ClinVar Miner

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

gnomAD frequency: 0.00004  dbSNP: rs369162678
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000171146 SCV000221342 likely pathogenic not provided criteria provided, single submitter research
Illumina Laboratory Services, 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 Laboratory Services, 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000346948 SCV001225018 uncertain significance Nephronophthisis 2022-10-04 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1359 of the NPHP4 protein (p.Arg1359Trp). This variant is present in population databases (rs369162678, gnomAD 0.08%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 190975). 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 NPHP4 protein function. 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.
GeneDx RCV000171146 SCV001989307 uncertain significance not provided 2019-05-28 criteria provided, single submitter clinical testing Identified in the heterozygous state in several individuals in a study to estimate carrier frequency for various Mendelian disorders in a large Saudi Arabian population (Abouelhoda et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 27124789)
Fulgent Genetics, Fulgent Genetics RCV002478540 SCV002776383 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2021-10-28 criteria provided, single submitter clinical testing

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