPs all fall in the low allelic fraction rangeWhen we launched this test we did not filter any of the variants out was a significant burdenBut after about a year we implemented a filtration threshold Toady more resources available, can get access to well sequenced samples and establish this kind of analysis early on

ALLELIC FRACTION THRESHOLDS SNVs + IN/DELS

See also: Allhoff et al. BMC Bioinformatics 2013 14 (Suppl 5):S1 doi:10.1186/1471-2105-14-S5-S1

READ 1READ 2

A T C C G T G G A T T T C G T T A C A C G T TTTTTTSTRAND BIAS

ANALYSIS THRESHOLDS QUALITY BY DEPTH

Assessment of NGS calling thresholds during test validation. FSB = Fishers Strand Bias, QD = quality by depth. Dotted lines are thresholds chosen for operations. Filtered out true positives (blue dots) were all part of difficult sequence contexts (3 out of 4 = highly homologous regions) and led to modifications (e.g. manual review of the CFTR intron 9 in IGV to accurately assess status of the Poly T/TG tract) 38

QUALITY CONTROL STEPS

Q/C Approach?Individual steps? End-to-end? Both is best!End-to-end critical measuresCompletenessAccuracy

Part of this process includes developing quality control stops and pass/fail criteriaShown here is the entire NGS testing process starting with extraction and ending with interpretation and reportingIndicated some commonly used Q/C measuresThe lab decides on the overall Q/C approachEach step?EtcI will point out that as long as the end to end performance q/c is done right the intermediate steps become more an operational toolDetect failures earlySave cost

39

Difficult to prescribe standard reduced quality at this step can be acceptable depending on the overall test design (fill in, confirmation)EXAMPLE Q/C STEPS - CLUSTER DENSITY (HiSeq)

One example of a commonly used Q/C measureCluster densityRaw clusters + those that pass filter are shown for each of the 8 lanesLeft: OK cluster densityRight: too high lead to a much lower number of clusters that passedIt is important to get this rightToo lowToo highBut can one standardize the perofrmance??40

Laboratory for Molecular Medicine 2013, unpublished data (HiSeq2000, 50b PE)When initial performance assessment reveals high FP rate one needs to plan for orthogonal confirmationDETERMINE NEED FOR ORTHOGONAL CONFIRMATION OF VARIANTSToday, NGS is deemed of high enough accuracy for SNVs such that confirmation may not needed

TEST VALIDATION

DESIGNSelect test contentsCharacterize contentsClinical needsTechnical limitationsSupplemental assays?Fill-in and variant confirmation ?Establish development + validation plan

LIBRARY PREPCAPTURESEQANALYSIS

DEVELOPMENTTest each stepString togetherOptimizeLock down protocol

VALIDATIONTest analytical performance using locked down protocol

4242Finally the test is optimized and we proceed to clinical validation

Genetic testing traditionally synonymous with genotyping (assessing whether known pathogenic variants are present)Sequencing based tests predominantly used to screen the entire coding sequence enables novel variant detectionCore issuesCannot validate every theoretically possible variantThe NGS testing process is highly complex (many steps)Increased requirement for bioinformatic processingKnowledge required for interpretation does not scale proportionally

WHY IS NGS DIFFERENT?These issues are not entirely new but are an order of magnitude worse compared to traditional methods (e.g. Sanger sequencing)NGS pushed us over the edge - catalyzed awareness and a push for novel approaches and standards

See also: Mattocks 2010: Eur J Hum Genet 18:1276CDC MMWR 2009 Vol 58 (www.cdc.gov/mmwr)Jennings 2009 Arch Pathol Lab Med.133:743755DESCRIPTION EXAMPLESENSSPECACCPRECLODQuantitative Test Result can have any value between 2 limits)Heteroplasmy of mitochondrial variantsQualitative TestTrue quantitative signal can only have one of two possible valuesSequencing (WT or variant allele)

Different approaches depending on type of testSens:SensitivitySpec:SpecificityAcc:AccuracyPrec:PrecisionLOD:Limit of DetectionANALYTICAL PERFORMANCE METRICS

Following slides selected 2 metrics44

Base line (methods-based approach)Maximize # of variants tested to achieve high statistical confidence Pathogenicity doesnt matterDetermine separately by variant type (SNV, indel, CNV)Critical importance of confidence interval!!

Disease/gene specific add-onsTest samples with common disease causing mutationsExample: validate the mutations present on the ACMG 23 panel for CF if NGS test covers CFTRANALYTICAL SENSITIVITY

DefinitionAbility to return a negative result when no variant is presentReflects frequency of false positives: TN / TN + FPCommon practice count WT bases correctly identified as WT20 kb sequenced: 5 FP 19995 true negativesSpecificity = 19995 / 20000 = 99.98%

Not very useful other metrics are more meaningfulTechnical Positive Predictive Value (likelihood that a variant call is FP): TP/ TP + FPNumber of FPs per TEST Particularly important if lab doesnt confirm variants!ANALYTICAL SPECIFICITY

Well character. gene+ n samples (e.g. frequent pathogenic variants)In/del rich gene+ n samplesMosaicism+ n samplesTIER 2: DISEASE/GENE SPECIFIC CONSIDERATIONS

CNV rich gene+ n samples

Test 1(100 genes)

NA12878Test 2(70 genes)Test 3(30 genes)Test 4(200genes)Variants600300100800Analytical sensitivity (+CI)(=TP/TP+FN)

TIER 1: BASE LINE (METHODS BASED, CUMULATIVE)VALIDATION LAYERS EXAMPLE: ANALYTICAL SENSITIVITY

Need for more reference materials!

There are really 2 layers of validationWhat I call base line validationThis is methods based, so one can add up results across different tests as long as the protocol is the sameThe emphasis is on maximizing the number of variants that are tested Goal is to derive a base line sensitivity with a confidence interval that is as tight as possible

The community is starting to create great reference materials for thisYou all know NISTs high quality variant call set for NA12878

But then there are disease or gene specific considerations that may need to be taken into accountFor a well characterized gene one may want to add refernece samples that carry.etc47

c.3628-41_3628-17del (outside region interpreted by many labs)MAF = 4-8% in SE AsiaHet: Mild/late onset HCM (high lifetime penetrance) OR ~6Hom: Severe and early onset disease, often Heart FailureDhandapany et al. Nat Genet. 2009. 41(2):187-9125 bp deletion (intron 32, MYBPC3)

4848

WHAT NGS DOES NOT DO WELL CURRENT NGS LIMIATIONS

NGS HAS PROBLEMS WITHRegions of high homologyRepeat expansionsLarge in/dels, CNVs and other structural variantsLESS PROBLEMATIC FOR GENE PANELSTesting labs typically have clinical domain expertiseContents typically highly curated + well understoodAdd-on tests typically available for difficult genesKNOWLEDGE DOES NOT SCALE EASILYSequencing understanding

http://www.trizic.com/the-devil-is-in-the-details-how-prepared-are-you-for-a-presence-exam/THE DEVIL IS IN THE DETAILS

SEQUENCING GENES WITH HOMOLOGY1

100% identical incl. introns

29STRC (nonsyndromic hearing loss)99.6% identical across cds (98.9% incl. introns)First half of gene 100% identical (incl. introns)Mandelker 2014, J. Mol. Diagn.

maps to pseudogene

STRC: 10% of recessive nonsyndromic hearing lossCYP21A2: Nearly all of congenital adrenal hyperplasiaVWF: Von Willebrandts disease (common coagulopathy)PMS2: Colorectal CA (on ACMG Incidental Findings gene list)Diana Mandelker, Himanshu Sharma, Mark BowserExome wide clinical grade resource to be shared via Get-RM (in progress)

NGS IN THE CLINIC

REAL WORLD CHALLENGES

A WORD OF CAUTION

THE NGS PROCESS IS HIGHLY COMPLEX

EVEN THE BEST INFORMATICS AND Q/C MEASURES DO NOT REPLACE A CRITICAL MIND

WATCH OUT FOR RESULTS THAT DONT MAKE SENSE

CASE EXAMPLE9 year old boy with suspected Noonan syndrome

TEST ORDEREDNoonan Spectrum Panel (12 genes tested via NGS)NEGATIVE

FAMILY HISTORY REVISITED

some featuresPhysician ordered whole exomePathogenic missense variant in SOS1Gene WAS covered by our testWhat went wrong?Variant in untested region of SOS1 or variant type not detectable?Technical false negative?.at this point the lab director received an unpleasant email

SOS1 Thr734Pro: strand bias = 97.48Highest strand bias observed in technical validation = 1.78Used threshold of 20 since

DIGGING IN THE TRASH.

FILTERED (REMOVED FROM ANALYSIS) SECTION

TEST LIMITATIONS IN CLINICAL PRACTICE100% sensitive for SNVsCI = 99.3-100%

Technical false negatives will happen

LMMHeidi RehmMatt LeboSami AmrHeather McLaughlinHeather Mason-SuaresJun ShenOperationsLisa MahantaRobin Hill CookLaura HutchinsonShangtao LiuAshley FrisellaTimothy FioreJiyeon KimMaya MiatkowskiWilliam CamaraEli PasackowIT TeamSandy AronsonNatalie BoutinAll team membersLeadership and FacultyScott WeissMeini Sumbada-ShinRobert GreenImmaculata deVivoMason FreemanJohn IafrateMira IronsIsaac KohaneRaju KucherlapatiCynthia MortonSoumya RaychaudhuriPatrick SlussTransl. Genomics CoreSami AmrAll team membersBioinformaticsMatt LeboRimma ShakhbatyanJason EvansHimanshu SharmaPeter RossettiEllen TsaiChet GrahamDevelopmentBirgit FunkeBeth Duffy-HynesMark BowserDiana MandelkerFellowsOzge BirsoyYan MengAhmad A. TayounJillian BuchanFahad HakamiHana ZoukGenetic CounselorsAmy LoveletteMelissa KellyMitch DillonShana WhiteAndrea MuirheadDanielle MettervilleACKNOWLEDGMENTSMarketingPriscilla CepedaOfficePeta-Gaye BrooksKim OBrienLauren SalviatiCharlotte MaillyCassandra NovickClinGen leadership and cardiovascular domain working group

THANKS!

61

Title, Location, Date63

Chart141589411712885232240020011100000000010001

# of Variants

Charts

Charts41589411712885232240020011100000000010001

# of Variants

Statistics415894117128852322414152171811122232425262728293013233341

# of Variants# of Families# of Variants

Sheet1# of Families# of Variants% of TotalPath/LPVUSBenign/LBOther*Total Non-MYBPC3 MutationsTotal Non-MYBPC3 Missense Mutations141567.48%MYBPC31677269All Non_Inc36131528914.47%Missense555517All_Path2382123416.67%In-Frame InDel500All_VUS1231034172.76%Frameshift43005121.95%Nonsense2800681.30%Extension100781.30%Intronic3515660MYBPC3 Non-Truncating850.81%Silent0246106MYBPC3 Truncating920.33%MYH712154831030.49%Missense116462206Other Sarcomere Non-Truncating1120.33%In-Frame InDel5007Other Sarcomere Truncating1220.33%Frameshift0101340.65%Nonsense0000LAMP2 Non-Truncating1400.00%Intronic06611LAMP2 Truncating1500.00%Silent01751620.33%MYL217797PRKAG2 Non-Truncating1700.00%Missense15700PRKAG2 Truncating1800.00%In-Frame InDel0001910.16%Frameshift1006GLA Non-Truncating2010.16%Nonsense1001GLA Truncating2110.16%Intronic0032200.00%Silent0062300.00%MYL38542400.00%Missense8502500.00%In-Frame InDel0002600.00%Frameshift0002700.00%Nonsense0002800.00%Intronic0012900.00%Silent0033000.00%PRKAG2711273110.16%Missense7943200.00%In-Frame InDel0003300.00%Frameshift0103400.00%Nonsense0003510.16%Intronic014615Silent001910 or more18TNNI326415Missense2332In-Frame InDel100# of Families# of VariantsFrameshift0001415Nonsense000289Start Codon100341Intronic114417Silent009512TNNT225121668Missense206178In-Frame InDel20085Frameshift00092Nonsense100103Intronic255112Silent009122TPM1121213134Missense1211014In-Frame InDel00015Frameshift000162Nonsense00017Intronic01418Silent009191ACTC4412201Missense440211In-Frame InDel00022Frameshift00023Nonsense00024Intronic00125Silent001026GLA77827Missense67028In-Frame InDel00029Frameshift00030Nonsense000311Intronic10332Silent00533LAMP2117934Missense152351In-Frame InDel000Frameshift200Nonsense400Intronic420Silent007Total405195265Total Non-MYBPC3 MutationsTotal Non-MYBPC3 Missense Mutations414nonreported variants8651279

ExclusionsNEED TO UPDATE AND MAKE SURE ALL VARIANTS ARE CLASSIFIED CORRECTLY - DONE 12/27/10IS_PATH+IS_VUS+IS_BENIGN +GENEDNAAAREGIONCAT_DISRPTFAMDNA_TYPEAA_TYPEFREQALIASESSOURCEDBSNPREFSINTERPRETATION_TEXTCOUNTIS_PATHIS_VUSIS_BENIGNIS_MISSENSEIS_INTRONICIS_NONSENSEIS_FRAMESHIFTIS_IN_FRAME_INDELIS_START_CODONIS_SILENTIS_MISSENSEIS_INTRONICIS_NONSENSEIS_FRAMESHIFTIS_IN_FRAME_INDELIS_START_CODONIS_SILENTIS_MISSENSEIS_INTRONICIS_NONSENSEIS_FRAMESHIFTIS_IN_FRAME_INDELIS_START_CODONIS_SILENTIS_MISSENSEIS_INTRONICIS_SILENTMYH7c.2742G>Tp.Gln914HisEXON 23(Uncl) (myopathy), Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) : The Gln914His variant has not been reported in the literature nor has it been detected in over 1500 chromosomes screened by our laboratory. This residue is highly conserved across divergent species including several mammals, salmon, lizard, and fr11110000000000000000MYBPC3c.2498C>Tp.Ala833ValEXON 25Benign1313SUBSTITUTIONMISSENSEC16154TMAF=0.042 (AA only)rs3729952Alders 2003,11100PRKAG2c.298G>Ap.Gly100SerEXON 3Benign1616SUBSTITUTIONMISSENSE11100MYBPC3c.1144C>Tp.Arg382TrpEXON 13Benign2727SUBSTITUTIONMISSENSESeidman PM 2005, LMM SNP Data, dbSNP, Cardiogenomics - polymorphismrs11570076Van 2004,11100MYBPC3c.977G>Ap.Arg326GlnEXON 12Benign4632SUBSTITUTIONMISSENSEdbSNPrs34580776Niimura 2002, Jaaskelainen 2002, Morner 2003, Maron 2001, Van 2004, Ingles 2005The Arg326Gln variant is thought to be a common variant found in over 5% of individuals from certain populations (Jaaskelainen et al. 2002, dbSNP rs34580786). Therefore, it is highly unlikely that this variant is disease-causing.11100MYH7c.4472C>Gp.Ser1491CysEXON 32Benign5451SUBSTITUTIONMISSENSESeidman PM 2005, dbSNP; Cardiogenomics - polymorphismsrs3729823Hougs 2005, Blair 2002, Van 2004,11100TNNT2c.758A>Gp.Lys253ArgEXON 14Benign125123SUBSTITUTIONMISSENSEI253RSeidman PM 2005, dbSNP rs3730238rs3730238Morner 2003, Miliou 2005, Watkins 1995,11100MYBPC3c.472G>Ap.Val158MetEXON 4Benign289281SUBSTITUTIONMISSENSESeidman PM 2005, dbSNP, Cardiogenomics - polymorphism rs3729986Morner 2003, Alders 2003,11100MYBPC3c.706A>Gp.Ser236GlyEXON 6Benign363342SUBSTITUTIONMISSENSESer236ValSeidman PM 2005, dbSNP, Cardiogenomics - polymorphism rs3729989Jaaskelainen 2002, Morner 2003, Alders 2003, , Van 200411100MYL2c.381G>Ap.Ala127AlaEXON 6Benign77SUBSTITUTIONSILENTLMM SNP Databasers223326111001MYH7c.3864C>Gp.Ser1288SerEXON 29Benign99SUBSTITUTIONSILENTLMM SNP Datars4550169411001TNNT2c.444G>Cp.Arg148ArgEXON 10Benign1616SUBSTITUTIONSILENTLMM SNP Databasers3591432511001MYH7c.1002C>Tp.Asn334AsnEXON 12Benign2222SUBSTITUTIONSILENTMAF= 2.8% (AA)rs3480378111001MYH7c.3351G>Ap.Glu1117GluEXON 27Benign2323SUBSTITUTIONSILENTLMM SNP Database11001MYH7c.3153G>Ap.Ala1051AlaEXON 25Benign2424SUBSTITUTIONSILENTdbSNP (MAF=0.019); Cardiogenomicsrs4554083111001MYH7c.1767C>Tp.Asn589AsnEXON 16Benign2625SUBSTITUTIONSILENTdbSNP (Afr Am popul only)rs372981611001MYBPC3c.2601C>Tp.Ile867IleEXON 25Benign2727SUBSTITUTIONSILENTdbSNP (Afr Am)rs11570097This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. In addition, this variant has been identified in 3.3% of the Black population (dbSNP:rs11570097). In sum11001MYH7c.4716C>Tp.Ile1572IleExon 34Benign3030SUBSTITUTIONSILENTdbSNP, LMM SNP Data rs714019611001MYL3c.69C>Tp.Pro23ProEXON 1Benign3939SUBSTITUTIONSILENTLMM SNP Database, dbSNP11001MYH7c.4566T>Cp.Thr1522ThrEXON 33Benign4242SUBSTITUTIONSILENTdbSNP (MAF=0.006), LMM SNP Datbase; Cardiogenomicsrs275415511001PRKAG2c.1623T>Cp.Ile541IleEXON 15Benign4444SUBSTITUTIONSILENTdbSNPrs2876399811001MYH7c.975C>Tp.Asp325AspEXON 11Benign5149SUBSTITUTIONSILENTSeidman PM 200511001MYH7c.597A>Gp.Ala199AlaEXON 7Benign5252SUBSTITUTIONSILENTg.7647A>GSeidman PM 2005, LMM SNP Databasers2069541The Ala199Ala silent variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. In addition, it is present in 1-3% of the general population (dbSNP rs2069541).11001MYH7c.1605A>Gp.Glu535GluEXON 16Benign5453SUBSTITUTIONSILENTMAF: 0.029 (African Am), not polymorphic in other ethnicitiesrs2069543This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. In addition, this variant has been identified in 2.9% of the Black population (dbSNP:rs2069543). In sum11001ACTCc.927T>Cp.Pro309ProEXON 5Benign5555SUBSTITUTIONSILENT11001TNNI3c.198G>Ap.Glu66GluEXON 5Benign5757SUBSTITUTIONSILENTMAF 11.7% in Afr Am (not polymorphic in Cauc)rs372971011001LAMP2c.927C>Tp.Ser309SerEXON 7Benign6565SUBSTITUTIONSILENT11001MYBPC3c.492C>Tp.Gly164GlyEXON 4Benign119119SUBSTITUTIONSILENTg.3654C>TSeidman PM 200511001TNNI3c.204G>Tp.Arg68ArgEXON 5Benign133129SUBSTITUTIONSILENTSeidman PM 200511001MYBPC3c.537C>Tp.Ala179AlaExon 5Benign132132SUBSTITUTIONSILENTg.3789C>TSeidman PM 2005, dbSNP rs1157005111001TPM1c.486T>Cp.Tyr162TyrEXON 4Benign145144SUBSTITUTIONSILENTSeidman PM 2005; WIPGA_03_32711001MYL2c.132T>Cp.Ile44IleEXON 3Benign158154SUBSTITUTIONSILENTSeidman PM 200511001MYBPC3c.2547C>Tp.Val849ValEXON 25Benign164161SUBSTITUTIONSILENTSeidman PM 200511001MYH7c.1062C>Tp.Gly354GlyExon 12Benign183183SUBSTITUTIONSILENTSeidman PM 200511001TNNI3c.537G>Ap.Glu179GluExon 7Benign204201SUBSTITUTIONSILENTSeidman PM 2005, LMM SNP Database11001TNNT2c.207G>Ap.Ser69SerExon 8Benign221219SUBSTITUTIONSILENTSeidman PM 2005, LMM SNP Database11001MYBPC3c.786C>Tp.Thr262ThrEXON 7Benign339323SUBSTITUTIONSILENTSeidman PM 200511001MYH7c.1128C>Tp.Asp376AspExon 12Benign329325SUBSTITUTIONSILENTSeidman PM 200511001MYH7c.1095G>Ap.Lys365LysExon 12Benign363358SUBSTITUTIONSILENTSeidman PM 200511001MYH7c.5106G>Ap.Ala1702AlaEXON 35Benign434427SUBSTITUTIONSILENTCardiogenomics11001MYH7c.732C>Tp.Phe244PheExon 8Benign525523SUBSTITUTIONSILENTg.7864C>TSeidman PM 200511001LAMP2c.156A>Tp.Val52ValExon 2Benign549542SUBSTITUTIONSILENTdbSNP, LMM SNP Database, Seidman SNPsrs1209711001MYH7c.2967T>Cp.Ile989IleExon 24Benign831819SUBSTITUTIONSILENTSeidman PM 200511001MYBPC3c.3288G>Ap.Glu1096GluEXON 30Benign10571027SUBSTITUTIONSILENTg.20412G>ASeidman PM 200511001MYH7c.189T>Cp.Thr63ThrExon 3Benign11401123SUBSTITUTIONSILENTSeidman PM 200511001TPM1c.453C>Ap.Ala151AlaExon 4Benign12151204SUBSTITUTIONSILENTSeidman PM 200511001TNNT2c.318C>Tp.Ile106IleExon 9Benign13301309SUBSTITUTIONSILENTSeidman PM 200511001GLAc.639+866_867delAGINTRON 4Benign66IVS4+866_867delAG11010TNNT2c.264+7G>AINTRON 8Benign1414SUBSTITUTIONIVS8+7G>ALMM SNP DatabaseThis variant is not expected to have clinical significance because it is not located in the conserved region of the splicing consensus sequence and it is a common variant in the Black population.11010MYH7c.3337-3_3337-2insCIntron 26Benign173173INSERTIONIVS26-2_-3insCLMM11010MYBPC3c.506-12_506-11insCINTRON 4Benign448445INSERTIONIVS4-11_-12insCSeidman PM 200511010TNNI3c.25-8T>AINTRON 2Benign702693SUBSTITUTIONIVS2-8T>ASeidman PM 2005 rs3729836 (DBSNP)11010TNNT2c.53-11_53-7delCTTCTIntron 3Benign11191103DELETIONIVS3-11_-7delCTTCT; IVS3-12_-16delCTTCTSeidman PM Database 41/49 (83%)11010MYBPC3c.3413G>Ap.Arg1138HisEXON 31Likely Benign11SUBSTITUTIONMISSENSESeidman PM 2005, Cardiogenomics - polymorphismJaaskelainen 2002, Garca-Castro 200911100MYBPC3c.206G>Ap.Arg69GlnEXON 2Likely Benign31SUBSTITUTIONMISSENSEKondrashov 200211100PRKAG2c.739G>Cp.Glu247GlnEXON 5Likely Benign31SUBSTITUTIONMISSENSE11100PRKAG2c.325T>Gp.Ser109AlaEXON 3Likely Benign21SUBSTITUTIONMISSENSE11100LAMP2c.299C>Tp.Ala100ValEXON 03Likely Benign41SUBSTITUTIONMISSENSE11100TNNI3c.235C>Tp.Arg79CysExon 5Likely Benign44SUBSTITUTIONMISSENSECardioGenomics, dbSNP, LMM Databasers3729712Mogensen 2004, , Kimura 199711100MYBPC3c.3106C>Tp.Arg1036CysEXON 29Likely Benign115SUBSTITUTIONMISSENSEChanged to likely benign due to its high prevelence in the non-Caucasian population.11100MYH7c.3981C>Ap.Asn1327LysEXON 30Likely Benign145SUBSTITUTIONMISSENSECardioGenomicsHougs 200511100MYBPC3c.1519G>Ap.Gly507ArgEXON 17Likely Benign108SUBSTITUTIONMISSENSECardioGenomicsrs35736435Erdmann 2001, Van 200411100MYBPC3c.478C>Tp.Arg160TrpEXON 4Likely Benign88SUBSTITUTIONMISSENSEAnan 2006, Anan 2007The Arg160Trp variant has been identified in one Japanese proband with older onset, sporadic HCM, and was absent from 200 control chromosomes, suggesting that it may be pathogenic (Anan 2007). However, the variant has now been identified by our laboratory11100MYBPC3c.2992C>Gp.Gln998GluEXON 28Likely Benign119SUBSTITUTIONMISSENSEdbSNP, Cardiogenomics - variant of uncertain effectrs11570112Van 2004, Konno 2006, Bahrudin 2008, Garca-Castro 200911100MYBPC3c.2497G>Ap.Ala833ThrEXON 25Likely Benign139SUBSTITUTIONMISSENSESeidman PM 2005, Cardiogenomics - variant of uncertain effectMorner 2003, Alders 2003, Van 2004The significance of the Ala833Thr variant was initially debated. It was initially reported in three HCM probands, two of which carried a second, likely disease causing HCM variant (Morner 2003, Alders 2003, Van Driest 2004). In addition, the variant was d11100MYBPC3c.3004C>Tp.Arg1002TrpEXON 29Likely Benign1412SUBSTITUTIONMISSENSECardiogenomics - polymorphism, Seidman PM 2005, dbSNPrs3729799Fitzpatrick 1988, Sanchis 2004, Niimura 200211100MYBPC3c.530G>Ap.Arg177HisEXON 5Likely Benign1413SUBSTITUTIONMISSENSEArg177His in exon 5 of the MYBPC3 gene: This variant has not been reported in the literature. Although it changes an amino acid, it appears to be common in the Black population as it has been identified in 10 Black probands (6 with HCM, 4 with DCM) and no11100MYBPC3c.565G>Ap.Val189IleEXON 5Likely Benign2015SUBSTITUTIONMISSENSESeidman PM 2005, LMM Database, dbSNP, Cardiogenomics - polymorphismrs11570052Girolami 2004, Olivotto, 2004,The Val189Ile variant in exon 5 of MYBPC3 was initially reported in an individual with a clinical diagnosis of HCM and was not detected in 200 control chromosomes (Girolami 2004). However, our laboratory has detected this variant in over 15 patients with11100TNNI3c.244C>Tp.Pro82SerEXON 5Likely Benign1917SUBSTITUTIONMISSENSEUncertain: 3% of Afro-Carribbeans but earlier report as pathogenic. NOTE: P82T = polymorphismGomes 2004, Frazier 2008, Niimura 2002, Mogensen 2004Although this variant changes an amino acid, it has been reported to be present 3% of healthy Afro-Caribbean controls (Mogensen et al. 2004). In addition, approximately half of the probands in this laboratory who had this variant also had other variants o11100LAMP2c.1171G>Ap.Val391IleEXON 9BLikely Benign2217SUBSTITUTIONMISSENSE11100MYBPC3c.833G>Ap.Gly278GluEXON 8Likely Benign1818SUBSTITUTIONMISSENSECardioGenomicsRichard 2003The Gly278Glu variant has been reported in one HCM proband of unknown racial origin while absent from 200 control chromosomes, suggesting that it may be disease causing (Richard et al, 2003). However, we have now identified it in 16 probands, 12 of whom w11100PRKAG2c.59G>Tp.Ser20IleEXON 1Likely Benign2218SUBSTITUTIONMISSENSEAlthough this variant changes an amino acid, our laboratory has identified it in 14% of Black probands (>14%). Given this frequency we feel that this variant is not likely to be contributing to disease.11100MYBPC3c.2686G>Ap.Val896MetEXON 26Likely Benign3726SUBSTITUTIONMISSENSECardioGenomics - polymorphism, Seidman PM 2005, LMM Databasers35078470Moolman-Smook 1999, Keller 2004, Jaaskelainen 2002, Morner 2003Val896Met in exon 26 of MYBPC3: The V896M variant was originally reported to be disease causing or have a modifying role (Moolman-Smook 1999; Jaaskelainen 2002; Morner et al. 2003, Keller et al. 2004). However, it has now been reported in the SNP database11100MYH7c.4806C>Tp.Asp1602AspExon 34Likely Benign11SUBSTITUTIONSILENT11001TNNI3c.384G>Ap.Leu128LeuExon 7Likely Benign11SUBSTITUTIONSILENTThe Leu128Leu variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. However, on rare occasions, base changes that do not result in amino acid changes can be associa11001MYH7c.2799T>Cp.Asn933AsnExon 23Likely Benign11SUBSTITUTIONSILENT11001MYH7c.2802T>Gp.Ala934AlaExon 23Likely Benign11SUBSTITUTIONSILENT11001ACTCc.903A>Gp.Leu301LeuExon 5Likely Benign11SUBSTITUTIONSILENTLMM SNP data (found in patient PM05-00419)11001LAMP2c.591G>Ap.Val197ValExon 5Likely Benign11SUBSTITUTIONSILENT11001MYL2c.342G>Ap.Leu114LeuExon 5Likely Benign11SUBSTITUTIONSILENT11001MYH7c.2358G>Ap.Thr786ThrEXON 21Likely Benign11SUBSTITUTIONSILENTJskelinen 199811001MYH7c.2472C>Tp.Val824ValExon 22Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.960C>Tp.Asp320AspExon 12Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.2274C>Tp.Gly758GlyExon 23Likely Benign11SUBSTITUTIONSILENT11001TNNT2c.744C>Tp.Phe248PheExon 14Likely Benign11SUBSTITUTIONSILENT11001MYH7c.474C>Tp.Ser158SerExon 5Likely Benign11SUBSTITUTIONSILENTLMM SNP Database11001MYH7c.1518C>Tp.Ile506IleExon 15Likely Benign11SUBSTITUTIONSILENT11001MYH7c.1983C>Tp.Asn661AsnExon 18Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.2499G>Ap.Ala833AlaExon 25Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.2196C>Tp.Asp732AspExon 23Likely Benign11SUBSTITUTIONSILENTLMM SNP Data (found in patient PM05-00459)11001MYBPC3c.2163C>Tp.Thr721ThrExon 23Likely Benign11SUBSTITUTIONSILENT11001MYH7c.5421C>Gp.Gly1807GlyExon 37Likely Benign11SUBSTITUTIONSILENT11001MYH7c.3754T>Cp.Leu1252LeuEXON 28Likely Benign11SUBSTITUTIONSILENT11001MYH7c.480C>Tp.Asn160AsnEXON 05Likely Benign11SUBSTITUTIONSILENTrs4550070011001GLAc.48T>Gp.Leu16LeuEXON 1Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.993T>Cp.Tyr331TyrEXON 8Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.1071A>Tp.Thr357ThrEXON 10Likely Benign11SUBSTITUTIONSILENT11001MYH7c.930T>Cp.Tyr310TyrEXON 11Likely Benign11SUBSTITUTIONSILENT11001MYH7c.2922G>Ap.Lys974LysEXON 23Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.1704G>Ap.Thr568ThrEXON 16Likely Benign11SUBSTITUTIONSILENT11001MYH7c.297C>Tp.Pro99ProEXON 4Likely Benign11SUBSTITUTIONSILENTVan 200411001MYH7c.957C>Tp.Thr319ThrEXON 11Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.2997C>Tp.Gly999GlyEXON 29Likely Benign11SUBSTITUTIONSILENT11001TNNI3c.39C>Gp.Arg13ArgEXON 3Likely Benign11SUBSTITUTIONSILENT11001MYH7c.5421C>Tp.Gly1807GlyEXON 37Likely Benign11SUBSTITUTIONSILENT11001ACTCc.219C>Tp.Ile73IleEXON 2Likely Benign11SUBSTITUTIONSILENT11001MYH7c.4005G>Ap.Ser1335SerEXON 30Likely Benign11SUBSTITUTIONSILENT11001MYH7c.396G>Tp.Pro132ProExon 5Likely Benign11SUBSTITUTIONSILENT11001GLAc.129C>Tp.Gly43GlyEXON 1Likely Benign11SUBSTITUTIONSILENT11001MYH7c.156G>Ap.Val52ValEXON 03Likely Benign11SUBSTITUTIONSILENT11001TNNI3c.246G>Tp.Pro82ProEXON 5Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.618G>Tp.Pro206ProEXON 4Likely Benign11SUBSTITUTIONSILENT11001MYH7c.1332T>Cp.Asn444AsnEXON 14Likely Benign11SUBSTITUTIONSILENT11001GLAc.714T>Cp.Ser238SerEXON 5Likely Benign11SUBSTITUTIONSILENT11001ACTCc.918T>Ap.Thr306ThrEXON 5Likely Benign11SUBSTITUTIONSILENT11001ACTCc.1053G>Ap.Leu351LeuEXON 06Likely Benign11SUBSTITUTIONSILENT11001ACTCc.1092C>Tp.Tyr364TyrExon 06Likely Benign11SUBSTITUTIONSILENT11001TPM1c.252C>Tp.Asp84AspExon 3Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.450C>Tp.Pro150ProEXON 4Likely Benign11SUBSTITUTIONSILENT11001MYH7c.5739C>Tp.Ala1913AlaEXON 39Likely Benign11SUBSTITUTIONSILENT11001LAMP2c.672A>Gp.Ser224SerEXON 5Likely Benign11SUBSTITUTIONSILENT11001MYH7c.4911C>Tp.Ala1637AlaEXON 34Likely Benign21SUBSTITUTIONSILENT11001MYH7c.4515G>Tp.Leu1505LeuEXON 32Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.594G>Ap.Pro198ProExon 4Likely Benign11SUBSTITUTIONSILENT11001TNNT2c.421C>Ap.Arg141ArgEXON 10Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.114G>Ap.Pro38ProEXON 1Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.240C>Ap.Gly80GlyEXON 3Likely Benign11SUBSTITUTIONSILENT11001MYL2c.243G>Tp.Val81ValEXON 4Likely Benign11SUBSTITUTIONSILENT11001GLAc.978G>Ap.Lys326LysEXON 6Likely Benign11SUBSTITUTIONSILENT11001TNNI3c.105C>Ap.Ala35AlaEXON 3Likely Benign11SUBSTITUTIONSILENT11001MYH7c.1323G>Ap.Thr441ThrEXON 14Likely Benign11SUBSTITUTIONSILENT11001MYH7c.4188G>Ap.Arg1396ArgEXON 31Likely Benign11SUBSTITUTIONSILENT11001TPM1c.549T>Cp.Ala183AlaExon 5Likely Benign11SUBSTITUTIONSILENT11001TNNT2c.807C>Tp.Asn269AsnEXON 15Likely Benign11SUBSTITUTIONSILENT11001TNNT2c.63T>Gp.Val21ValEXON 4Likely Benign11SUBSTITUTIONSILENTThis variant was not described in the literature. It is a silent variant meaning that the amino acid is not altered at this residue. Furthermore, this variant does not occur within a known consensus splice site. Therefore, this variant is likely to be ben11001MYBPC3c.3285G>Ap.Thr1095ThrEXON 30Likely Benign11SUBSTITUTIONSILENT11001MYH7c.4077C>Tp.Arg1359ArgEXON 30Likely Benign11SUBSTITUTIONSILENTdbSNPrs4552383511001MYH7c.4395G>Tp.Ser1465SerEXON 32Likely Benign11SUBSTITUTIONSILENT11001LAMP2c.333T>Cp.Ile111IleEXON 3Likely Benign21SUBSTITUTIONSILENT11001PRKAG2c.897C>Tp.Asn299AsnEXON 7Likely Benign11SUBSTITUTIONSILENT11001MYL3c.516G>Ap.Leu172LeuEXON 5Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.2784G>Ap.Ser928SerEXON 27Likely Benign11SUBSTITUTIONSILENT11001ACTCc.516T>Cp.Ala172AlaEXON 3Likely Benign11SUBSTITUTIONSILENT11001MYH7c.5115G>Ap.Glu1705GluEXON 35Likely Benign11SUBSTITUTIONSILENT11001MYH7c.5718A>Cp.Ala1906AlaEXON 39Likely Benign11SUBSTITUTIONSILENTrs4552323311001MYBPC3c.2178C>Tp.Arg726ArgEXON 23Likely Benign11SUBSTITUTIONSILENT11001MYH7c.5703C>Tp.His1901HisEXON 39Likely Benign11SUBSTITUTIONSILENTThis variant is not expected to have clinical significance because it is does not change the amino acid at this position. Therefore, it is unlikely that this variant is disease-causing.11001MYBPC3c.207G>Cp.Arg69ArgEXON 2Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.1602G>Ap.Ala534AlaEXON 17Likely Benign11SUBSTITUTIONSILENT11001TNNI3c.6G>Ap.Ala2AlaEXON 1Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.93C>Tp.Ala31AlaEXON 2Likely Benign11SUBSTITUTIONSILENTThis variant is not expected to have clinical significance because it does not change an amino acid residue and is not located in the conserved region of the splicing consensus sequence.11001MYBPC3c.1914C>Tp.Phe638PheEXON 20Likely Benign11SUBSTITUTIONSILENT11001TNNI3c.273G>Ap.Ala91AlaEXON 5Likely Benign11SUBSTITUTIONSILENT11001MYH7c.261C>Tp.Ile87IleEXON 4Likely Benign11SUBSTITUTIONSILENT11001MYH7c.2388C>Tp.Leu796LeuEXON 21Likely Benign11SUBSTITUTIONSILENT11001PRKAG2c.1098A>Gp.Pro366ProEXON 10Likely Benign11SUBSTITUTIONSILENT11001MYH7c.1608G>Ap.Glu536GluEXON 16Likely Benign11SUBSTITUTIONSILENT11001MYH7c.3273C>Tp.Asn1091AsnEXON 26Likely Benign11SUBSTITUTIONSILENT11001TNNT2c.537C>Tp.Ser179SerEXON 11Likely Benign11SUBSTITUTIONSILENTHo 200011001MYBPC3c.1719T>Gp.Val573ValEXON 18Likely Benign11SUBSTITUTIONSILENTThis variant is not expected to have clinical significance because it is not located in the conserved region of the splicing consensus sequence.11001ACTCc.294G>Ap.Val98ValEXON 2Likely Benign11SUBSTITUTIONSILENT11001MYBPC3c.1803G>Ap.Leu601LeuEXON 19Likely Benign11SUBSTITUTIONSILENT11001MYH7c.2979C>Tp.Thr993ThrEXON 24Likely Benign11SUBSTITUTIONSILENT11001MYH7c.3918C>Tp.Leu1306LeuEXON 29Likely Benign11SUBSTITUTIONSILENT11001MYH7c.3777C>Tp.His1259HisEXON 28Likely Benign11SUBSTITUTIONSILENTThis variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. Therefore, it is unlikely that this variant is disease-causing.11001MYBPC3c.558G>Tp.Pro186ProEXON 5Likely Benign22SUBSTITUTIONSILENTLMM SNP Data (found in patient PM05-00607)11001MYBPC3c.132C>Tp.Arg44ArgExon 2Likely Benign22SUBSTITUTIONSILENT11001MYH7c.2637C>Tp.Ser879SerExon 22Likely Benign22SUBSTITUTIONSILENTLMM SNP Database11001MYH7c.1755C>Ap.Ile585IleExon 16Likely Benign22SUBSTITUTIONSILENT11001MYH7c.4293C>Tp.Asp1431AspExon 31Likely Benign22SUBSTITUTIONSILENT11001MYH7c.5397A>Gp.Glu1799GluExon 37Likely Benign22SUBSTITUTIONSILENT11001MYBPC3c.3102C>Tp.Ala1034AlaExon 29Likely Benign22SUBSTITUTIONSILENTg.20003C>TSeidman PM 200511001MYBPC3c.3315C>Ap.Ala1105AlaEXON 30Likely Benign22SUBSTITUTIONSILENTfound in patient 04-062011001MYH7c.4239G>Ap.Ser1413SerEXON 31Likely Benign22SUBSTITUTIONSILENTfound in patient PM05-A00259rs3729821The Ser1413Ser variant is not expected to have clinical significance because it does not alter an amino acid and is not located near a splice junction. In addition, it has been observed in 1/38 control samples (dbSNP rs3729821).11001MYL3c.81T>Cp.Pro27ProExon 1Likely Benign22SUBSTITUTIONSILENT11001MYL2c.33G>Ap.Gly11GlyExon 2Likely Benign22SUBSTITUTIONSILENT11001MYBPC3c.1290C>Tp.Asp430AspEXON 15Likely Benign32SUBSTITUTIONSILENT11001TPM1c.726G>Ap.Ala242AlaEXON 08Likely Benign22SUBSTITUTIONSILENT11001MYH7c.2229G>Ap.Glu743GluEXON 20Likely Benign22SUBSTITUTIONSILENT11001ACTCc.513C>Tp.Tyr171TyrEXON 3Likely Benign22SUBSTITUTIONSILENT11001MYH7c.5562G>Ap.Thr1854ThrEXON 38Likely Benign22SUBSTITUTIONSILENT11001PRKAG2c.312C>Tp.Thr104ThrEXON 3Likely Benign22SUBSTITUTIONSILENT11001MYBPC3c.2544G>Ap.Ala848AlaEXON 25Likely Benign22SUBSTITUTIONSILENT11001PRKAG2c.471C>Tp.Ser157SerExon 04Likely Benign22SUBSTITUTIONSILENT11001ACTCc.798C>Tp.Pro266ProExon 04Likely Benign22SUBSTITUTIONSILENT11001PRKAG2c.123C>Tp.Ser41SerEXON 2Likely Benign22SUBSTITUTIONSILENT11001MYH7c.2553C>Ap.Ser851SerEXON 22Likely Benign22SUBSTITUTIONSILENT11001TPM1c.180C>Tp.Tyr60TyrEXON 2Likely Benign22SUBSTITUTIONSILENTrs1785019411001MYH7c.3156G>Ap.Lys1052LysEXON 25Likely Benign22SUBSTITUTIONSILENT11001TPM1c.27G>Ap.Gln9GlnEXON 1Likely Benign22SUBSTITUTIONSILENT11001MYBPC3c.933G>Cp.Ser311SerEXON 12Likely Benign22SUBSTITUTIONSILENT11001MYH7c.4974C>Tp.Asp1658AspEXON 35Likely Benign22SUBSTITUTIONSILENTThis variant has not yet been reported. It is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction.11001GLAc.945C>Tp.Asp315AspEXON 6Likely Benign22SUBSTITUTIONSILENT11001MYH7c.327C>Tp.Tyr109TyrEXON 4Likely Benign22SUBSTITUTIONSILENTVan 2004This silent variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. Silent variants can disrupt DNA sequence motifs that are important for mRNA splicing; however, the11001PRKAG2c.111T>Ap.Ile37IleExon 1Likely Benign33SUBSTITUTIONSILENT11001PRKAG2c.1296G>Ap.Thr432ThrExon 12Likely Benign33SUBSTITUTIONSILENT11001MYH7c.2349C>Tp.Arg783ArgExon 21Likely Benign33SUBSTITUTIONSILENT11001MYBPC3c.3003C>Tp.Pro1001ProExon 29Likely Benign33SUBSTITUTIONSILENT11001TNNT2c.240C>Gp.Pro80ProExon 8Likely Benign33SUBSTITUTIONSILENT11001PRKAG2c.531G>Tp.Leu177LeuExon 4Likely Benign33SUBSTITUTIONSILENTLMM SNP Database11001TPM1c.522C>Tp.Ser174SerExon 5Likely Benign43SUBSTITUTIONSILENT11001MYH7c.1395C>Tp.Phe465PheEXON 14Likely Benign33SUBSTITUTIONSILENTrs4550829311001MYBPC3c.12G>Ap.Pro4ProEXON 1Likely Benign33SUBSTITUTIONSILENT11001MYH7c.2334C>Tp.Asp778AspEXON 21Likely Benign33SUBSTITUTIONSILENTrs206954411001MYH7c.2907C>Tp.His969HisExon 23Likely Benign33SUBSTITUTIONSILENT11001MYH7c.3960G>Ap.Glu1320GluExon 29Likely Benign33SUBSTITUTIONSILENT11001MYL2c.36C>Tp.Gly12GlyEXON 2Likely Benign33SUBSTITUTIONSILENT11001LAMP2c.339C>Tp.Ser113SerEXON 3Likely Benign64SUBSTITUTIONSILENT(HCM) :11001MYH7c.3036C>Tp.Ala1012AlaEXON 24Likely Benign55SUBSTITUTIONSILENTB 2005This silent variant has been previously reported (Yu 2005, please note that the variant is listed as A1022A). It is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. Silen11001MYH7c.2769C>Tp.Asn923AsnExon 23Likely Benign55SUBSTITUTIONSILENTrs36211716; Seidman PM 200511001MYH7c.4452C>Tp.Leu1484LeuExon 32Likely Benign66SUBSTITUTIONSILENTLMM SNP Database11001TPM1c.618A>Gp.Ala206AlaExon 6aLikely Benign77SUBSTITUTIONSILENTLMM SNP DatabaseThis variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located near a splice junction. Silent variants can disrupt DNA sequence motifs that are important for mRNA splicing; however, splicing v11001MYH7c.4788G>Ap.Ser1596SerExon 34Likely Benign88SUBSTITUTIONSILENTLMM SNP Database11001PRKAG2c.639C>Tp.Thr213ThrExon 4Likely Benign1010SUBSTITUTIONSILENT11001PRKAG2c.207G>Ap.Pro69ProExon 3Likely Benign1111SUBSTITUTIONSILENTLMM SNP Database11001PRKAG2c.1593G>Ap.Arg531ArgExon 15Likely Benign1313SUBSTITUTIONSILENTLMM SNP Database11001MYBPC3c.1608T>Ap.Ala536AlaExon 17Likely Benign1514SUBSTITUTIONSILENTLMM SNP Data11001TPM1c.563+10C>TIntron 5Likely Benign11SUBSTITUTIONIVS5+10C>TLMM SNP Database (found in PM05-00459)11010TNNT2c.459+7_459+8insGINTRON 10Likely Benign11INSERTIONIVS10+7_+8insGLMM Database11010TPM1c.241-9T>CIntron 2Likely Benign11SUBSTITUTIONIVS2-9T>C11010PRKAG2*3G>AEXON 3'UTRLikely Benign11SUBSTITUTION11010MYL2c.274+8C>TINTRON 4Likely Benign11SUBSTITUTIONIVS4+8C>T11010MYBPC3c.1624+9G>AINTRON 17Likely Benign11SUBSTITUTIONIVS17+9G>A11010TNNI3c.373-4C>GINTRON 6Likely Benign11SUBSTITUTIONIVS6-4C>Grs2288530Kimura 199711010MYBPC3c.2309-20G>AINTRON 23Likely Benign11SUBSTITUTIONIVS23-20G>APM08-0073211010TNNT2c.170-4C>GINTRON 6Likely Benign11SUBSTITUTIONIVS6-4C>G11010GLAc.1-12G>ALikely Benign11SUBSTITUTIONrs302758511010MYBPC3c.772+10C>TINTRON 6Likely Benign11SUBSTITUTIONIVS6C>T11010MYH7c.5656-4G>CINTRON 38Likely Benign11SUBSTITUTION11010TPM1c.563+6C>AINTRON 5Likely Benign11SUBSTITUTION11010PRKAG2c.685-8C>TINTRON 4Likely Benign11SUBSTITUTION11010MYL2c.274+26_274+27insGTIntron 4Likely Benign22INSERTION282_283ins, IVS4+26_+27insGTLMM SNP Data11010MYH7c.5559+8G>AIntron 37Likely Benign22SUBSTITUTIONIVS37+8G>A11010TNNI3c.12-7delCIntron 1Likely Benign22DELETIONIVS1-7delC11010MYL2c.274+9G>AINTRON 04Likely Benign22SUBSTITUTION11010PRKAG2c.1106+9G>CIntron 10Likely Benign22SUBSTITUTIONIVS10+9G>C11010MYL3c.559+6C>TIntron 5Likely Benign33SUBSTITUTIONIVS5+6C>TLMM SNP Database11010MYBPC3c.926+8C>TIntron 11Likely Benign54SUBSTITUTIONThis variant is not expected to have clinical significance because it is not located in the conserved region of the splicing consensus sequence.11010MYBPC3c.1790+7G>AINTRON 18Likely Benign44SUBSTITUTIONIVS18+7G>A11010TPM1c.375-5T>CINTRON 3Likely Benign74SUBSTITUTION11010TNNT2c.52+7G>AIntron 3Likely Benign55SUBSTITUTIONIVS3+7G>ALMM Database11010MYH7c.4353+10G>AIntron 31Likely Benign66SUBSTITUTIONIVS31+10G>ALMM SNP Database11010MYH7c.2162+4G>AIntron 19Likely Benign66SUBSTITUTIONIVS19+4G>ALMM SNP Database11010ACTCc.454+9G>AINTRON 2Likely Benign66SUBSTITUTIONIVS3+911010PRKAG2c.1584+7C>TIntron 14Likely Benign87SUBSTITUTIONIVS14+7C>T11010GLA-10C>TLikely Benign87SUBSTITUTIONrs207122511010TNNI3c.550-10C>TINTRON 7Likely Benign88SUBSTITUTIONThis variant has not been reported in the literature but has been identified in 8 probands, 5 of whom were black, 2 of mixed race, and 1 of unspecified race. Five of the probands had a second variant in another gene, one of which is known to be pathogeni11010MYH7c.3853+7C>TIntron 28Likely Benign1817SUBSTITUTIONMost likely benign (splice consensus goes up to +6)rs4546739711010GLAc.196G>Cp.Glu66GlnEXON 2Likely Pathogenic (Fabry disease, HCM)11SUBSTITUTIONMISSENSETakata 1997, Ishii 1992, Okumiya 1995, Sugawara 2008, Nakao 2003, Yoshitama 2001, Ishii 2007, Park 2009, Shimotori 2008(Fabry disease, HCM) :11110000000000000000GLAc.386T>Cp.Leu129ProLikely Pathogenic (Fabry disease, HCM)11SUBSTITUTIONMISSENSESchfer 2005, Whybra 2001(Fabry disease, HCM) :11110000000000000000MYBPC3c.1513_1515delAAGp.Lys505delExon 17Likely Pathogenic (HCM)11DELETIONDELETIONK504delCardioGenomicsCardim 2005(HCM) :11100001000000000000MYBPC3c.2441_2443delAGAp.Lys814delExon 25Likely Pathogenic (HCM)31DELETIONDELETIONEx25delLys, K811del, Lys811del, 2440_2442delAAGCardioGenomicsJaaskelainen 2002, Van 2004, Song 2005, Cardim 2005(HCM) :11100001000000000000MYBPC3c.1814_1816delACGp.Asp605delEXON 19Likely Pathogenic (HCM)71DELETIONDELETION(HCM) :11100001000000000000MYBPC3c.3767_3769delCCAp.Thr1256delEXON 33Likely Pathogenic (HCM)11DELETIONDELETION(HCM) : This is a reassessment of the novel variant Thr1256del. A 3767_3769delCCA mutation in exon 33 results in an in frame deletion of Thr at position 1256 . This variant has not been reported in the literature. Our records indicate that this variant w11100001000000000000MYH7c.5186_5188delAGAp.Lys1729delEXON 36Likely Pathogenic (HCM)11DELETIONDELETIONCardiogenomics - other mutations - Laing distal myopathyMeredith 2004(HCM) :11100001000000000000MYH7c.2627_2629delAGAp.Lys876delEXON 22Likely Pathogenic (HCM)11DELETIONDELETION(HCM) :11100001000000000000MYH7c.5015_5020delp.Ala1672_Ile1673delEXON 35Likely Pathogenic (HCM)11DELETIONDELETION(HCM) :11100001000000000000MYH7c.2539_2541delAAGp.Lys847delEXON 22Likely Pathogenic (HCM)33DELETIONDELETIONCardiogenomicsVan 2004(HCM) :11100001000000000000MYBPC3c.3742_3759dupp.Gly1248_Cys1253dupEXON 33Likely Pathogenic (HCM)165DUPLICATIONDUPLICATIONInsGGIYVC/Ins18bp1163CardioGenomicsVan 2004, Brown 2002, Watkins 1995, Maron 2001(HCM) : The G1248_C1253dup variant has been previously reported (Watkins 1995, Maron 2001, Brown 2002). Segregation studies and absence from healthy controls support a pathogenic role (Watkins 1995); however, one report classified this variant as a benign11100001000000000000LAMP2c.217_218insAp.Thr73fsEXON 3Likely Pathogenic (HCM)11INSERTIONFRAMESHIFT(HCM) :11100010000000000000LAMP2c.191delTp.Val64fsExon 3Likely Pathogenic (HCM)11DELETIONFRAMESHIFTV64fsX9(HCM) :11100010000000000000MYBPC3c.1699_1700delGAp.Glu567fsExon 18Likely Pathogenic (HCM)31DELETIONFRAMESHIFTC566 fs/3CardioGenomicsVan 2004(HCM) :11100010000000000000MYBPC3c.2558delGp.Gly853fsEXON 25Likely Pathogenic (HCM)71DELETIONFRAMESHIFTI852fs/25CardioGenomicsVan 2004(HCM) :11100010000000000000MYBPC3c.3332_3335dupAGTGp.Trp1112fsExon 31Likely Pathogenic (HCM)11DUPLICATIONFRAMESHIFT(HCM) :11100010000000000000MYBPC3c.3600_3609delp.Cys1201fsExon 32Likely Pathogenic (HCM)21DELETIONFRAMESHIFTLMM Database(HCM) :11100010000000000000MYBPC3c.2943_2947delGACCAp.Gln981fsExon 28Likely Pathogenic (HCM)31DELETIONFRAMESHIFTLMM Database(HCM) :11100010000000000000MYBPC3c.3735delCp.Phe1246fsEXON 33Likely Pathogenic (HCM)101DELETIONFRAMESHIFTP1245fs(HCM) : The Phe1246fs variant has not been reported in the literature. This variant is predicted to cause a frameshift, which alters the protein's terminal 29 amino acids, abolishes the stop codon and adds an additional 55 amino acids. Frameshift variants11100010000000000000MYBPC3c.984_1054delp.Pro329fsExon 12Likely Pathogenic (HCM)11DELETIONFRAMESHIFT(HCM) :11100010000000000000MYBPC3c.2555_2556insTp.Gly853fsExon 25Likely Pathogenic (HCM)31INSERTIONFRAMESHIFTGly853LeufsX31NOTE! Observed in cis with 2557G>T(HCM) :11100010000000000000MYBPC3c.3288delGp.Glu1096fsExon 30Likely Pathogenic (HCM)11DELETIONFRAMESHIFTLekanne 2006(HCM) :11100010000000000000MYBPC3c.2394_2395insTp.Gly799fsEXON 24Likely Pathogenic (HCM)11INSERTIONFRAMESHIFT(HCM) :11100010000000000000MYBPC3c.1678delGp.Asp560fsEXON 18Likely Pathogenic (HCM)11DELETIONFRAMESHIFTD560Tfsx19(HCM) :11100010000000000000MYBPC3c.3166_3167insGp.Ala1056fsEXON 29Likely Pathogenic (HCM)11INSERTIONFRAMESHIFTA1056fsX8(HCM) :11100010000000000000MYBPC3c.2311_2312insGp.Val771fsEXON 24Likely Pathogenic (HCM)11INSERTIONFRAMESHIFTV771GfsX62(HCM) :11100010000000000000MYBPC3c.1999_2000delinsGp.Leu667fsEXON 21Likely Pathogenic (HCM)11INSERTION_DELETIONFRAMESHIFTL667fsX15(HCM) :11100010000000000000MYBPC3c.1863delCp.Phe621fsEXON 19Likely Pathogenic (HCM)11DELETIONFRAMESHIFTPhe621LeufsX42(HCM) :11100010000000000000MYBPC3c.3476_3477delTTp.Phe1159fsEXON 31Likely Pathogenic (HCM)11DELETIONFRAMESHIFT(HCM) :11100010000000000000MYBPC3c.2875_2876delACp.Thr959fsEXON 27Likely Pathogenic (HCM)11DELETIONFRAMESHIFTT959GfsX91(HCM) :11100010000000000000MYBPC3c.533delTp.Val178fsEXON 5Likely Pathogenic (HCM)31DELETIONFRAMESHIFTVal178GlyfsX7(HCM) :11100010000000000000MYBPC3c.3297dupGp.Tyr1100fsEXON 30Likely Pathogenic (HCM)31DUPLICATIONFRAMESHIFTY1100fsX49, 3297_3298insG(HCM) :11100010000000000000MYBPC3c.3690_3691delCAp.Phe1230fsEXON 33Likely Pathogenic (HCM)11DELETIONFRAMESHIFT(HCM) :11100010000000000000MYBPC3c.551_552insTp.Lys185fsEXON 5Likely Pathogenic (HCM)21INSERTIONFRAMESHIFTp. Lys185GlufsX56(HCM) :11100010000000000000MYBPC3c.362delCp.Pro121fsEXON 3Likely Pathogenic (HCM)21DELETIONFRAMESHIFTp.Pro121ArgfsX38(HCM) :11100010000000000000MYBPC3c.2780_2781delCAp.Thr927fsExon 27Likely Pathogenic (HCM)72DELETIONFRAMESHIFTLMM Database(HCM) :11100010000000000000MYBPC3c.1357_1358delCCp.Pro453fsEXON 16Likely Pathogenic (HCM)22DELETIONFRAMESHIFTP453CfsX21CardioGenomics, LMM DatabaseWaldmuller 2003(HCM) :11100010000000000000MYBPC3c.3192_3193insCp.Lys1065fsExon 30Likely Pathogenic (HCM)22INSERTIONFRAMESHIFTK1065QfsX12Cardiogenomics (Seidman)(HCM) :11100010000000000000MYBPC3c.2604_2605delinsAp.S871fsEXON 26Likely Pathogenic (HCM)42INSERTION_DELETIONFRAMESHIFTSer871AlafsX8(HCM) :11100010000000000000MYBPC3c.3624_3625insCp.Lys1209fsEXON 32Likely Pathogenic (HCM)32INSERTIONFRAMESHIFTK1209QfsX33(HCM) :11100010000000000000MYL2c.45_46delinsTp.Asn16fsExon 2Likely Pathogenic (HCM)32INSERTION_DELETIONFRAMESHIFTN16fsX34(HCM) :11100010000000000000MYBPC3c.3624delCp.Pro1208fsEXON 32Likely Pathogenic (HCM)53DELETIONFRAMESHIFTdelC1208CardioGenomicsBarr,(HCM) :11100010000000000000MYBPC3c.459delCp.Ile154fsEXON 4Likely Pathogenic (HCM)63DELETIONFRAMESHIFT(HCM) :11100010000000000000MYBPC3c.177_187delAGAGGGCACACp.Glu60fsExon 02Likely Pathogenic (HCM)105DELETIONFRAMESHIFTE60AfsX49(HCM) :11100010000000000000TNNI3c.1A>Gp.Met1?Exon 1Likely Pathogenic (HCM)21SUBSTITUTIONINITIATING_METH(HCM) :11100000100000000000ACTCc.28C>Ap.Leu10MetEXON 1Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000ACTCc.76G>Ap.Asp26AsnEXON 1Likely Pathogenic (HCM)41SUBSTITUTIONMISSENSELaing 2009(HCM) : The Asp26Asn variant has not been reported in the literature. We have previously identified this variant in one Hispanic proband and in one affected relative. Aspartic Acid (Asp) at position 26 is highly conserved across several species, indicati11110000000000000000MYBPC3c.3746G>Tp.Gly1249ValEXON 33Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYBPC3c.836G>Cp.Gly279AlaExon 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomics(HCM) :11110000000000000000MYBPC3c.2003G>Ap.Arg668HisEXON 21Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardioGenomicsMorner 2003, Song 2005(HCM) :11110000000000000000MYBPC3c.1037G>Ap.Arg346HisEXON 12Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.2320G>Ap.Ala774ThrEXON 24Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1343T>Cp.Phe448SerEXON 15Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.844C>Tp.Arg282TrpEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsErdmann 2001, Erdmann 2003, Govada 2008(HCM) :11110000000000000000MYBPC3c.1591G>Cp.Gly531ArgEXON 17Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardioGenomicsGirolami 2006(HCM) :11110000000000000000MYBPC3c.2459G>Ap.Arg820GlnEXON 25Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSESeidman PM 2005, dbSNP, Cardiogenomics - variant of uncertain effectShimizu 2005, Konno 2003, Nanni 2003, Alders 2003(HCM) :11110000000000000000MYBPC3c.3049G>Ap.Glu1017LysExon 29Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardioGenomics(HCM) :11110000000000000000MYBPC3c.3373G>Ap.Val1125MetExon 31Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardioGenomics(HCM) :11110000000000000000MYBPC3c.3763G>Ap.Ala1255ThrExon 33Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSEG21524ACardioGenomics(HCM) :11110000000000000000MYBPC3c.2993A>Gp.Gln998ArgExon 28Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSEVan Driest 2004 (novel), Bos 2006 (compound het)Van 2004, Bos 2006(HCM) :11110000000000000000MYBPC3c.2269G>Ap.Val757MetEXON 23Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardioGenomics(HCM) :11110000000000000000MYBPC3c.103C>Tp.Arg35TrpEXON 2Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSELMM Database; Cardiogenomics(HCM) :11110000000000000000MYBPC3c.223G>Ap.Asp75AsnExon 2Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.2449C>Tp.Arg817TrpEXON 25Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1418T>Cp.Phe473SerEXON 16Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.2533C>Tp.Arg845CysEXON 25Likely Pathogenic (HCM)41SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.3548T>Gp.Phe1183CysEXON 32Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.290C>Tp.Ala97ValEXON 2Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.636C>Gp.Ser212ArgEXON 5Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1505G>Tp.Arg502LeuEXON 17Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1672G>Ap.Ala558ThrEXON 18Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.3472G>Ap.Val1158IleExon 31Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1814A>Gp.Asp605GlyEXON 19Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.3605G>Ap.Cys1202TyrExon 32Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.3G>Cp.M1?EXON 1Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1456T>Gp.Trp486GlyEXON 16Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.481C>Ap.Pro161ThrEXON 4Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.3797G>Ap.Cys1266TyrEXON 33Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.2170C>Tp.Arg724TrpEXON 23Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.2312T>Cp.Val771AlaEXON 24Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSEGarca-Castro 2005(HCM) : The Val771Ala variant has not been reported in the literature. This individual's racial origin is reported to be Caucasian and the Val771Ala variant has not been identified in over 1500 Caucasian probands (3000 chromosomes) tested by our laborator11110000000000000000MYBPC3c.1540A>Gp.Ile514ValEXON 17Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1496A>Gp.Glu499GlyExon 15Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSELMM DatabaseMoolman-Smook 1999(HCM) :11110000000000000000MYH7c.743T>Cp.Ile248ThrEXON 9Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1318G>Ap.Val440MetExon 14Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardiogenomicsVan 2004(HCM) :11110000000000000000MYH7c.4066G>Ap.Glu1356LysExon 30Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardiogenomicsVan 2004, Perrot 2005(HCM) :11110000000000000000MYH7c.830T>Cp.Leu277ProEXON 10Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2191C>Gp.Pro731AlaEXON 20Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2708A>Gp.Glu903GlyExon 23Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYH7c.2845G>Ap.Glu949LysEXON 23Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsWatkins 1992(HCM) :11110000000000000000MYH7c.5302G>Ap.Glu1768LysEXON 37Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseVan 2004(HCM) :11110000000000000000MYH7c.5561C>Tp.Thr1854MetEXON 38Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.3158G>Ap.Arg1053GlnEXON 25Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomics - HCM or DCMKrkkinen 2004(HCM) :11110000000000000000MYH7c.1608G>Tp.Glu536AspEXON 16Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYH7c.2555T>Cp.Met852ThrEXON 22Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSEFHC Database, LMM Database FHC0177Richard 2003, Morita 2008(HCM) :11110000000000000000MYH7c.1357C>Ap.Arg453SerExon 14Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardioGenomics, LMM SNP DatabaseAckerman 2002, Garcia-Castro 2003, Perrot 2005, Greber-Platzer 2001, Nanni 2003(HCM) :11110000000000000000MYH7c.2129C>Tp.Pro710LeuEXON 19Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.3169G>Ap.Gly1057SerExon 25Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardioGenomicsVan 2004(HCM) :11110000000000000000MYH7c.632C>Tp.Pro211LeuExon 7Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsWoo 2003, Perrot 2005(HCM) :11110000000000000000MYH7c.976G>Cp.Ala326ProEXON 11Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsCoviello 1997(HCM) :11110000000000000000MYH7c.2198G>Ap.Gly733GluExon 20Likely Pathogenic (HCM)121SUBSTITUTIONMISSENSECardiogenomicsRichard 2003(HCM) :11110000000000000000MYH7c.505A>Gp.Arg169GlyExon 6Likely Pathogenic (HCM)101SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYH7c.1490A>Gp.Glu497GlyEXON 15Likely Pathogenic (HCM)51SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2572C>Gp.Arg858GlyEXON 22Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSESeidman PM 2005, dbSNP; Cardiogenomics - polymorphismsrs2754158(HCM) :11110000000000000000MYH7c.1370T>Cp.Ile457ThrEXON 14Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2080C>Tp.Arg694CysEXON 19Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsAndersen 1999, Van 2004, Van 2004, Andersen 2004(HCM) :11110000000000000000MYH7c.2899G>Ap.Glu967LysEXON 23Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2342T>Cp.Leu781ProEXON 21Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1273G>Ap.Gly425ArgExon 14Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsSong 2005(HCM) :11110000000000000000MYH7c.1532T>Cp.Ile511ThrExon 15Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsVan 2004(HCM) :11110000000000000000MYH7c.1283C>Tp.Ala428ValExon 14Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsRichard 2003, Van 2004(HCM) :11110000000000000000MYH7c.1436A>Gp.Asn479SerEXON 15Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsRichard 2003, Mohiddin 2003(HCM) :11110000000000000000MYH7c.2221G>Cp.Gly741ArgEXON 20Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSECardiogenomicsSong 2005, Fananapazir 1993(HCM) :11110000000000000000MYH7c.2644C>Gp.Gln882GluEXON 22Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsMohiddin 2003, Arai 1995(HCM) :11110000000000000000MYH7c.5326A>Gp.Ser1776GlyEXON 37Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardiogenomicsBlair 2002(HCM) :11110000000000000000MYH7c.1969A>Cp.Lys657GlnEXON 18Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.5380C>Ap.Gln1794LysEXON 37Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2129C>Ap.Pro710HisEXON 19Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2744T>Cp.Leu915ProEXON 23Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.968T>Ap.Ile323AsnEXON 11Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.4283T>Cp.Leu1428SerEXON 31Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.707T>Cp.Val236AlaEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.848A>Gp.Tyr283CysEXON 10Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.5192A>Tp.Asp1731ValEXON 36Likely Pathogenic (HCM)41SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.5287G>Ap.Ala1763ThrEXON 37Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2602G>Cp.Ala868ProEXON 22Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1562T>Cp.Ile521ThrExon 15Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.506G>Ap.Arg169LysEXON 6Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2513C>Tp.Pro838LeuEXON 22Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSEKaram 2008(HCM) :11110000000000000000MYH7c.5696T>Cp.Val1899AlaEXON 39Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.5344A>Gp.Met1782ValEXON 37Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1405G>Ap.Asp469AsnEXON 14Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) : The Asp469Asn variant has not been reported in the literature. Aspartic acid (Asp) at position 469 is evolutionarily conserved in mammals and chicken, increasing the likelihood that the change is pathogenic. In addition, another variant (p.Asp469T11110000000000000000MYH7c.2432T>Cp.Leu811ProEXON 22Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) : The Leu811Pro variant has not been reported in the literature. Leucine (Leu) at position 811 is conserved across mammals and in distantly related species, increasing the likelihood that the change is pathogenic. In addition, the vast majority of11110000000000000000MYH7c.5156A>Gp.Gln1719ArgEXON 35Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) : The Gln1719Arg variant has not been reported in the literature. This variant has been detected in one proband in our laboratory (of more than 1500 Caucasion probands or 3000 chromosomes tested) and was found to segregate with disease in one additi11110000000000000000MYH7c.3994G>Ap.Ala1332ThrEXON 30Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.507A>Tp.Arg169SerEXON 6Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.739T>Cp.Phe247LeuEXON 9Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSEGarca-Castro 2009(HCM) :11110000000000000000MYH7c.4124A>Gp.Tyr1375CysEXON 30Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.141C>Ap.Asn47LysEXON 3Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsAndersen 2001, CardioGenomics , Szczesna-Cordary 2004(HCM) :11110000000000000000MYL2c.482A>Gp.His161ArgEXON 07Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.119G>Ap.Arg40LysEXON 3Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.239C>Ap.Thr80AsnEXON 4Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.275G>Tp.Gly92ValEXON 5Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.170G>Ap.Gly57GluEXON 4Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.358C>Tp.Arg120TrpEXON 6Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.392C>Gp.Ser131CysEXON 6Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.488A>Cp.Glu163AlaExon 7Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSEMayo Clinic Research Study (2% of patients with HCM)(HCM) :11110000000000000000MYL2c.80A>Gp.Gln27ArgEXON 2Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.459G>Cp.Lys153AsnEXON 7Unknown Significance11SUBSTITUTIONMISSENSE(HCM) :11100000001000000000MYL3c.466G>Ap.Val156MetEXON 4Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardiogenomics - uncertainMorita 2006(HCM) :11110000000000000000MYL3c.517A>Gp.Met173ValEXON 5Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYL3c.461G>Ap.Arg154HisExon 4Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardiogenomicsPoetter 1996(HCM) :11110000000000000000MYL3c.170C>Gp.Ala57GlyEXON 3Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsLee 2001(HCM) :11110000000000000000MYL3c.11A>Gp.Lys4ArgEXON 1Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL3c.466G>Tp.Val156LeuEXON 4Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL3c.532G>Ap.Asp178AsnEXON 5Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000PRKAG2c.1516G>Cp.Glu506GlnEXON 14Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSEBayraka 2006, Kelly 2009(HCM) : The Glu506Gln variant has been reported in the literature in an infant proband with severe biventricular HCM and ventricular pre-excitation; the variant was also identified in two of the patient's affected family members (Kelly et al, 2009). It h11110000000000000000PRKAG2c.967T>Ap.Phe323IleExon 08Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000PRKAG2c.1508A>Gp.Gln503ArgEXON 14Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000PRKAG2c.1390G>Ap.Asp464AsnEXON 12Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNI3c.497C>Tp.Ser166PheEXON 7Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsVan 2003, Van 2004, Erdmann 2003, Mogensen 2004(HCM) :11110000000000000000TNNI3c.625G>Ap.Glu209LysExon 8Likely Pathogenic (HCM)61SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000TNNI3c.485G>Cp.Arg162ProEXON 7Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseRichard 2003, Ingles 2005, Doolan 2005(HCM) :11110000000000000000TNNI3c.434G>Ap.Arg145GlnEXON 7Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsTakahashi-Yanaga 2001, Mogensen 2004, Kimura 1997(HCM) :11110000000000000000TNNI3c.592C>Gp.Leu198ValEXON 8Likely Pathogenic (HCM)51SUBSTITUTIONMISSENSECardiogenomics(HCM) :11110000000000000000TNNI3c.526G>Ap.Val176MetEXON 7Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNI3c.602T>Cp.Met201ThrEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNI3c.575G>Tp.Arg192LeuEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNI3c.167T>Cp.Ile56ThrEXON 5Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNI3c.574C>Tp.Arg192CysEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNT2c.311C>Tp.Ala104ValEXON 9Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsNakajima-Taniguchi 1997, Palm 2001, Hinkle 2003(HCM) :11110000000000000000TNNT2c.247G>Ap.Glu83LysEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsHarada 2004, Mogensen 2003(HCM) :11110000000000000000TNNT2c.257A>Cp.Asp86AlaExon 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSECardiogenomicsVan 2003(HCM) :11110000000000000000TNNT2c.388C>Tp.Arg130CysEXON 10Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSECardiogenomicsWang 2007, Song 2005, Torricelli 2003(HCM) :11110000000000000000TNNT2c.732G>Tp.Glu244AspEXON 14Likely Pathogenic (HCM)41SUBSTITUTIONMISSENSECardiogenomicsrs45466197Yanaga 1999, Watkins 1995(HCM) :11110000000000000000TNNT2c.785A>Gp.Asn262SerEXON 15Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) : The Asn262Ser variant has not been identified in over 1500 Caucasian probands (3000 chromosomes) tested by our laboratory. In addition, asparagine (Asn) at position 262 is conserved across evolutionary distant species (including several mammals, c11110000000000000000TNNT2c.249G>Cp.Glu83AspEXON 8Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNT2c.330T>Gp.Phe110LeuExon 9Likely Pathogenic (HCM)41SUBSTITUTIONMISSENSETorricelli 2003(HCM) :11110000000000000000TNNT2c.773A>Tp.Lys258IleExon 14Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNT2c.807C>Ap.Asn269LysEXON 15Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.559G>Cp.Glu187GlnEXON 5Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.46G>Cp.Glu16GlnEXON 1Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.842T>Cp.Met281ThrExon 9Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSELMM SNP Database, CardiogenomicsVan 2003(HCM) :11110000000000000000TPM1c.343G>Ap.Glu115LysEXON 3Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.835A>Cp.Asn279HisEXON 9Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.609C>Gp.Asn203LysEXON 6BLikely Pathogenic (HCM)51SUBSTITUTIONMISSENSEF002814Denz 2004(HCM) :11110000000000000000TPM1c.790A>Gp.Lys264GluEXON 9Likely Pathogenic (HCM)31SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.82G>Ap.Asp28AsnExon 01Likely Pathogenic (HCM)21SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.676A>Cp.Lys226GlnEXON 07Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TPM1c.58G>Ap.Asp20AsnEXON 1Likely Pathogenic (HCM)11SUBSTITUTIONMISSENSE(HCM) :11110000000000000000ACTCc.793C>Gp.Gln265GluExon 04Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.814C>Tp.Arg272CysEXON 7Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSEZeller et al (2006) J Mol MEd 84:682Zeller 2006, Ehlermann 2008(HCM) :11110000000000000000MYBPC3c.2374T>Cp.Trp792ArgExon 24Likely Pathogenic (HCM)42SUBSTITUTIONMISSENSECardioGenomicsVan 2004(HCM) :11110000000000000000MYBPC3c.1790G>Ap.Arg597GlnExon 18Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYBPC3c.1468G>Ap.Gly490ArgExon 17Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardioGenomicsVan 2004(HCM) :11110000000000000000MYBPC3c.532G>Ap.Val178MetEXON 5Likely Pathogenic (HCM)82SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYBPC3c.1213A>Gp.Met405ValEXON 13Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2782G>Ap.Asp928AsnEXON 23Likely Pathogenic (HCM)62SUBSTITUTIONMISSENSECardioGenomics, LMM SNP DatabaseGimeno 2009, Erdmann 2003, Perrot 2005(HCM) :11110000000000000000MYH7c.2221G>Ap.Gly741ArgEXON 20Likely Pathogenic (HCM)42SUBSTITUTIONMISSENSECardiogenomicsRayment 1995, Fananapazir 1993, Richard 2003, Van 2004(HCM) :11110000000000000000MYH7c.2608C>Tp.Arg870CysEXON 22Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseWoo 2003, Anan 2000, CardioGenomics(HCM) : This variant has been reported in 3 probands with clinical features of HCM and was absent from at least 312 control chromosomes tested across several studies (Anan 2000, Woo 2003, CardioGenomics 2008). In addition, our laboratory has identified th11110000000000000000MYH7c.2779G>Ap.Glu927LysExon 23Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSECardioGenomicsB 2005(HCM) :11110000000000000000MYH7c.715G>Ap.Asp239AsnExon 8Likely Pathogenic (HCM)42SUBSTITUTIONMISSENSEg.7847G>APersonal Communication with Ivan Macciocca (Australia)(HCM) :11110000000000000000MYH7c.428G>Ap.Arg143GlnExon 5Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardiogenomicsWang 2008, Kimura 2010, Song 2005, Van 2004(HCM) : The Arg143Gln variant has been reported in 2 probands with a clinical diagnosis of HCM (Song 2005, Van Driest 2004) and was absent from over 1140 control chromosomes. In addition, this variant has been identified by our laboratory in three proban11110000000000000000MYH7c.2788G>Cp.Glu930GlnEXON 23Likely Pathogenic (HCM)92SUBSTITUTIONMISSENSECardiogenomicsGirolami 2006(HCM) :11110000000000000000MYH7c.788T>Cp.Ile263ThrEXON 9Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSEI263WCardiogenomicsTesson 1998, Richard 2003, Tesson 1997, Brito 2003(HCM) :11110000000000000000MYH7c.1063G>Ap.Ala355ThrExon 12Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSECardiogenomicsRichard 2003(HCM) :11110000000000000000MYH7c.2011C>Tp.Arg671CysEXON 18Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSECardiogenomicsRichard 2003, Mohiddin 2003(HCM) :11110000000000000000MYH7c.2606G>Ap.Arg869HisEXON 22Likely Pathogenic (HCM)72SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseVan 2004, Girolami 2006, Cecchi 2006, Anan 2000(HCM) :11110000000000000000MYH7c.28G>Cp.Gly10ArgEXON 3Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1549C>Ap.Leu517MetEXON 15Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardiogenomicsNanni 2003(HCM) :11110000000000000000MYH7c.1727A>Gp.His576ArgExon 16Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSECardiogenomicsPerrot 2005(HCM) :11110000000000000000MYH7c.1598T>Ap.Ile533AsnExon 16Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.2539A>Gp.Lys847GluExon 22Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSEFananapazir 1999(HCM) :11110000000000000000MYH7c.1003G>Tp.Ala335SerEXON 12Likely Pathogenic (HCM)62SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.3236G>Ap.Arg1079GlnEXON 25Likely Pathogenic (HCM)62SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.872C>Tp.Ser291PheEXON 10Likely Pathogenic (HCM)52SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYH7c.1012G>Ap.Val338MetEXON 12Likely Pathogenic (HCM)142SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.485G>Ap.Gly162GluEXON 7Likely Pathogenic (HCM)52SUBSTITUTIONMISSENSELMM DatabaseOlivotto 2008(HCM) :11110000000000000000MYL2c.260G>Cp.Gly87AlaEXON 4Likely Pathogenic (HCM)22SUBSTITUTIONMISSENSE(HCM) :11110000000000000000TNNI3c.586G>Ap.Asp196AsnExon 8Likely Pathogenic (HCM)52SUBSTITUTIONMISSENSECardiogenomicsNiimura 2002, Richard 2003, Mogensen 2004(HCM) :11110000000000000000TNNI3c.611G>Ap.Arg204HisEXON 8Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardioGenomicsDoolan 2005, Ingles 2005(HCM) :11110000000000000000TNNI3c.484C>Tp.Arg162TrpEXON 7Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardiogenomicsElliott 2000, Takahashi-Yanaga 2001, Murphy 2004, Kimura 1997(HCM) :11110000000000000000TNNT2c.857G>Ap.Arg286HisEXON 16Likely Pathogenic (HCM)42SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseVan 2003, Van 2004(HCM) :11110000000000000000TNNT2c.244G>Ap.Gly82ArgEXON 8Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000TNNT2c.536C>Tp.Ser179PheExon 11Likely Pathogenic (HCM)32SUBSTITUTIONMISSENSECardiogenomicsHo 2000(HCM) : The Ser179Phe variant has been previously identified in 1 consanguineous family with HCM where it was present in heterozygosity in two mildly affected individuals and in homozygosity in an individual who died early due to a severe form of HCM. The11110000000000000000MYBPC3c.2573G>Ap.Ser858AsnEXON 25Likely Pathogenic (HCM)53SUBSTITUTIONMISSENSEMorita 2008(HCM) : The Ser858Asn variant has been reported in one individual with childhood-onset HCM who carried a second, pathogenic variant in the MYBPC3 gene (Arg502Trp). The variant was not present among over 1200 control chromosomes (Morita 2008), supporting a11110000000000000000MYBPC3c.624G>Cp.Gln208HisEXON 5Likely Pathogenic (HCM)33SUBSTITUTIONMISSENSECardioGenomics, LMM Database(HCM) :11110000000000000000MYBPC3c.1813G>Ap.Asp605AsnExon 19Likely Pathogenic (HCM)63SUBSTITUTIONMISSENSECardioGenomics - variant of uncertain effect, Seidman PM 2005, LMM DatabaseAlders 2003, Van 2004, Kaski 2009, Morita 2008(HCM) : The Asp605Asn variant has been reported in four individuals with a clinical diagnosis of HCM and was absent from 600 control chromosomes (400 Caucasian chromosomes and 200 African American chromosomes; Alders 2003, Morita 2008, Van Driest 2004, Ka11110000000000000000MYBPC3c.710A>Cp.Tyr237SerEXON 6Likely Pathogenic (HCM)93SUBSTITUTIONMISSENSECardiogenomicsGovada 2008, Morner 2003(HCM) :11110000000000000000MYBPC3c.1483C>Gp.Arg495GlyEXON 17Likely Pathogenic (HCM)63SUBSTITUTIONMISSENSELMM DatabaseNiimura 1998, Maron 2001(HCM) :11110000000000000000MYBPC3c.3392T>Cp.Ile1131ThrEXON 31Likely Pathogenic (HCM)43SUBSTITUTIONMISSENSESeidman PM 2005, CardiogenomicsAlders 2003, Van 2004(HCM) :11110000000000000000MYBPC3c.1591G>Ap.Gly531ArgEXON 17Likely Pathogenic (HCM)53SUBSTITUTIONMISSENSEGirolami 2006(HCM) :11110000000000000000MYH7c.4377G>Tp.Lys1459AsnEXON 32Likely Pathogenic (HCM)43SUBSTITUTIONMISSENSELMM Database, CardiogenomicsVan 2004(HCM) :11110000000000000000MYH7c.2302G>Ap.Gly768ArgEXON 21Likely Pathogenic (HCM)63SUBSTITUTIONMISSENSECardiogenomicsRichard 2003(HCM) :11110000000000000000MYH7c.2360G>Ap.Arg787HisEXON 21Unknown Significance33SUBSTITUTIONMISSENSECardiogenomicsRichard 2003, Rai 2009, Laredo 2006, Garca-Castro 2009, B 2005(HCM) :11100000001000000000MYH7c.1757T>Cp.Val586AlaExon 16Likely Pathogenic (HCM)103SUBSTITUTIONMISSENSELMM Database(HCM) :11110000000000000000MYH7c.2681A>Gp.Glu894GlyEXON 23Likely Pathogenic (HCM)33SUBSTITUTIONMISSENSECardiogenomicsVan 2004, Van 2004, B 2005(HCM) :11110000000000000000MYH7c.596C>Tp.Ala199ValExon 7Likely Pathogenic (HCM)53SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL2c.401A>Cp.Glu134AlaEXON 6Likely Pathogenic (HCM)63SUBSTITUTIONMISSENSE(HCM) :11110000000000000000MYL3c.281G>Ap.Arg94HisEXON 3Likely Pathogenic (HCM)33SUBSTITUTIONMISSENSEFokstuen 2008(HCM) :11110000000000000000TNNI3c.509G>Ap.Arg170GlnEXON 7Likely Pathogenic (HCM)33SUBSTITUTIONMISSENSEKubo 2007, Kaski 2009(HCM) :11110000000000000000MYH7c.1987C>Tp.Arg663CysExon 18Likely Pathogenic (HCM)74SUBSTITUTIONMISSENSECardiogenomicsSong 2005, Van 2004(HCM) :11110000000000000000MYH7c.2207T>Cp.Ile736ThrExon 20Likely Pathogenic (HCM)74SUBSTITUTIONMISSENSECardiogenomicsErdmann 2000, Liu 2006, Ingles 2005, Mohiddin 2003, Perrot 2005(HCM) :11110000000000000000TNNI3c.422G>Ap.Arg141GlnEXON 7Likely Pathogenic (HCM)74SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseRichard 2003, Van 2003, Mogensen 2004(HCM) : The Arg141Gln variant has been reported in 4 HCM probands and was absent from over 500 control chromosomes (Richard 2003, Van Driest 2003, Mogensen 2004). In addition, our laboratory has detected this variant in two affected family members in each11110000000000000000TNNT2c.281G>Ap.Arg94HisEXON 9Likely Pathogenic (HCM)54SUBSTITUTIONMISSENSECardioGenomics(HCM) :11110000000000000000MYBPC3c.655G>Cp.Val219LeuExon 6Likely Pathogenic (HCM)75SUBSTITUTIONMISSENSECardioGenomics, LMM DatabaseVan 2004(HCM) : The Val219Leu variant has been reported in one individual with clinical features of HCM and was absent from 200 White and 200 Black control chromosomes (Van Driest 2004). Including this individual, the Val219Leu variant has been identified by our11110000000000000000MYBPC3c.442G>Ap.Gly148ArgEXON 4Unknown Significance95SUBSTITUTIONMISSENSE(HCM) :11100000001000000000MYH7c.4130C>Tp.Thr1377MetEXON 30Likely Pathogenic (HCM)105SUBSTITUTIONMISSENSEwrong nomenclature), E1377M (RichardCardiogenomicsRichard 2003, Van 2004(HCM) :11110000000000000000MYH7c.1491G>Tp.Glu497AspEXON 15Likely Pathogenic (HCM)135SUBSTITUTIONMISSENSECardioGenomicsArad 2005(HCM) :11110000000000000000MYBPC3c.2308G>Ap.Asp770AsnEXON 23Likely Pathogenic (HCM)86SUBSTITUTIONMISSENSECardioGenomicsrs36211723Girolami 2006, Tanjore 2008, Van 2004(HCM) :11110000000000000000MYH7c.5135G>Ap.Arg1712GlnExon 35Likely Pathogenic (HCM)117SUBSTITUTIONMISSENSECardiogenomics, LMM DatabaseHougs 2005, Morita 2008(HCM) : The Arg1712Gln missense variant has been previously reported in the literature in 13 probands (Morita et al., 2008; www.gencor.nl) and has been identified by our laboratory in six other probands (out of over 1900 Caucasian probands) with clinical11110000000000000000TPM1c.574G>Ap.Glu192LysExon 6bLikely Pathogenic (HCM)128SUBSTITUTIONMISSENSECardiogenomicsBrown 2005, Van 2003(HCM) :11110000000000000000MYBPC3c.1484G>Ap.Arg495GlnExon 17Likely Pathogenic (HCM)179SUBSTITUTIONMISSENSECardioGenomicsMaron 2001, Niimura 1998, Van 2004(HCM) : The Arg495Gln variant meets our criteria for pathogenicity (http://pcpgm.