ClinVar Miner

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

gnomAD frequency: 0.00065  dbSNP: rs143451766
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176699 SCV000228396 uncertain significance not provided 2018-09-12 criteria provided, single submitter clinical testing
Invitae RCV000814429 SCV000954839 likely benign Nephronophthisis 2024-01-29 criteria provided, single submitter clinical testing
Illumina Laboratory Services, 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 Laboratory Services, Illumina RCV001147809 SCV001308655 uncertain significance NPHP3-related Meckel-like syndrome 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 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.
CeGaT Center for Human Genetics Tuebingen RCV000176699 SCV001501878 uncertain significance not provided 2020-07-01 criteria provided, single submitter clinical testing
GeneDx RCV000176699 SCV001824778 likely benign not provided 2020-11-09 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 12872122, 21228398)
Preventiongenetics, part of Exact Sciences RCV003416083 SCV004115053 uncertain significance NPHP3-related condition 2023-05-19 criteria provided, single submitter clinical testing The NPHP3 c.3756C>G variant is predicted to result in the amino acid substitution p.Ser1252Arg. This variant was reported in one family with nephronophthisis 3 and a second variant in NPHP3 was not identified (Family F50, Olbrich et al 2003. PubMed ID: 12872122). This variant is reported in 0.12% of alleles in individuals of European (Non-Finnish) descent in gnomAD, including on homozygous individual (http://gnomad.broadinstitute.org/variant/3-132401603-G-C) which may be too frequent to be a disease causing variant. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Clinical Genetics, Academic Medical Center RCV000176699 SCV001919178 uncertain significance not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000176699 SCV001964048 uncertain significance not provided no assertion criteria provided clinical testing

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