The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: MYO7A vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000260.4(MYO7A):c.3527G>A (p.Ser1176Asn)

CA242907

196099 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 981fcdec-991d-4878-a19d-3e45b688fc3b
Approved on: 2024-12-18
Published on: 2025-03-26

HGVS expressions

NM_000260.4(MYO7A):c.3527G>A
NM_000260.4:c.3527G>A
NM_000260.4(MYO7A):c.3527G>A (p.Ser1176Asn)
NC_000011.10:g.77189367G>A
CM000673.2:g.77189367G>A
NC_000011.9:g.76900412G>A
CM000673.1:g.76900412G>A
NC_000011.8:g.76578060G>A
NG_009086.1:g.66103G>A
NG_009086.2:g.66122G>A
ENST00000409709.9:c.3527G>A
ENST00000670577.1:c.1368G>A
ENST00000409619.6:c.3494G>A
ENST00000409709.7:c.3527G>A
ENST00000458169.2:c.1070G>A
ENST00000458637.6:c.3527G>A
ENST00000467137.1:n.54G>A
ENST00000481328.7:n.1070G>A
NM_000260.3:c.3527G>A
NM_001127180.1:c.3527G>A
NM_001127180.2:c.3527G>A
NM_001369365.1:c.3494G>A
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Uncertain Significance

Met criteria codes 1
BP2
Not Met criteria codes 4
PM3 PM2 PP3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.3527G>A variant in MYO7A is a missense variant predicted to cause substitution of serine by asparagine at amino acid 1176. The highest population minor allele frequency in gnomAD v4.1 is 0.0005863 (44/75046 alleles) in the African/African-American population (PM2_Supporting and BS1_Supporting are not met). The computational predictor REVEL gives a score of 0.638, which is neither above nor below the thresholds predicting a damaging or benign impact on MYO7A function (PP3 not met). The variant has been observed in at least 3 individuals with Usher syndrome type 1. However, in one proband the c.3527G>A variant in the homozygous state was observed with another homozygous pathogenic/likely pathogenic variant in MYO7A (BP2 met; PMID: 26969326). The remaining probands did not have a second pathogenic/likely pathogenic variant in MYO7A identified (PM3 and PP4 not met; PMID: 27344577, 27460420, 31479088). While this variant has also been identified in individuals with hearing loss, they either had no other pathogenic/likely pathogenic variant or an alternate molecular basis for disease was identified (PMID:33297549, LabCorp Genetics (formerly Invitae) internal data ClinVar SCV001418817.4, GeneDx internal data ClinVar SCV000714448.1). In summary, this variant has been classified as a variant of uncertain significance for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: BP2 (ClinGen Hearing Loss VCEP specifications version 2; 12/18/2024).
Met criteria codes
BP2
Observed in cis with another pathogenic/likely pathogenic variant in MYO7A, which was in the homozygous state (PMID: 26969326).
Not Met criteria codes
PM3
Observed in at least 3 individuals with Usher syndrome type 1; however, these probands either had possible alternate mechanisms of disease or only carried another VUS with phase unknown (PMID: 27344577, 27460420, 31479088, 26969326).
PM2
The highest population minor allele frequency in gnomAD v4.1 is 0.0005863 (44/75046 alleles) in the African/African-American population (PM2_Supporting and BS1_Supporting are not met).
PP3
The computational predictor REVEL gives a score of 0.638, which is neither above nor below the thresholds predicting a damaging or benign impact on MYO7A function (PP3 not met).
BS1
The highest population minor allele frequency in gnomAD v4.1 is 0.0005863 (44/75046 alleles) in the African/African-American population (PM2_Supporting and BS1_Supporting are not met).
Curation History
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