ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3311A>G (p.Tyr1104Cys)

gnomAD frequency: 0.00002  dbSNP: rs571618016
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000735161 SCV000863362 uncertain significance not provided 2018-09-13 criteria provided, single submitter clinical testing
Invitae RCV000802714 SCV000942556 uncertain significance Nephronophthisis 2022-08-08 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 1104 of the NPHP3 protein (p.Tyr1104Cys). This variant is present in population databases (rs571618016, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 598704). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002294376 SCV002587488 uncertain significance Kidney disorder 2021-06-24 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002477735 SCV002783618 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-12-18 criteria provided, single submitter clinical testing

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