Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Clin |
RCV000036241 | SCV001245160 | likely pathogenic | Usher syndrome | 2022-08-03 | reviewed by expert panel | curation | The c.6560G>A variant in MYO7A is a missense variant predicted to cause substitution of glycine by aspartic acid at amino acid 2187. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00001190 (1/84018 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Hearing Loss VCEP threshold (<0.00007) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.915, which is above the threshold of 0.7, evidence that correlates with impact to MYO7A (PP3). At least one patient with this variant displayed profound congenital deafness and retinitis pigmentosa, which is highly specific for Usher syndrome (PP4, PMID:10930322). This variant has been detected in at least two individuals with Usher syndrome. Of those individuals, both were compound heterozygous for the variant and a pathogenic or likely pathogenic variant published by multiple submitters in ClinVar (c.2904G>T (p.Glu968Asp) and c.3719G>A (p.R1240Q)) and both of those were presumed in trans (1 PM3 point, PMID:10930322, LMM) (PM3). In summary, this variant was reviewed by the ClinGen Hearing Loss VCEP and classified as likely pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_P, PP3, PP4, PM3 (ClinGen Hearing Loss VCEP specifications version 2; 7/20/2022). |
| Laboratory for Molecular Medicine, |
RCV000036241 | SCV000059893 | likely pathogenic | Usher syndrome | 2019-03-13 | criteria provided, single submitter | clinical testing | The p.Gly2187Asp variant in MYO7A has been reported in 1 individual with Usher syndrome (Bharadwaj 2000) and identified by our laboratory in 1 individual with profound congenital hearing loss and vestibular problems. Both individuals were compound heterozygous for a second pathogenic or likely pathogenic MYO7A variant. This variant has been identified in 0.001% (1/84018) of European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs397516332). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analysis suggest that the p.Gly2187Asp variant may impact the protein. In summary, although additional studies are required to fully establish its clinical significance, the p.Gly2187Asp variant is likely pathogenic. ACMG/AMP Criteria applied: PM3_Strong, PM2, PP3 |
| Counsyl | RCV000675126 | SCV000800695 | uncertain significance | Autosomal recessive nonsyndromic hearing loss 2; Usher syndrome type 1 | 2018-04-13 | criteria provided, single submitter | clinical testing | |
| Natera, |
RCV001275540 | SCV001460755 | likely pathogenic | Usher syndrome type 1B | 2020-09-16 | no assertion criteria provided | clinical testing |