rs730880603

chr11-47332115-G-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PM2 PM5 PP3_Strong PP5

The NM_000256.3(MYBPC3):c.3771C>A(p.Asn1257Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N1257S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MYBPC3 NM_000256.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:3
• Conservation: PhyloP100: 1.20

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 11 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 16 uncertain in NM_000256.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-47332117-T-C is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.952
• PP5: Variant 11-47332115-G-T is Pathogenic according to our data. Variant chr11-47332115-G-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 181022.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=1, Uncertain_significance=2, Likely_pathogenic=2}. Variant chr11-47332115-G-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPC3	NM_000256.3	c.3771C>A	p.Asn1257Lys	missense_variant	33/35	ENST00000545968.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPC3	ENST00000545968.6	c.3771C>A	p.Asn1257Lys	missense_variant	33/35	5	NM_000256.3	P4
MYBPC3	ENST00000399249.6	c.3771C>A	p.Asn1257Lys	missense_variant	32/34	5		A2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 26, 2016	Variant classified as Uncertain Significance - Favor Pathogenic. The p.Asn1257Ly s variant in MYBPC3 has been reported in at least 7 individuals with HCM (Lopes 2013, Kapplinger 2014, Lopes 2015). This variant was absent from large populatio n studies. Computational prediction tools and conservation analysis suggest that the p.Asn1257Lys variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some s uspicion for a pathogenic role, the clinical significance of the p.Asn1257Lys va riant is uncertain. -
Uncertain significance, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Oct 01, 2013	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.Asn1257Lys Based on the data reviewed below we classify this variant as a variant of uncertain significance that is likely disease causing. The variant is novel. This is a semi-conservative amino acid change with a neutral, polar asparagine replaced with a basic polar lysine. The asparagine at position 1257 is highly conserved across species. In silico analysis (PolyPhen) predicts the variant to be possibly damaging. Variants at surrounding residues (p.Ala1255Thr, p.Gly1260Asp) have been reported in association with cardiomyopathy. In total the variant has not been seen in 5600 published controls and publicly available population datasets. There is no variation at codon 1257 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~5300 Caucasian and African American individuals (as of 3/28/2012). There is also no variation at this codon listed in dbSNP or 1000 genomes (as of 3/28/2012). -

Primary familial dilated cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

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not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

May 31, 2022

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies suggest a damaging effect in HEK293A cells (Helms et al., 2020); This variant is associated with the following publications: (PMID: 23396983, 24510615, 24793961, 27532257, 12818575, 25351510, 29030401, 33782553, 32841044) -

Hypertrophic cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 17, 2023

This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 1257 of the MYBPC3 protein (p.Asn1257Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with known and suspected hypertrophic cardiomyopathy (HCM) (PMID: 23396983, 24510615, 24793961, 27532257, 29030401; Invitae). ClinVar contains an entry for this variant (Variation ID: 181022). 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. Experimental studies have shown that this missense change affects MYBPC3 function (PMID: 32841044). For these reasons, this variant has been classified as Pathogenic. -

Asymmetric septal hypertrophy Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

NIHR Bioresource Rare Diseases, University of Cambridge

Jan 01, 2018

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Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 08, 2023

The p.N1257K variant (also known as c.3771C>A), located in coding exon 33 of the MYBPC3 gene, results from a C to A substitution at nucleotide position 3771. The asparagine at codon 1257 is replaced by lysine, an amino acid with similar properties. This variant has been observed in multiple individuals reported to have hypertrophic cardiomyopathy (HCM); however, clinical details were limited (Kapplinger JD et al. J Cardiovasc Transl Res, 2014 Apr;7:347-61; Bos JM et al. Mayo Clin. Proc., 2014 Jun;89:727-37; Walsh R et al. Genet. Med., 2017 02;19:192-203; Cirino AL et al. Circ Cardiovasc Genet, 2017 Oct;10:[Epub ahead of print]). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
CardioboostCm	Uncertain	0.37
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
Cadd	Benign	23
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.88	D;T;T
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Benign	0.21	N
LIST_S2	Pathogenic	0.98	D;D;D
M_CAP	Pathogenic	0.40	D
MetaRNN	Pathogenic	0.95	D;D;D
MetaSVM	Uncertain	0.64	D
MutationAssessor	Pathogenic	4.6	H;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-5.5	D;.;D
REVEL	Uncertain	0.57
Sift	Uncertain	0.0010	D;.;D
Sift4G	Pathogenic	0.0	D;D;D
Vest4		0.99
MVP		0.93
MPC		0.89
ClinPred		1.0	D
GERP RS		4.3
Varity_R		0.89
gMVP		1.0

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: rs730880603; hg19: chr11-47353666;