rs397515905

chr11-47342719-G-Achr11-47342719-G-Cchr11-47342719-G-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PM5 PP3_Moderate PP5_Very_Strong

The NM_000256.3(MYBPC3):c.1483C>T(p.Arg495Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R495L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: MYBPC3 NM_000256.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:13
• Conservation: PhyloP100: 2.76

Genes affected

MYBPC3 (HGNC:7551): (myosin binding protein C3) MYBPC3 encodes the cardiac isoform of myosin-binding protein C. Myosin-binding protein C is a myosin-associated protein found in the cross-bridge-bearing zone (C region) of A bands in striated muscle. MYBPC3 is expressed exclusively in heart muscle and is a key regulator of cardiac contraction. Mutations in this gene are a frequent cause of familial hypertrophic cardiomyopathy. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 12 uncertain in NM_000256.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-47342719-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 42537.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.926
• PP5: Variant 11-47342719-G-A is Pathogenic according to our data. Variant chr11-47342719-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 164114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-47342719-G-A is described in Lovd as [Pathogenic]. Variant chr11-47342719-G-A is described in Lovd as [Likely_benign]. Variant chr11-47342719-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPC3	NM_000256.3	c.1483C>T	p.Arg495Trp	missense_variant	17/35	ENST00000545968.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPC3	ENST00000545968.6	c.1483C>T	p.Arg495Trp	missense_variant	17/35	5	NM_000256.3	P4
MYBPC3	ENST00000399249.6	c.1483C>T	p.Arg495Trp	missense_variant	16/34	5		A2
MYBPC3	ENST00000544791.1	c.1483C>T	p.Arg495Trp	missense_variant, NMD_transcript_variant	17/27	5

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152202 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000753 AC: 11 AN: 1461678 Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7 AN XY: 727130

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000989

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152202 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74360

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000151

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:13

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 09, 2023	This missense variant is located in the Ig-like domain C3 of the MYBPC3 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in at least 10 unrelated individuals affected with hypertrophic cardiomyopathy and in a few asymptomatic relatives (PMID: 18713777, 19150014, 20433692, 23283745, 25351510, 27532257, 28356264, 28771489, 31919335, 32492895, 33495597). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at this codon, p.Arg495Gln and p.Arg495Gly, are known to be pathogenic (ClinVar variation ID: 164113, 42537), indicating that arginine at this position is important for the MYBPC3 protein function. Based on the available evidence, this variant is classified as Likely Pathogenic. -
Likely pathogenic, no assertion criteria provided	research	Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	Dec 06, 2019	The MYBPC3 Arg495Trp variant has been reported in at least >10 HCM cases (see literature), and was found to segregate in one family (García-Castro M, et al., 2009). We have identified this variant in a HCM proband of East Asian descent, with no family history of disease. The variant is present at a low frequency in the Genome Aggregation Database (AF=0.000007; http://gnomad.broadinstitute.org/). In silico tools SIFT, PolyPhen-2 and MutationTaster predict this variant to be deleterious. Furthermore different rare variants at this position (Arg495Gln and Arg495Gly) have been reported as pathogenic, suggesting that an amino acid substitution at this site may not be tolerated. Based on the adapted ACMG criteria (Kelly MA, et al., 2018) the variant has been reported in more than 10 HCM probands (PS4_supporting), is rare in the general population (PM2), other amino acid changes at this position have been classified as pathogenic (PM5) and multiple in silico tools predict that this variant is deleterious (PP3), therefore we classify MYBPC3 Arg495Trp as 'likely pathogenic'. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 20, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 495 of the MYBPC3 protein (p.Arg495Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 19150014, 22765922, 27532257). ClinVar contains an entry for this variant (Variation ID: 164114). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant disrupts the p.Arg495 amino acid residue in MYBPC3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11499718, 18403758, 19659763, 20019025, 20624503, 22857948, 23396983, 24093860, 27532257). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 06, 2023	The p.Arg495Trp variant in MYBPC3 has been reported in at least 15 individuals with hypertrophic cardiomyopathy (HCM; Rodríguez-García 2010 PMID: 20433692, Coto 2012 PMID: 22765922, Rubattu 2016 PMID: 27483260, Walsh 2017 PMID: 27532257, Restrepo-Cordoba 2017 PMID: 28138913, Kim 2020 PMID: 32492895, Lipari 2020 PMID: 31919335, Sepp 2022 PMID: 35626289, LMM data), including in 1 individual who also had another pathogenic variant in MYBPC3 (Berge 2014 PMID: 24111713). This variant was also been identified by other clinical laboratories in ClinVar (Variation ID: 164114) and has also been identified in 0.001% (1/68028) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. Additionally, a variant involving this codon (p.Arg495Gln) have been identified in individuals with HCM and has been classified as pathogenic by this laboratory. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4, PM2_Supporting, PM5. -

Hypertrophic cardiomyopathy 4 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	May 19, 2023	The MYBPC3 c.1483C>T (p.Arg495Trp) missense variant has been identified in a heterozygous state in at least five individuals with hypertrophic cardiomyopathy (PMID: 19150014; PMID: 22765922; PMID: 27532257). The variant has also been found in a heterozygous state in asymptomatic individuals suggesting reduced penetrance (PMID: 19150014). The c.1483C>T variant was not observed in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. Additionally, two different amino acid substitutions at the same codon [(p.Arg495Gln) and (p.Arg495Gly)] have been reported in individuals with hypertrophic cardiomyopathy (PMID: 27532257; ClinVar). Multiple lines of computational evidence suggest the variant may impact the gene or gene product. This variant has been classified as pathogenic or likely pathogenic by at least three submitters in ClinVar. Based on the available evidence, the c.1483C>T (p.Arg495Trp) variant is classified as likely pathogenic for hypertrophic cardiomyopathy. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	Mar 01, 2023	The missense variant c.1483C>T(p.Arg495Trp) in MYBPC3 gene has been observed in heterozygous state in multiple individuals with hypertrophic cardiomyopathy (Coto et. al., 2012; García-Castro et. al., 2009). The p.Arg495Trp variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic / Likely_pathogenic (multiple submitters). The amino acid change p.Arg495Trp in MYBPC3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant disrupts the p.Arg495 amino acid residue in MYBPC3. Other variant(s) that disrupt this residue have been determined to be pathogenic (Marsiglia JD et. al., 2013). The amino acid Arg at position 495 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. Functional studies will be required to confirm the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	Oct 22, 2019	This variant has been previously reported as a heterozygous change in patients with hypertrophic cardiomyopathy or dilated cardiomyopathy (PMID: 19150014, 22765922, 27532257). It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. The c.1483C>T (p.Arg495Trp) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.1483C>T (p.Arg495Trp) variant is classified as Pathogenic. -

Cardiomyopathy Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 05, 2022	This missense variant is located in the Ig-like domain C3 of the MYBPC3 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in at least 10 unrelated individuals affected with hypertrophic cardiomyopathy and in a few asymptomatic relatives (PMID: 18713777, 19150014, 20433692, 23283745, 25351510, 27532257, 28356264, 28771489, 31919335, 32492895, 33495597). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at this codon, p.Arg495Gln and p.Arg495Gly, are known to be pathogenic (ClinVar variation ID: 164113, 42537), indicating that arginine at this position is important for the MYBPC3 protein function. Based on the available evidence, this variant is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Apr 01, 2022	- -

not provided Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Primary familial hypertrophic cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 13, 2019

Variant summary: MYBPC3 c.1483C>T (p.Arg495Trp) results in a non-conservative amino acid change located in the Immunoglobulin subtype 2 (IPR003598) domain and Immunoglobulin I-set (IPR013098) domain of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 249906 control chromosomes (gnomAD) but has been reported in the literature in individuals affected with Hypertrophic Cardiomyopathy (Garcia-Castro_2009, Coto_2012, Rodriguez-Garcia_2010, Walsh_2017). These data indicate that the variant may be associated with disease. However, this variant was also found in two asymptomatic family members (Garcia-Castro_2009), suggesting incomplete penetrance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Another missense change at this codon has been classified as pathogenic by our laboratory (p.Arg495Gly). Two submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 12, 2024

The p.R495W variant (also known as c.1483C>T), located in coding exon 17 of the MYBPC3 gene, results from a C to T substitution at nucleotide position 1483. The arginine at codon 495 is replaced by tryptophan, an amino acid with dissimilar properties. In one family, this variant was detected in a proband and maternal grandfather both reported to have hypertrophy, and was also detected in the proband's unaffected mother (García-Castro M et al. Rev Esp Cardiol, 2009 Jan;62:48-56). This variant has also been detected in other probands reported to have hypertrophic cardiomyopathy (HCM) and in HCM cohorts where, in some cases, clinical detail was limited or another variant was also detected (Zou Y et al. Mol. Biol. Rep., 2013 Jun;40:3969-76; Berge KE et al. Clin. Genet., 2014 Oct;86:355-60; Lopes LR et al. Heart. 2015 Feb;101(4):294-301; Rubattu S et al. Int J Mol Sci, 2016 Jul;17(8); Walsh R et al. Genet. Med., 2017 02;19:192-203;Lipari M et al. Pol Arch Intern Med, 2020 02;130:89-99). This alteration was also reported in one individual from a dilated cardiomyopathy (DCM) cohort (Mazzarotto F et al. Circulation, 2020 02;141:387-398). Another alteration at the same codon, p.R495Q (c.1484G>A), has been reported in association with HCM (Niimura H et al. N. Engl. J. Med. 1998 Apr;338(18):1248-57). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
CardioboostCm	Uncertain	0.62
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
Cadd	Uncertain	25
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.74	D;T;T
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.97	D;D;D
M_CAP	Pathogenic	0.38	D
MetaRNN	Pathogenic	0.93	D;D;D
MetaSVM	Uncertain	0.11	D
MutationAssessor	Pathogenic	3.5	M;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-5.2	D;.;D
REVEL	Pathogenic	0.70
Sift	Uncertain	0.010	D;.;D
Sift4G	Uncertain	0.0090	D;D;D
Vest4		0.97
MVP		0.90
MPC		0.85
ClinPred		0.99	D
GERP RS		3.7
Varity_R		0.44
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs397515905; hg19: chr11-47364270; COSMIC: COSV99921153;