The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000260.4(MYO7A):c.631A>G (p.Ser211Gly)

CA278707

43325 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: fe99b50b-ba3f-4ebf-9816-12fa2f37b939

HGVS expressions

NM_000260.4:c.631A>G
NM_000260.4(MYO7A):c.631A>G (p.Ser211Gly)
NM_000260.3:c.631A>G
NM_001127179.2:c.631A>G
NM_001127180.1:c.631A>G
NM_001127180.2:c.631A>G
NM_001369365.1:c.598A>G
ENST00000409619.6:c.598A>G
ENST00000409709.7:c.631A>G
ENST00000409893.5:c.631A>G
ENST00000458637.6:c.631A>G
ENST00000620575.4:c.631A>G
NC_000011.10:g.77156900A>G
CM000673.2:g.77156900A>G
NC_000011.9:g.76867946A>G
CM000673.1:g.76867946A>G
NC_000011.8:g.76545594A>G
NG_009086.1:g.33637A>G
NG_009086.2:g.33655A>G

Likely Pathogenic

Met criteria codes 4
PM3_Strong PM2_Supporting PP3 PP4

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.631A>G (p.Ser211Gly) variant in MYO7A was present in 0.009% (6/64570) of non-Finnish European chromosomes in gnomAD, which is a low enough frequency to apply PM2_Supporting based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss (PM2_Supporting). This variant has been observed in at least 3 probands with Usher syndrome who carried other pathogenic or likely pathogenic variants in MYO7A; in two cases the other variant was confirmed to be in trans (PM3_Strong; PMID: 25472526; Laboratory for Molecular Medicine internal data, SCV000059882.6). All three of these probands displayed hearing loss and retinitis pigmentosa, features highly specific for MYO7A and Usher syndrome (PP4). The REVEL computational prediction analysis tool produced a score of 0.96, which is above the threshold necessary to apply PP3. In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive Usher syndrome based on ACMG/AMP criteria applied as specified by the Hearing Loss Expert Panel (PM2_Supporting, PM3_Strong, PP3, PP4).
Met criteria codes
PM3_Strong
1 published case and 2 from LMM, for 2.5 PM3 points total. Both LMM probands had likely pathogenic variants identified in trans.

PM2_Supporting
Present in 0.005453% (7/128370) of non-Finnish European chromosomes in gnomAD v2.1.1. Not present in any other subpopulations. In v3, present in 0.009292% (6/64570) of non-Finnish European chromosomes; also seen in 1 Latino chromosome.
PP3
REVEL score 0.957. Alamut does not predict an impact to splicing. Entirely conserved in UCSC database.
PP4
Both LMM probands and the published proband had a combination of SNHL and RP.
Approved on: 2020-05-06
Published on: 2020-05-12
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.