rs727503185

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM5PP3_Moderate

The NM_000256.3(MYBPC3):c.2573G>A(p.Ser858Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,603,490 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S858R) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

MYBPC3
NM_000256.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:5

Conservation

PhyloP100: 7.57

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 Likely_pathogenic. Variant got 6 ACMG points.

PM1

In a domain Fibronectin type-III 1 (size 96) in uniprot entity MYPC3_HUMAN there are 50 pathogenic changes around while only 6 benign (89%) in NM_000256.3

PM5

Other missense variant is known to change same aminoacid residue: Variant chr11-47337421-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 635763.Status of the report is criteria_provided_single_submitter, 1 stars.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.906

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYBPC3	NM_000256.3 linkuse as main transcript	c.2573G>A	p.Ser858Asn	missense_variant	25/35	ENST00000545968.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYBPC3	ENST00000545968.6 linkuse as main transcript	c.2573G>A	p.Ser858Asn	missense_variant	25/35	5	NM_000256.3	P4	Q14896-1
MYBPC3	ENST00000399249.6 linkuse as main transcript	c.2573G>A	p.Ser858Asn	missense_variant	24/34	5		A2
MYBPC3	ENST00000544791.1 linkuse as main transcript	c.*78G>A		3_prime_UTR_variant, NMD_transcript_variant	25/27	5

Frequencies

GnomAD3 genomes

AF:

0.0000131

AC:

AN:

152190

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:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000413

AC:

AN:

242216

Hom.:

AF XY:

0.00

AC XY:

AN XY:

131522

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000914

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000110

AC:

AN:

1451300

Hom.:

Cov.:

AF XY:

0.0000111

AC XY:

AN XY:

720608

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000145

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000131

AC:

AN:

152190

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74348

show subpopulations

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:

0.0000294

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000622

Hom.:

Bravo

AF:

0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:5

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hypertrophic cardiomyopathy

Pathogenic:1Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 20, 2020	The p.Ser858Asn variant in MYPBC3 has been identified in at least 12 individuals with HCM and segregated with disease in 1 affected family member (Walsh 2017 PMID: 27532257, Ambry pers. comm., GeneDx pers. comm., Invitae pers. comm., LMM data). Additionally, it was identified in several individuals, some with earlier onset or more severe presentations, who carried additional pathogenic variants in other cardiomyopathy related genes (Ambry pers. Comm., Invitae pers. Comm., GeneDx pers. comm.). This variant has also been reported in ClinVar (Variation ID # 164070) and has been identified in 2/124800 of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that this variant may impact the protein. 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, PP3. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Jan 18, 2024	This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 858 of the MYBPC3 protein (p.Ser858Asn). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 20378854, 27532257, 31006259). ClinVar contains an entry for this variant (Variation ID: 164070). 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. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not specified

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 12, 2019	The c.2573G>A p.Ser858Asn variant (rs727503185) has been reported in at least 6 individuals with hypertrophic cardiomyopathy (Morita. 2008, and Walsh 2017). However, in at least one individual the p.Ser858Asn variant was identified with another pathogenic variant of MYBPC3 and family segregation data of the p.Ser858Asn variant was not readily available for any of the individuals. This variant is reported as a variant of uncertain significance by 5 laboratories in ClinVar (Variation ID: 164070). This variant is only observed on two alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The serine at codon 858 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Due to limited information, the clinical significance of the p.Ser858Asn variant is uncertain at this time. -
Uncertain significance, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Nov 20, 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. p.Ser858Asn (c.2573G>A). in MYBPC3 Given the lack of case data, we consider this variant a variant of uncertain significance and we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). Per ClinVar, LMM also classifies it as a variant of uncertain significance (last reviewed by them in 2010, evidence and internal data not provided). The variant has been seen in at least one case of HCM (not including this patient's family), though that patient carried another pathogenic variant. Morita et al (2008) reported the presence of this variant in one individual with HCM. This patient was diagnosed early in childhood and also carried an additional variant in the MYBPC3 gene which is very likely disease causing and is actually the most common HCM-causing variant, present in 2.4% of patients with HCM (p.Arg502Trp). The authors did not report data on segregation or phasing. This is likely the same case that was reported by Saltzman et al (2010). Serine is highly conserved across species at position 858 in MYBPC3 gene. The amino acid change is chemically conservative, with a polar, neutral Serine being replaced by a polar, neutral Asparagine. Three is no variation at codon 858 listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of August 27th, 2015). There is adequate coverage.This variant was not identified in 680 presumed healthy controls (Morita et al 2008). -

not provided

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jun 13, 2022

Reported in association with cardiomyopathy; however, at least one family harbored an additional pathogenic variant in the MYBPC3 gene (Morita et al., 2008; Saltzman et al., 2010; Ho et al., 2013; Walsh et al., 2017); 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; This variant is associated with the following publications: (PMID: 23549607, 20378854, 18403758, 18761664, 27532257, 25228707, 31006259) -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 18, 2023

The p.S858N variant (also known as c.2573G>A), located in coding exon 25 of the MYBPC3 gene, results from a G to A substitution at nucleotide position 2573. The serine at codon 858 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in patients with hypertrophic cardiomyopathy (HCM) and HCM genetic testing cohorts; however, other variants in cardiomyopathy-associated genes were detected in some cases and/or clinical detail was limited (Morita H et al. N. Engl. J. Med. 2008;358:1899-908; Walsh R et al. Genet. Med. 2017;19:192-203; Norrish G et al. Circulation. 2019 Jul;140(3):184-192; Field E et al. J Med Genet. 2022 Aug;59(8):768-775). 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

0.94

CardioboostCm

Uncertain

0.68

BayesDel_addAF

Uncertain

0.095

BayesDel_noAF

Benign

-0.10

Cadd

Uncertain

Dann

Uncertain

1.0

DEOGEN2

Uncertain

0.46

T;T;T

Eigen

Pathogenic

0.99

Eigen_PC

Pathogenic

0.86

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.97

D;D;D

M_CAP

Pathogenic

0.62

MetaRNN

Pathogenic

0.91

D;D;D

MetaSVM

Uncertain

0.76

MutationAssessor

Pathogenic

4.7

H;.;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.57

PROVEAN

Uncertain

-2.7

D;.;D

REVEL

Pathogenic

0.71

Sift

Uncertain

0.0010

D;.;D

Sift4G

Uncertain

0.0040

D;D;D

Vest4

0.94

MVP

0.93

MPC

0.80

ClinPred

0.99

GERP RS

4.6

Varity_R

0.82

gMVP

0.81

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

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