ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3281G>A (p.Arg1094Gln) (rs146890274)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000724039 SCV000228091 uncertain significance not provided 2017-10-05 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000194551 SCV000248268 uncertain significance not specified 2015-03-11 criteria provided, single submitter clinical testing
Invitae RCV001066929 SCV001231953 uncertain significance Nephronophthisis 2019-12-30 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 1094 of the NPHP3 protein (p.Arg1094Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs146890274, ExAC 0.07%). This variant has not been reported in the literature in individuals with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 195784). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.
Illumina Clinical Services Laboratory,Illumina RCV001147011 SCV001307778 uncertain significance Nephronophthisis 3 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 RCV001147012 SCV001307779 uncertain significance Renal-hepatic-pancreatic dysplasia 1 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 RCV001147013 SCV001307780 uncertain significance Meckel syndrome type 7 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.

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