ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.4075C>T (p.Arg1359Trp) (rs369162678)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000308383 SCV000358394 uncertain significance Senior-Loken syndrome 4 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Clinical Services Laboratory,Illumina RCV001093794 SCV000358395 uncertain significance Nephronophthisis 4 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Invitae RCV000346948 SCV001225018 uncertain significance Nephronophthisis 2019-12-29 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 1359 of the NPHP4 protein (p.Arg1359Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs369162678, ExAC 0.09%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals with NPHP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 190975). 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: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre RCV000171146 SCV000221342 likely pathogenic not provided no assertion criteria provided research

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