ClinVar Miner

Submissions for variant NM_174878.3(CLRN1):c.606T>G (p.Asn202Lys)

gnomAD frequency: 0.00001  dbSNP: rs746128095
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001246907 SCV001420299 pathogenic not provided 2023-09-29 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 202 of the CLRN1 protein (p.Asn202Lys). This variant is present in population databases (rs746128095, gnomAD 0.01%). This missense change has been observed in individual(s) with Usher syndrome (PMID: 25743179). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 971183). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive.
Dept Of Ophthalmology, Nagoya University RCV003887969 SCV004705686 uncertain significance Retinal dystrophy 2023-10-01 criteria provided, single submitter research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004690033 SCV005186073 likely pathogenic Usher syndrome 2024-05-29 criteria provided, single submitter clinical testing Variant summary: CLRN1 c.606T>G (p.Asn202Lys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251094 control chromosomes (gnomAD). c.606T>G has been reported in the literature in homozygous individuals affected with Usher Syndrome (Yoshimura_2015). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 25743179). ClinVar contains an entry for this variant (Variation ID: 971183). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005038009 SCV005664958 likely pathogenic Retinitis pigmentosa 61; Usher syndrome type 3A 2024-05-30 criteria provided, single submitter clinical testing

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