ClinVar Genomic variation as it relates to human health

This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported as disease-causing by following sources [PMID: 25097241, 20507924, 25472526, 22004887, ClinVar ID: 197932]

The USH2A c.10073G>A 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: PS1, PM2, PM3, PP3. Based on this evidence we have classified this variant as Likely Pathogenic.

The p.Cys3358Tyr variant in USH2A has been reported in over 15 individuals with retinitis pigmentosa, with at least 9 of these individuals being compound heterozygous for a pathogenic variant on the remaining copy of USH2A (Calzetti 2018 PMID:29953849, Garcia-Garcia 2011 PMID:22004887, LeQuesne Stabej 2012 PMID:22135276, Lenassi 2015 PMID:25649381, McGee 2010 PMID:20507924, Neveling 2012 PMID:22334370, Stone 2018 PMID:28559085, van Huet 2015 PMID:25999674, Wang 2014 PMID:25097241, Zhao 2015 PMID:25472526, Avila-Fernandez 2010 PMID:21151602). Two of these individuals were reported to have features of atypical type 2 Usher syndrome, with a later onset hearing loss (Garcia-Garcia 2011 PMID:22004887, Lenassi 2015 PMID:25649381), and one was reported to have hearing loss though age of onset was not noted (Calzetti 2018 PMID:29953849). The variant has been identified in 98/128872 European chromosomes by gnomAD (http://gnomad.broadinstitute.org); however its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analysis suggest an impact to the protein. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive retinitis pigmentosa and/or atypical type 2 Usher syndrome, based on the previously reported individuals. ACMG/AMP criteria applied: PM3_VeryStrong, PM2_Supporting, PP3.

The p.Cys3358Tyr 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: PS1, PM2, PM3, PP3. 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.

Variant summary: USH2A c.10073G>A (p.Cys3358Tyr) 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 0.00035 in 251094 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in USH2A causing Usher Syndrome (0.00035 vs 0.011), allowing no conclusion about variant significance. c.10073G>A has been reported in the literature in multiple individuals affected with Usher Syndrome/Retinitis Pigmentosa/Inherited Retinal Diseases (IRD) (example, Garcia-Garcia_2011, LeQuesneStabej_2012, Lenassi_2015, Neveling_2012, Wang_2014, Calzetti_2018, McGee_2010, Weisschuh_2020). 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.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Usher syndrome, type 2A (MIM#276901) and retinitis pigmentosa (MIM# 6138093). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from cysteine to tyrosine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 111 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in at least ten individuals with both Usher syndrome, type 2A (MIM#276901) and retinitis pigmentosa (MIM# 6138093), and classified as both like pathogenic and pathogenic by diagnostic laboratories in Clinvar (PMID: 22004887, 25649381). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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: 28559085, 32531858, 34758253, 22334370, 25472526, 22004887, 20507924, 25649381, 22135276, 21151602, 25999674, 25097241, 26667666, 29953849, 31456290, 31980526, 32176120, 32581362, 31589614, 33576794, 33258288, 33737949, 32037395, 32326409, 36011334, 35266249, 38219857, 37217489, 36672815, 34906470, 31964843, 36819107, 33749171, 36646238, 38351866, 36909829)

The c.10073G>A (p.Cys3358Tyr) missense variant in the USH2A gene has been previously reported in several individuals affected with Usher Syndrome or Retinitis Pigmentosa. This allele was observed in 13 cases out of 914 affected alleles (Lenassi et al., 2015) and is significantly higher than the allele frequency in the ExAC database (13/121292). This variant is often seen in trans with other pathogenic variants (Garcia-Garcia et al., 2011; Le Quesne Stabej et al., 2012; Neveling et al., 2012; Lenassi et al., 2015). This c.10073G>A allele has been reported at low frequency, or is absent in other population databases (Exome Sequencing Project [ESP] = 0.058%, 1000 Genomes = NA). Multiple in silico algorithms predict this variant to have a deleterious effect GERP = 5.76; CADD = 22.4; PolyPhen = 1; SIFT = 0). Reputable diagnostic laboratories have reported this variant as either Likely Pathogenic or Pathogenic for either, Retinitis Pigmentosa or Usher Syndrome, Type 2A. Therefore, this collective evidence supports the classification of the c.10073G>A (p.Cys3358Tyr) as a recessive Likely Pathogenic variant for Usher syndrome, type IIA.

This variant is interpreted as a Likely Pathogenic, for Retinitis pigmentosa 39, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM3-Strong => PM3 upgraded in strength to Strong (PMID:22334370) (PMID:25649381).

NM_206933.2(USH2A):c.10073G>A(C3358Y) is classified as likely pathogenic in the context of USH2A-related disorders and is primarily associated with retinitis pigmentosa. Sources cited for classification include the following: PMID 22004887, 22334370, 26667666, 25472526, 25097241, 25649381 and 20507924. Classification of NM_206933.2(USH2A):c.10073G>A(C3358Y) is based on the following criteria: This variant has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

Clinical significance based on ACMG v2.0

This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 3358 of the USH2A protein (p.Cys3358Tyr). This variant is present in population databases (rs148660051, gnomAD 0.07%). This missense change has been observed in individual(s) with Usher syndrome or retinal disease (PMID: 22004887, 22135276, 25472526, 28559085). 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: 197932). 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 with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

The USH2A c.10073G>A variant is predicted to result in the amino acid substitution p.Cys3358Tyr. This variant has been reported along with a second pathogenic variant in many individuals with autosomal recessive nonsyndromic retinitis pigmentosa or Usher syndrome (Calzetti et al. 2018. PubMed ID: 29953849; Table S4, Colombo et al. 2021. PubMed ID: 33576794; Lynn et al. 2023. PubMed ID: 36672815; Molina-Ramírez et al. 2020. PubMed ID: 32176120; Table S4, Panneman et al. 2023. PubMed ID: 36819107), although it has been associated primarily with nonsyndromic retinal degeneration in patients without early onset hearing loss (Leanassi et al. 2015. PubMed ID: 25649381). This variant is reported in 0.076% of alleles in individuals of European (non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.