ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3756C>G (p.Ser1252Arg) (rs143451766)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000176699 SCV000228396 uncertain significance not provided 2018-09-12 criteria provided, single submitter clinical testing
Invitae RCV000814429 SCV000954839 uncertain significance Nephronophthisis 2019-12-20 criteria provided, single submitter clinical testing This sequence change replaces serine with arginine at codon 1252 of the NPHP3 protein (p.Ser1252Arg). The serine residue is highly conserved and there is a moderate physicochemical difference between serine and arginine. This variant is present in population databases (rs143451766, ExAC 0.1%), including at least one homozygous and/or hemizygous individual. This variant has been observed in a family with nephronophthisis, but no second variant was identified (PMID: 12872122). ClinVar contains an entry for this variant (Variation ID: 195996). 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.
Illumina Clinical Services Laboratory,Illumina RCV001147808 SCV001308654 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 RCV001147809 SCV001308655 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.
Illumina Clinical Services Laboratory,Illumina RCV001147810 SCV001308656 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.

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