ClinVar Genomic variation as it relates to human health

The p.Trp3521Arg variant in USH2A has been reported in at least 10 individuals w ith Usher syndrome (Dreyer 2008, McGee 2010, Le Quesne Stabej 2012, Glockle 2014 ). At least 4 of these individuals were reported to carry another pathogenic USH 2A variant in trans (Le Quesne Stabej 2012). This variant has also been identifi ed by our laboratory in 3 Caucasian individuals with Usher syndrome, all of whom carried a second, loss-of-function variant in the USH2A gene. The Exome Aggrega tion Consortium (ExAC, http://exac.broadinstitute.org) has identified this varia nt in 2/66552 European chromosomes (dbSNP rs111033264). Although this variant ha s been seen in the general population, its frequency is low enough to be consist ent with a recessive carrier frequency. Computational prediction tools and conse rvation analysis suggest that the variant may impact the protein. In summary, th e p.Trp3521Arg variant meets our criteria to be classified as pathogenic for Ush er syndrome in an autosomal recessive manner (http://pcpgmwww.partners.org/perso nalizedmedicince/LMM).

ACMG categories: PS3,PM2,PP1,PP3,PP4,PP5

This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 3521 of the USH2A protein (p.Trp3521Arg). This variant is present in population databases (rs111033264, gnomAD 0.006%). This missense change has been observed in individual(s) with retinitis pigmentosa (RP) or Usher syndrome (PMID: 24265693, 26969326). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 48352). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt USH2A protein function. For these reasons, this variant has been classified as Pathogenic.

USH2A: PM3:Very Strong, PM2

The USH2A c.10561T>C variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PM2, PM3, PP3, PP4. Based on this evidence we have classified this variant as Likely Pathogenic.

Variant summary: USH2A c.10561T>C (p.Trp3521Arg) results in a non-conservative amino acid change located in the Fibronectin type III domain (IPR003961) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.4e-05 in 251148 control chromosomes. c.10561T>C has been reported in the literature as a biallelic genotype in multiple individuals affected with Usher Syndrome (example, Eisenberger_2013, Bonnet_2016). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26969326, 20507924, 23591405, 27460420, 28041643, 30718709, 32531858, 24265693, 18273898, 22135276, 27318125, 28559085, 32581362, 36011334, 35266249, 32037395, 31964843, 36524988, 32313182, 34440443, 34662339, 25999674, 34906470, 36785559, 27957503, 32281467, 28944237)

The USH2A c.10561T>C variant is predicted to result in the amino acid substitution p.Trp3521Arg. This variant has been reported in multiple individuals with Usher syndrome type IIa or non-syndromic retinitis pigmentosa (see for examples Dreyer et al. 2008. PubMed ID: 18273898; Eisenberger et al. 2013. PubMed ID: 24265693; McGee et al. 2010. PubMed ID: 20507924, Supplementary table 1, Weisschuh et al. 2024. PubMed ID: 37734845). This variant is reported in 0.0054% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant has been interpreted as pathogenic or likely pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/48352). Given the evidence, we interpret c.10561T>C (p.Trp3521Arg) as pathogenic.