ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.10073G>A (p.Cys3358Tyr) (rs148660051)

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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000482080 SCV000231295 pathogenic not provided 2017-04-05 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000505000 SCV000245680 pathogenic Retinitis pigmentosa 2021-03-29 criteria provided, single submitter clinical testing 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.
Knight Diagnostic Laboratories, Oregon Health and Sciences University RCV000190637 SCV000538073 likely pathogenic Usher syndrome, type 2A 2016-01-27 criteria provided, single submitter clinical testing 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.
GeneDx RCV000482080 SCV000565648 pathogenic not provided 2020-11-18 criteria provided, single submitter clinical testing 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, 22334370, 25472526, 22004887, 20507924, 25649381, 22135276, 21151602, 25999674, 25097241, 26667666, 29953849, 31456290, 31980526, 32176120, 32581362, 31589614, 33576794, 33258288)
Fulgent Genetics,Fulgent Genetics RCV000515419 SCV000611246 likely pathogenic Usher syndrome, type 2A; Retinitis pigmentosa 39 2017-05-18 criteria provided, single submitter clinical testing
SIB Swiss Institute of Bioinformatics RCV000179099 SCV000803576 likely pathogenic Retinitis pigmentosa 39 2018-05-31 criteria provided, single submitter curation 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).
Invitae RCV000482080 SCV000952339 pathogenic not provided 2020-10-09 criteria provided, single submitter clinical testing This sequence change replaces cysteine with tyrosine at codon 3358 of the USH2A protein (p.Cys3358Tyr). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and tyrosine. This variant is present in population databases (rs148660051, ExAC 0.05%). This variant has been observed in individual(s) with Usher syndrome or retinal disease (PMID: 22004887, 28559085, 22135276, 25472526). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 197932). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. For these reasons, this variant has been classified as Pathogenic.
Myriad Women's Health, Inc. RCV000190637 SCV001193786 likely pathogenic Usher syndrome, type 2A 2019-12-17 criteria provided, single submitter clinical testing 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.
Blueprint Genetics RCV001073681 SCV001239234 pathogenic Retinal dystrophy 2019-08-15 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000482080 SCV001246252 pathogenic not provided 2018-08-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001174974 SCV001338457 likely pathogenic Usher syndrome 2020-04-09 criteria provided, single submitter clinical testing 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 (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in USH2A causing Usher syndrome (0.00035 vs 0.013), allowing no conclusion about variant significance. c.10073G>A has been reported in the literature in individuals affected with Usher syndrome and other USH2A related diseases (e.g. Garcia-Garcia_2011, LeQuesneStabej_2012, Lenassi_2015, Calzetti_2018). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Twelve ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic (n= 9) and pathogenic (n=3). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV000190637 SCV001520105 likely pathogenic Usher syndrome, type 2A 2019-09-30 criteria provided, single submitter clinical testing 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]
Ocular Genomics Institute, Massachusetts Eye and Ear RCV000179099 SCV001573662 likely pathogenic Retinitis pigmentosa 39 2021-04-08 criteria provided, single submitter research 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.
Broad Institute Rare Disease Group, Broad Institute RCV000505000 SCV001950390 likely pathogenic Retinitis pigmentosa 2021-04-01 criteria provided, single submitter curation 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.
Division of Human Genetics,Children's Hospital of Philadelphia RCV000190637 SCV000536900 likely pathogenic Usher syndrome, type 2A 2016-07-19 no assertion criteria provided research
NIHR Bioresource Rare Diseases, University of Cambridge RCV000505000 SCV000598759 likely pathogenic Retinitis pigmentosa 2015-01-01 no assertion criteria provided research
Counsyl RCV000179099 SCV000678128 likely pathogenic Retinitis pigmentosa 39 2016-12-16 no assertion criteria provided clinical testing
Sharon lab,Hadassah-Hebrew University Medical Center RCV000505000 SCV001161345 likely pathogenic Retinitis pigmentosa 2019-06-23 no assertion criteria provided research
Genomics England Pilot Project,Genomics England RCV000179099 SCV001760012 pathogenic Retinitis pigmentosa 39 no assertion criteria provided clinical testing

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