NM_000256.3:c.1513_1515delAAG

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM4_SupportingPP5_Very_Strong

The NM_000256.3(MYBPC3):c.1513_1515delAAG(p.Lys505del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.00000991 in 1,613,944 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000096 ( 0 hom. )

Consequence

MYBPC3
NM_000256.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely pathogenic criteria provided, multiple submitters, no conflicts P:11U:2

Conservation

PhyloP100: 5.89

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 Pathogenic. Variant got 11 ACMG points.

PM1

In a domain Ig-like C2-type 3 (size 90) in uniprot entity MYPC3_HUMAN there are 33 pathogenic changes around while only 9 benign (79%) in NM_000256.3

PM4

Nonframeshift variant in NON repetitive region in NM_000256.3. Strenght limited to Supporting due to length of the change: 1aa.

PP5

Variant 11-47342686-CCTT-C is Pathogenic according to our data. Variant chr11-47342686-CCTT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 177699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-47342686-CCTT-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYBPC3	NM_000256.3 link	c.1513_1515delAAG	p.Lys505del	conservative_inframe_deletion	Exon 17 of 35	ENST00000545968.6	NP_000247.2	Q14896-1A5YM48

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
MYBPC3	ENST00000545968.6 link	c.1513_1515delAAG	p.Lys505del	conservative_inframe_deletion	Exon 17 of 35	5	NM_000256.3	ENSP00000442795.1	Q14896-1
MYBPC3	ENST00000399249.6 link	c.1513_1515delAAG	p.Lys505del	conservative_inframe_deletion	Exon 16 of 34	5		ENSP00000382193.2	A8MXZ9
MYBPC3	ENST00000544791.1 link	n.1513_1515delAAG		non_coding_transcript_exon_variant	Exon 17 of 27	5		ENSP00000444259.1	F5GZR4

Frequencies

GnomAD3 genomes

AF:

0.0000131

AC:

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000802

AC:

AN:

249264

Hom.:

AF XY:

0.0000148

AC XY:

AN XY:

135220

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:

0.0000177

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000958

AC:

AN:

1461698

Hom.:

AF XY:

0.00000825

AC XY:

AN XY:

727134

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000447

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:

0.0000166

GnomAD4 genome

AF:

0.0000131

AC:

AN:

152246

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000151

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:11Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hypertrophic cardiomyopathy

Pathogenic:4

Dec 31, 2018

Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 10, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes an in-frame deletion of one amino acid at codon 505 in the Ig-like domain C3 of the MYBPC3 protein. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over ten individuals affected with hypertrophic cardiomyopathy (PMID: 12707239, 16566405, 20433692, 24093860, 27532257, 28138913, 28771489, 31006259, 32268277, 32841044; Sabater-Molina et al 2013). It has been shown that this variant segregates with disease in three families (PMID: 20433692, 28771489; communication with an external laboratory, ClinVar SCV000203959.5). This variant has also been reported in one individual affected with left ventricular non-compaction (PMID: 24602869); in three individuals affected with dilated cardiomyopathy (PMID: 30847666, 32826072, 37904629); and in two individuals affected with sudden cardiac death (PMID: 28255936, 33336002), one of whom also carried a pathogenic truncation variant in the same gene (PMID: 33336002). This variant has been identified in 3/280658 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Jan 12, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant, c.1513_1515del, results in the deletion of 1 amino acid(s) of the MYBPC3 protein (p.Lys505del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs727504287, gnomAD 0.003%). This variant has been observed in individuals with clinical features of MYBPC3-related conditions (PMID: 12707239, 16566405, 20433692, 24093860, 24602869, 27532257, 28138913, 28255936, 30847666; internal data). This variant is also known as Del [10957-10959] (Del K504). ClinVar contains an entry for this variant (Variation ID: 177699). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

May 24, 2021

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Lys505del variant in MYBPC3 has been reported in at least 15 heterozygous individuals with HCM, 1 individual with SCD, 2 individuals with DCM and 1 infant with severe early-onset left ventricular noncompaction, who carried a second pathogenic variant in MYBPC3. Additionally, it segregated with disease in 3 affected individuals from 3 families (Cardim 2005 PMID: 16566405, Mademont-Soler 2017 PMID: 28771489, Marsiglia 2013 PMID: 24093860, Richard 2003 PMID: 12707239 , Rodriguez-Garcia 2010 PMID: 20433692, Schaefer 2014 PMID: 24602869, Sabater-Molina 2013 DOI:10.4081/cardiogenetics.2013.e5, Campuzano 2017 PMID: 28255936, Norrish 2019 PMID: 31006259, van Lint 2019 PMID: 30847666, Ambry pers. comm., Invitae pers. comm., Bristol Genetics Laboratory pers. comm., LMM data). It has also been identified in 1/35360 Latino chromosomes and 2/128444 European chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org). This variant is a deletion of 1 amino acid at position 505 and is not predicted to alter the protein reading-frame; it is unclear if this deletion will 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_Strong, PM2_Supporting, PM4_Supporting, PP1. -

not provided

Pathogenic:1Uncertain:2

Clinical Genetics, Academic Medical Center

Significance: Uncertain significance

Review Status: flagged submission

Collection Method: clinical testing

- -

Apr 19, 2023

Mayo Clinic Laboratories, Mayo Clinic

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_supporting, PM4, PS4 -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Uncertain significance

Review Status: flagged submission

Collection Method: clinical testing

- -

Cardiomyopathy

Pathogenic:2

Sep 18, 2024

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1513_1515del variant in MYBPC3 is predicted to cause an in-frame deletion of 1 amino acid at codon 505. It has also been previously reported as p.Lys504del using alternate nomenclature. It has a Grpmax Filtering Allele Frequency of 0.0003% in control populations in the Genome Aggregation Database (gnomAD). It has been previously reported in at least 15 apparently unrelated individuals with hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and left ventricular non-compaction cardiomyopathy (LVNC) (PMID 12707239, 16566405, 20433692, 24093860, 24602869, 27532257, 32268277, 34400558, 32826072, 31006259, 30847666 and others; ClinVar database, CHEO internal data). It was reported in a compound heterozygous state in an infant with a severe form of LVNC who carried a secondary pathogenic variant in MYBPC3 (p.Pro955fs); the p.Lys505del variant was inherited from an unaffected mother, while the p.Pro955fs variant was inherited from a father with HCM (PMID 24602869). This variant has also been reported in a compound heterozygous state in two other individuals: a postmortem case of cardiac death with suspected LVNC in which the proband also carried a pathogenic MYBPC3 variant (p.Pro955Argfs*95) (PMID 33336002), and in a patient with HCM who also carried a pathogenic TNNT2 variant (p.W287*) (PMID 28771489). This variant was reported to segregate with disease in at least 3 families (PMID 20433692, ClinVar database). In silico prediction programs predict that this variant is unlikely to affect splicing. However, this prediction has not been confirmed by RNA functional studies. This variant is listed in ClinVar (VCV000177699). Based on the above information, we categorize this variant as likely pathogenic. -

Apr 28, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant causes an in-frame deletion of one amino acid at codon 505 of the MYBPC3 protein. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over ten individuals affected with hypertrophic cardiomyopathy (PMID: 12707239, 16566405, 20433692, 24093860, 27532257, 28138913, 28771489, 31006259, 32268277; Sabater-Molina et al 2013). It has been shown that this variant segregates with disease in three families (PMID: 20433692, 28771489; communication with an external laboratory). This variant has also been reported in an individual affected with left ventricular non-compaction (PMID: 24602869), in individuals affected with dilated cardiomyopathy (PMID: 30847666, 32826072), and in an individual affected with sudden cardiac death (PMID: 28255936). This variant has been identified in 3/280658 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hypertrophic cardiomyopathy 4

Pathogenic:1

Laboratory of Genetics and Molecular Cardiology, University of São Paulo

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cardiovascular phenotype

Pathogenic:1

Oct 08, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1513_1515delAAG variant (also known as p.K505del) is located in coding exon 17 of the MYBPC3 gene. This variant results from an in-frame AAG deletion at nucleotide positions 1513 to 1515. This results in the in-frame deletion of a lysine at codon 505. This variant was reported in individuals with features consistent with hypertrophic cardiomyopathy (HCM) (Richard P et al. Circulation, 2003 May;107:2227-32; Cardim N et al. Rev Port Cardiol, 2005 Dec;24:1463-76; Marsiglia JD et al. Am Heart J, 2013 Oct;166:775-82; Schaefer E et al. Eur J Med Genet, 2014 Mar;57:129-32; Alejandra Restrepo-Cordoba M et al. J Cardiovasc Transl Res, 2017 Feb;10:35-46; Campuzano O et al. Sports Med, 2017 Oct;47:2101-2115; Walsh R et al. Genet Med, 2017 Feb;19:192-203; Field E et al. J Med Genet, 2022 Aug;59:768-775). Based on internal structural analysis, this variant is more disruptive than known pathogenic variants (Ambry internal data). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Hypertrophic cardiomyopathy 1

Pathogenic:1

Feb 20, 2020

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

MYBPC3-related disorder

Pathogenic:1

May 19, 2021

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS4, PM2, PM4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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