ClinVar Genomic variation as it relates to human health

The c.8682-9A>G variant in USH2A has been detected in patients with hearing loss in trans with at least 4 pathogenic or suspected-pathogenic variants (PM3_VS; PMID: 27318125, 25425308, 28944237, 23591405). The allele frequency of the c.8682-9A>G variant in the USH2A gene is 0.04% (5/10112) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2_Supporting based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss (PM2_P). At least one patient with this variant displayed features of retinitis pigmentosa and hearing loss which is consistent with Usher syndrome (PP4; PMID: 27318125, 25425308, 28944237, 23591405). Computational prediction tools and conservation analysis suggest that the c.8682-9A>G variant may impact the protein (PP3). 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_VS, PM2_Supporting, PP4, PP3.

_x000D_ Criteria applied: PM3_VSTR, PS1_SUP, PP3

The USH2A c.8682-9A>G 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.8682-9A>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: One predicts the variant abolishes canonical a 3 acceptor site. Two predict the variant creates a cryptic 3 acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 6.8e-05 in 250002 control chromosomes (gnomAD and publication data). This frequency is not significantly higher than expected for a pathogenic variant in USH2A causing Usher Syndrome (6.8e-05 vs 0.011), allowing no conclusion about variant significance. c.8682-9A>G has been reported in the literature in multiple individuals affected with Usher Syndrome and Hereditary retinal dystrophies (e.g. Glockle_2013, Zein_2014, Hartel_2016, Neuhanus_2017). 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. Nine ClinVar submitters (evaluation after 2014) cite the variant as pathogenic (n=4) and likely pathogenic (n=5), including one expert panel (ClinGen Hearing Loss Variant Curation Expert Panel) classified as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 23591405, 18273898, 25425308, 27318125, 30358468, 28944237, 31980526, 33576794)

The c.8682-9A>G variant in USH2A was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). 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. If you have any questions about the classification please reach out to the Pierce Lab.

This sequence change falls in intron 43 of the USH2A gene. It does not directly change the encoded amino acid sequence of the USH2A protein. This variant is present in population databases (rs372347027, gnomAD 0.05%). This variant has been observed in individual(s) with Usher syndrome type II (PMID: 18273898, 23591405, 25425308, 27318125, 28894305, 28944237). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 197510). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

The USH2A c.8682-9A>G variant is predicted to interfere with splicing. This variant has been reported as pathogenic for autosomal recessive Usher syndrome (Table S5, Glöckle et al. 2014. PubMed ID: 23591405; Zein et al. 2014. PubMed ID: 25425308; Colombo et al. 2021. PubMed ID: 34781295). This variant is reported in 0.048% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. This variant has been interpreted as pathogenic by the ClinGen Hearing Loss Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/197510/). This variant is interpreted as pathogenic.