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.5618G>A (p.Arg1873Gln)

CA278687

43292 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: ba742d08-69a6-4fa1-b737-dbd16b210ece
Approved on: 2019-11-26
Published on: 2019-11-26

HGVS expressions

NM_000260.4:c.5618G>A
NM_000260.4(MYO7A):c.5618G>A (p.Arg1873Gln)
NC_000011.10:g.77205599G>A
CM000673.2:g.77205599G>A
NC_000011.9:g.76916644G>A
CM000673.1:g.76916644G>A
NC_000011.8:g.76594292G>A
NG_009086.1:g.82335G>A
NM_000260.3:c.5618G>A
NM_001127180.1:c.5504G>A
ENST00000409619.6:c.5471G>A
ENST00000409709.7:c.5618G>A
ENST00000458169.2:n.3044G>A
ENST00000458637.6:c.5504G>A
ENST00000481328.7:n.3154G>A
ENST00000605744.1:n.239G>A
More

Pathogenic

Met criteria codes 6
PM2_Supporting PP3 PP4 PP1 PM5 PM3_Strong

Evidence Links 3

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The allele frequency of the p.Arg1873Gln variant in the MYO7A gene is 0.008% (2/24854) of European chromosomes by 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 detected in 2 probands with hearing loss and 2 probands with Usher syndrome. For 2 of those probands, a pathogenic or suspected-pathogenic variant was observed in trans, for 1 proband a pathogenic or suspected-pathogenic was suspected in trans, and for 1 of the probands, a rare variant of uncertain significance was observed in trans (PM3_Strong; PMID:23208854, 28000701, 29196752, Partners LMM internal data SCV000059849.6). The variant has been reported to segregate with hearing loss in one affected family member (PP1, Partners LMM internal data SCV000059849.6). A different pathogenic missense variant (p.Arg1873Trp) has been previously identified at this codon of MYO7A which may indicate that this residue is critical to the function of the protein (PM5; p.Arg1873Trp ClinVar Variation ID 43291). The REVEL computational prediction analysis tool produced a score of 0.936, which is above the threshold necessary to apply PP3. At least one of the above patients with the variant in this gene displayed features of Usher syndrome (PP4; Partners LMM internal data SCV000059849.6). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM3_Strong, PM2_Supporting, PM5, PP1, PP3, PP4.
Met criteria codes
PM2_Supporting
Variant is present in v2: 2/24854 European alleles 0.008% v3: 1/10472 European alleles 0.0095%
PP3
The REVEL score is 0.936, which is higher than our cutoff for pathogenicity of 0.7. The variant is entirely conserved.
PP4
This variant has been identified in 2 siblings with Congenital profound sensorineural hearing loss with retinitis pigmentosa (LMM internal data SCV SCV000059849.6)
PP1
This variant was identified with in two siblings with Usher syndrome. (LMM internal data SCV SCV000059849.6)
PM5
The p.Arg1873Trp variant is classified as a two star likely pathogenic/pathogenic variant in ClinVar. It has been observed in either the compound heterozygous or homozygous state in 5 patients with Usher syndrome.
PM3_Strong
There are 4 compound het observations: 2 with a known path/lp variant in trans (Schrauwen 2013 and Zazo Seco 2017, 2 pts), one with a VUS in trans (Baux 2017, 0.25 pts), and one with a LP/P variant phase unknown (LMM internal data SCV000059849.6, 0.5pts) 2.75pts total, Strong.

Curation History
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.