11-47346297-C-T

Position:

chr11-47346297-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM1PP3BP4_Moderate

The NM_000256.3(MYBPC3):c.1000G>A(p.Glu334Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,334 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000085 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00012 ( 0 hom. )

Consequence

MYBPC3
NM_000256.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:7B:4

Conservation

PhyloP100: 7.53

Variant links:

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]

MYBPC3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM1

In a helix (size 6) in uniprot entity MYPC3_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_000256.3

PP3

Multiple lines of computational evidence support a deleterious effect 8: AlphaMissense, BayesDel_noAF, Dann, M_CAP, MutationAssessor, phyloP100way_vertebrate, PrimateAI, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]

BP4

Computational evidence support a benign effect (MetaRNN=0.2173014).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYBPC3	NM_000256.3 linkuse as main transcript	c.1000G>A	p.Glu334Lys	missense_variant	12/35	ENST00000545968.6	NP_000247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYBPC3	ENST00000545968.6 linkuse as main transcript	c.1000G>A	p.Glu334Lys	missense_variant	12/35	5	NM_000256.3	ENSP00000442795	P4	Q14896-1
MYBPC3	ENST00000399249.6 linkuse as main transcript	c.1000G>A	p.Glu334Lys	missense_variant	11/34	5		ENSP00000382193	A2
MYBPC3	ENST00000544791.1 linkuse as main transcript	c.1000G>A	p.Glu334Lys	missense_variant, NMD_transcript_variant	12/27	5		ENSP00000444259

Frequencies

GnomAD3 genomes

AF:

0.0000854

AC:

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000251

AC:

AN:

247302

Hom.:

AF XY:

0.000231

AC XY:

AN XY:

134332

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00341

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000894

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000121

AC:

177

AN:

1461030

Hom.:

Cov.:

AF XY:

0.000124

AC XY:

AN XY:

726768

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00391

Gnomad4 SAS exome

AF:

0.0000813

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000450

Gnomad4 OTH exome

AF:

0.000166

GnomAD4 genome

AF:

0.0000854

AC:

AN:

152304

Hom.:

Cov.:

AF XY:

0.0000940

AC XY:

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000641

Hom.:

Bravo

AF:

0.0000982

ExAC

AF:

0.000297

AC:

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:7Benign:4

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Feb 08, 2021	Variant summary: MYBPC3 c.1000G>A (p.Glu334Lys) results in a conservative amino acid change located in the MyBP-C, tri-helix bundle domain (IPR040849) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00025 in 247302 control chromosomes, predominantly at a frequency of 0.0034 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in MYBPC3 causing Cardiomyopathy phenotype (0.001), suggesting that the variant may be a benign polymorphism found primarily in populations of East Asian origin. c.1000G>A has been reported in the literature in multiple individuals affected with cardiomyopathies (such as sporadic hypertrophic cardiomyopathy, hypertrophic cardiomyopathy, left ventricular noncompaction cardiomyopathy, restrictive cardiomyopathy (RCM)), in sudden cardiac arrest survivors and in patients suspected of genetic disorders (example: Anan_2007, Bahrudin_2008, Guo_2017, Jang_2015, Kim_2020, Liu_2020, Ntusi_2016, Olivotto_2008, Perkins_2017, Song_2017, Teramoto_2018, Wang_2014, Wu_2015). These report however, do not provide unequivocal conclusions about association of the variant with Cardiomyopathy. Co-occurrences with other pathogenic/likely pathogenic variants have been reported (MYH7 c.2123G>C, p.G708A; MYH7 c.2167C>T, p.R723C; MYH7 c.2207T>C, p.I736T; TNNI3 c.434G>A, p.R145Q; TNNI3 c.433C>T, p.R145W), providing supporting evidence for a benign role (Guo _2017, Wang_2014). In vitro over-expression studies in cell system resulted in reduced expression of the E334K mutant protein, caused Ubiquitin-proteasome system (UPS) impairment characterized by decreased level of 20S proteasome activity, increased the ratio of proapoptotic/antiapoptotic regulating protein, and increased apoptosis (Bahrudin_2008). It also enhanced Ca2+ transient amplitude resulting in cardiac electrophysiological dysfunction (Bahrudin_2011). Seven ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=4) or benign (n=2) or pathogenic (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 14, 2019	Variant classified as Uncertain Significance - Favor Benign. The p.Glu334Lys variant in MYBPC3 has been reported in >15 individuals with HCM (Anan 2007, Bahrudin 2008, Olivotto 2008, Gruner 2011, Zou 2013, Wang 2014, Jang 2015, Ntusi 2016, Guo 2017, Teramoto 2018, LMM data), 1 individual with DCM (Jang 2015), 1 individual with RCM (Wu 2015), and 1 individual with sudden cardiac death syndrome (Song 2017). However, no segregation data is available and at least 3 individuals with HCM carried additional variants that would be sufficient to explain their disease. Furthermore, the p.Glu334Lys variant has also been identified in 0.33% (65/19470) of East Asian chromosomes by gnomAD (gnomad.broadinstitute.org). This population frequency is significantly higher than expected for a variant causative of dominant HCM. In vitro functional studies provide some evidence that the p.Glu334Lys variant may impact protein function (Bahrudin 2011); however, these types of assays may not accurately represent biological function. Additionally, computational prediction tools and conservation analysis support that the p.Glu334Lys variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Finally, this variant has been reported with conflicting interpretations in ClinVar (Variation ID 177902). In summary, while its frequency suggests that it is more likely to be benign, the clinical significance of the p.Glu334Lys variant remains uncertain due to the presence of conflicting data. ACMG/AMP Criteria applied: PP3; PS3_Supporting; BA1. -
Uncertain significance, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jan 07, 2014	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. MYBPC3 p.Glu334Lys Based on the data reviewed below we would typically consider a variant like this to be likely disease causing. However, we are concerned about the fact that nearly all of the reported cases are Japanese and we have very few Japanese controls. Given that we are considering it a variant of uncertain significance, likely disease causing and recommending further segregation analysis and ideally waiting for more Japanese control data. The variant has been seen in at least 4 unrelated cases of cardiomyopathy. Anan et al (2007) reported the variant in one Japanese patient with HCM. Bahrudin et al (2008) observed the variant in three unrelated Japanese patients (which seem to not overlap with the report by Anan et al). Of note, given our patient's phenotype, this patient had "giant negative T-waves". These patients were reported as part of their HCM cohort, however, the authors noted that patients with this variant had systolic dysfunction (35%, 44%, 49%) and dilation (66, 50, 59). All three had left ventricular hypertrophy with IVS thicknesses of 16, 17, and 14 mm. Unfortunately only minimal clinical data is available and it is not clear if these patients first presented with classical HCM. Notably, Bahrudin et al observed the variant in 3 of 30 patients with HCM studied, which is unusually high prevalence for one variant, possibly suggesting that the variant is a common one in the Japanese population in general. They did not comment whether the patients had a shared haplotype. Gruner et al (2011) observed the variant in a patient with apical HCM from their cohort in Toronto, ancestry was not listed. In silico analysis with PolyPhen-2 predicts the variant to be benign while mutation taster predicts the variant to be disease causing. The glutamate at codon 334 is completely conserved across species, and neighboring amino acids are highly conserved. Another variant has been reported in association with disease at a nearby codon (p.Ile336Val). I could not find any other variants assocaited with disease at codon 334. Bahrudin et al (2008) reported that the myosin-binding protein was more quickly degraded by the ubiquitin-proteasome system. In total the variant has not been seen in at least ~6600 published controls and publicly available population datasets, though few of these match the ancestry of the published cases. There is no variation at codon 334 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~6400 Caucasian and African American individuals (as of 1/17/2013). There is also no variation at this codon listed in dbSNP or 1000 genomes (as of 1/17/2013), this probably includes 200 individuals of various Asian ancestries, though it is hard to be sure. There is no variation at codon 334 listed in the NIEHS exome data set, which includes 24 Asian individuals (as of 27th Sept 2012). The variant was not observed in the following published control samples: Anan et al (2007) did not see the variant in 100 controls (ancestry not noted). Bahrudin et al (2008) did not see the variant in 100 controls (ancestry not noted). -

Cardiomyopathy

Uncertain:1Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 15, 2023	This missense variant replaces glutamic acid with lysine at codon 334 of the MYBPC3 protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Experimental studies have shown that this variant may destabilize the protein through ubiquitin-proteasome system, modify the levels of channel proteins and induce apoptosis (PMID: 18929575, 21939669, 23740383). This variant has been reported in over 20 individuals affected with hypertrophic cardiomyopathy (PMID: 18929575, 21511876, 23283745, 23711808, 25132132, 26090888, 26163040, 32380161, 32492895, 33830315), in 5 individuals affected with dilated cardiomyopathy (PMID: 35284542), and in 1 individual affected with left ventricular non-compaction (PMID: 34853230), mostly of East Asian ancestry. This variant has also been identified in 66/278690 chromosomes (65/19470 East Asian chromosomes) in the general population by the Genome Aggregation Database (gnomAD). Although the high frequency of this variant in the general population suggests that it is unlikely to be disease-causing, available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Likely benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Jan 24, 2023	- -

Hypertrophic cardiomyopathy

Uncertain:1Benign:1

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 06, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Sep 05, 2023	This missense variant replaces glutamic acid with lysine at codon 334 of the MYBPC3 protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Experimental studies have shown that this variant may destabilize the protein through ubiquitin-proteasome system, modify the levels of channel proteins and induce apoptosis (PMID: 18929575, 21939669, 23740383). This variant has been reported in over 20 individuals affected with hypertrophic cardiomyopathy (PMID: 18929575, 21511876, 23283745, 23711808, 25132132, 26090888, 26163040, 32380161, 32492895, 33830315), in 5 individuals affected with dilated cardiomyopathy (PMID: 35284542), and in 1 individual affected with left ventricular non-compaction (PMID: 34853230), mostly of East Asian ancestry. This variant has also been identified in 66/278690 chromosomes (65/19470 East Asian chromosomes) in the general population by the Genome Aggregation Database (gnomAD). Although the high frequency of this variant in the general population suggests that it is unlikely to be disease-causing, available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Left ventricular noncompaction

Pathogenic:1

Likely pathogenic, flagged submission

clinical testing

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

- -

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jul 01, 2024

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17560888, 27731493, 29555771, 33830315, 21939669, 23283745, 18533079, 26163040, 24380728, 23711808, 19684034, 25132132, 23740383, 21511876, 28679633, 28518168, 20045868, 24574578, 27841901, 25856671, 22455086, 33407484, 33658040, 28323875, 31918855, 31980526, 26090888, 34853230, 35130036, 29398688, 35284542, 34621001, 32380161, 32492895, 38008210, 38186735, 18929575, 37652022, 28193612, 28202948, 35534676, 37653714) -

Hypertrophic cardiomyopathy 4

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Mendelics

May 28, 2019

- -

Left ventricular noncompaction 10

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -

Cardiovascular phenotype

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 11, 2020

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.84

CardioboostCm

Uncertain

0.11

BayesDel_addAF

Uncertain

0.041

BayesDel_noAF

Pathogenic

0.28

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.72

D;T;T

Eigen

Uncertain

0.58

Eigen_PC

Uncertain

0.58

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

1.0

D;D;D

M_CAP

Pathogenic

0.77

MetaRNN

Benign

0.22

T;T;T

MetaSVM

Uncertain

-0.027

MutationAssessor

Pathogenic

3.1

M;.;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Pathogenic

0.89

PROVEAN

Uncertain

-3.6

D;D;D

REVEL

Pathogenic

0.76

Sift

Uncertain

0.0020

D;D;D

Sift4G

Pathogenic

0.0

D;D;D

Polyphen

0.87

P;.;.

Vest4

0.86

MutPred

0.91

Gain of sheet (P = 0.0085);Gain of sheet (P = 0.0085);Gain of sheet (P = 0.0085);

MVP

0.92

MPC

0.36

ClinPred

0.34

GERP RS

4.7

Varity_R

0.57

gMVP

0.76

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over