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NM_000257.4(MYH7):c.715G>A (p.Asp239Asn) AND Hypertrophic cardiomyopathy 1

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Jan 24, 2024
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:
RCV000162339.9

Allele description [Variation Report for NM_000257.4(MYH7):c.715G>A (p.Asp239Asn)]

NM_000257.4(MYH7):c.715G>A (p.Asp239Asn)

Gene:
MYH7:myosin heavy chain 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q11.2
Genomic location:
Preferred name:
NM_000257.4(MYH7):c.715G>A (p.Asp239Asn)
Other names:
NM_000257.4(MYH7):c.715G>A
HGVS:
  • NC_000014.9:g.23431602C>T
  • NG_007884.1:g.9060G>A
  • NM_000257.4:c.715G>AMANE SELECT
  • NP_000248.2:p.Asp239Asn
  • LRG_384t1:c.715G>A
  • LRG_384:g.9060G>A
  • NC_000014.8:g.23900811C>T
  • NM_000257.2:c.715G>A
  • NM_000257.3:c.715G>A
  • c.715G>A
Protein change:
D239N
Links:
dbSNP: rs397516264
NCBI 1000 Genomes Browser:
rs397516264
Molecular consequence:
  • NM_000257.4:c.715G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hypertrophic cardiomyopathy 1
Synonyms:
Familial hypertrophic cardiomyopathy 1; MYH7-Related Familial Hypertrophic Cardiomyopathy
Identifiers:
MONDO: MONDO:0008647; MedGen: C3495498; OMIM: 192600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000212639Agnes Ginges Centre for Molecular Cardiology, Centenary Institute
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 4, 2019)
germlineresearch

PubMed (10)
[See all records that cite these PMIDs]

SCV001139419Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Likely pathogenic
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV0020581273billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 24, 2024)
germlineclinical testing

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

SCV005399438Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Feb 2, 2022)
germlineclinical testing

PubMed (9)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing, research
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Gene symbol: MYH7.

Iascone MR, Marchetti D, Ferrazzi P.

Hum Genet. 2007 Feb;120(6):916. No abstract available.

PubMed [citation]
PMID:
17438619

Prevalence of sarcomere protein gene mutations in preadolescent children with hypertrophic cardiomyopathy.

Kaski JP, Syrris P, Esteban MT, Jenkins S, Pantazis A, Deanfield JE, McKenna WJ, Elliott PM.

Circ Cardiovasc Genet. 2009 Oct;2(5):436-41. doi: 10.1161/CIRCGENETICS.108.821314. Epub 2009 Jul 16.

PubMed [citation]
PMID:
20031618
See all PubMed Citations (14)

Details of each submission

From Agnes Ginges Centre for Molecular Cardiology, Centenary Institute, SCV000212639.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (10)

Description

MYH7 Asp239Asn has been previously reported in multiple HCM cases (Walsh et al., 2017; Adler et al., 2016; Murphy et al., 2016; Garcia-Pavia et al., 2011; Kaski et al., 2009; Iascone et al., 2007) and has been found to segregate in their families (Garcia-Pavia et al., 2011; Ambry, ClinVar SCV000740109.2). We have also identified MYH7 Asp239Asn in a HCM proband (Ingles et al., 2017) as well as their 3 affected family members. This variant is present in the Genome Aggregation Database (http://gnomad.broadinstitute.org/) at an allele frequency of 0.000004. An in vitro functional study showed that the variant results in higher actin activated ATPase activity, higher actin gliding velocities and increased intrinsic force of the protein which results in hypercontractility (Adhikari et al., 2016). In a large HCM population study Walsh et al., showed that MYH7 variants identified in HCM cases were found to cluster between amino acids 181- 937 (2017), this implies that variants in this region are likely to cause a HCM phenotype. In silico tools PolyPhen2 and MutationTaster predict this variant to be deleterious, however SIFT predicts it to be "Tolerated". Based on the adapted ACMG criteria (Kelly MA, et al., 2018) this variant has been identified in at least 12 HCM probands without additional variants (PS4_moderate), shown to segregate strongly with disease across multiple families (PP1_Supporting), has been shown to have a damaging affect on protein in a functional study (PS3), it is located in a mutational hotspot (PM1) and is rare in the general population (PM2), therefore we classify MYH7 Asp239Asn as 'pathogenic'.

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

From Mendelics, SCV001139419.1

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

From 3billion, SCV002058127.2

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

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). Predicted Consequence/Location: The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PMID: 29300372). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.66 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.93 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000043100 /3billion dataset). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005399438.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as likely pathogenic. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established, however, missense variants have been proposed to act in a dominant negative manner (PMID: 24714796). (I) 0108 - This gene is associated with both recessive and dominant disease. Pathogenic variants in this gene are usually heterozygous, however a recessive inheritance pattern has been observed in severe cases (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 29300372). (I) 0200 - Variant is predicted to result in a missense amino acid change from aspartic acid to asparagine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. This variant is found within the head region, which is enriched with pathogenic missense variants (PMID: 29300372). (SP) 0710 - Another missense variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. An alternative change to a glutamic acid has been reported as a VUS in a HCM proband (PMID: 27247418). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple individuals with HCM (PMID: 27532257, 28615295, 21896538, 27247418, 26914223, ClinVar) and has been classified as likely pathogenic by the ClinGen cardiomyopathy variant curation expert panel. (SP) 0902 - This variant has moderate evidence for segregation with disease. This variant has been shown to segregate with HCM in five individuals from two families (PMID: 28615295, PMID: 21896538). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional analysis in mouse myoblast cells showed that this variant significant increased actin gliding velocity, intrinsic force, and ATPase activity compared to wild type (PMID: 27974200). (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: May 16, 2025