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NM_000256.3(MYBPC3):c.2827C>T (p.Arg943Ter) AND Hypertrophic cardiomyopathy 4

Germline classification:
Pathogenic (8 submissions)
Last evaluated:
Jun 24, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000030699.19

Allele description [Variation Report for NM_000256.3(MYBPC3):c.2827C>T (p.Arg943Ter)]

NM_000256.3(MYBPC3):c.2827C>T (p.Arg943Ter)

Gene:
MYBPC3:myosin binding protein C3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_000256.3(MYBPC3):c.2827C>T (p.Arg943Ter)
Other names:
p.R943*:CGA>TGA
HGVS:
  • NC_000011.10:g.47335120G>A
  • NG_007667.1:g.22583C>T
  • NM_000256.3:c.2827C>TMANE SELECT
  • NP_000247.2:p.Arg943Ter
  • LRG_386t1:c.2827C>T
  • LRG_386:g.22583C>T
  • LRG_386p1:p.Arg943Ter
  • NC_000011.9:g.47356671G>A
  • c.2827C>T
  • p.Arg943X
Protein change:
R943*; ARG943TER
Links:
OMIM: 600958.0023; dbSNP: rs387907267
NCBI 1000 Genomes Browser:
rs387907267
Molecular consequence:
  • NM_000256.3:c.2827C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
2

Condition(s)

Name:
Hypertrophic cardiomyopathy 4
Synonyms:
Familial hypertrophic cardiomyopathy 4
Identifiers:
MONDO: MONDO:0007268; MedGen: C1861862; OMIM: 115197

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000053360OMIM
no assertion criteria provided
Pathogenic
(Aug 1, 2010)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Lekanne Deprez, R. H., Muurling-Vlietman, J. J., Hruda, J., Baars, M. J. H., Wijnaendts, L. C. D., Stolte-Dijkstra, I., Alders, M., van Hagen, J. M. Two cases of severe neonatal hypertrophic cardiomyopathy caused by compound heterozygous mutations in the MYBPC3 gene. (Letter) J. Med. Genet. 43: 829-832, 2006.,

SCV000299253Center for Medical Genetics Ghent, University of Ghent
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 1, 2016)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

SCV000733034Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV000743547Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus
criteria provided, single submitter

(ACGS Guidelines, 2013)
Pathogenic
(Oct 8, 2014)
germlineclinical testing

Citation Link,

SCV000744834Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus
criteria provided, single submitter

(ACGS Guidelines, 2013)
Pathogenic
(Sep 21, 2015)
germlineclinical testing

Citation Link,

SCV0025213993billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 22, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV002580166MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 2, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005399406Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jun 24, 2022)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot provided1not providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Founder mutations in hypertrophic cardiomyopathy patients in the Netherlands.

Christiaans I, Nannenberg EA, Dooijes D, Jongbloed RJ, Michels M, Postema PG, Majoor-Krakauer D, van den Wijngaard A, Mannens MM, van Tintelen JP, van Langen IM, Wilde AA.

Neth Heart J. 2010 May;18(5):248-54.

PubMed [citation]
PMID:
20505798
PMCID:
PMC2871745

Unexpected myopathy associated with a mutation in MYBPC3 and misplacement of the cardiac myosin binding protein C.

Tajsharghi H, Leren TP, Abdul-Hussein S, Tulinius M, Brunvand L, Dahl HM, Oldfors A.

J Med Genet. 2010 Aug;47(8):575-7. doi: 10.1136/jmg.2009.072710. Epub 2009 Oct 26.

PubMed [citation]
PMID:
19858127
See all PubMed Citations (10)

Details of each submission

From OMIM, SCV000053360.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a female infant with fatal cardiomyopathy (CMH4; 115197) who also had evidence of skeletal myopathy, Tajsharghi et al. (2010) identified homozygosity for a 2827C-T transition, resulting in an arg943-to-ter (R943X) substitution in the MYBPC3 gene. Skeletal muscle biopsy at 2 months of age showed pronounced myopathic changes with numerous small fibers, which all expressed slow/beta-cardiac myosin heavy chain protein (MYH7; 160760). Electron microscopy revealed disorganization of the sarcomeres and partial depletion of thick filaments in the small fibers; immunohistochemical staining showed the presence of cardiac MYBPC in the small abnormal fibers. RT-PCR and sequencing demonstrated the mutation in transcripts of skeletal muscle. Tajsharghi et al. (2010) noted that cardiac MYBPC is not normally expressed in skeletal muscle, and stated that the reason for the ectopic expression of cardiac MYBPC remained unknown. The R943X mutation had previously been identified in compound heterozygosity with other truncating MYBPC3 mutations in 2 unrelated Dutch infants with fatal hypertrophic cardiomyopathy (Lekanne Deprez et al., 2006); skeletal myopathy was not mentioned in that report.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Center for Medical Genetics Ghent, University of Ghent, SCV000299253.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733034.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743547.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000744834.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002521399.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000037039 / PMID: 14563344 / 3billion dataset). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From MGZ Medical Genetics Center, SCV002580166.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005399406.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with hypertrophic cardiomyopathy 4 (HCM; MIM#115197). (I) 0108 - This gene is associated with both recessive and dominant disease. Dominant inheritance is frequently reported in adult onset conditions, however recessive inheritance results in a more severe early onset phenotype (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 32841044). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (4 heterozygotes, 0 homozygotes). (SP) 0701 - Other null variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. There are at least ten pathogenic NMD-predicted variants that have been reported (DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is a Dutch founder variant and has been classified as pathogenic by multiple diagnostic laboratories. This variant has also been reported to be compound heterozygous or homozygous in individuals with severe early-onset disease (ClinVar, PMID: 25335496). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Cardiomyocytes derived from induced pluripotent stem cells (iPSC-CMs) heterozygous for this variant demonstrated aberrant calcium signalling and prolonged relaxation kinetics compared to WT cells, with homozygous iPSC-CMs demonstrating more severe impairment (PMID: 30586709). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024