NM_000256.3:c.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC

Variant names:

• chr11-47346242-AGCCTCTTTAGCATGCCGCGCAGGTCAGTGACGCCGTACTGGAAGGCGATGCGCTCGTACTCAGATGGGGGT-A
• rs1555122751
• NM_000256.3:c.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1 PP5_Moderate

The NM_000256.3(MYBPC3):​c.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC​(p.Pro329GlnfsTer7) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYBPC3 NM_000256.3 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.55
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• hypertrophic cardiomyopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• hypertrophic cardiomyopathy 4

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• left ventricular noncompaction 10

  Inheritance: AR, AD Classification: DEFINITIVE, MODERATE, LIMITED Submitted by: Ambry Genetics
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• atrial fibrillation

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 11-47346242-AGCCTCTTTAGCATGCCGCGCAGGTCAGTGACGCCGTACTGGAAGGCGATGCGCTCGTACTCAGATGGGGGT-A is Pathogenic according to our data. Variant chr11-47346242-AGCCTCTTTAGCATGCCGCGCAGGTCAGTGACGCCGTACTGGAAGGCGATGCGCTCGTACTCAGATGGGGGT-A is described in ClinVar as Pathogenic. ClinVar VariationId is 42814.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYBPC3	NM_000256.3	c.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC	p.Pro329GlnfsTer7	frameshift_variant	Exon 12 of 35	ENST00000545968.6	NP_000247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYBPC3	ENST00000545968.6	c.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC	p.Pro329GlnfsTer7	frameshift_variant	Exon 12 of 35	5	NM_000256.3	ENSP00000442795.1
MYBPC3	ENST00000399249.6	c.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC	p.Pro329GlnfsTer7	frameshift_variant	Exon 11 of 34	5		ENSP00000382193.2
MYBPC3	ENST00000544791.1	n.984_1054delACCCCCATCTGAGTACGAGCGCATCGCCTTCCAGTACGGCGTCACTGACCTGCGCGGCATGCTAAAGAGGC		non_coding_transcript_exon_variant	Exon 12 of 27	5		ENSP00000444259.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypertrophic cardiomyopathy Pathogenic:1

Sep 17, 2010

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.5
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1555122751; hg19: chr11-47367793;