ClinVar Miner

Submissions for variant NM_001128178.3(NPHP1):c.14G>T (p.Arg5Leu)

gnomAD frequency: 0.00150  dbSNP: rs190983114
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory,University of Chicago RCV000117830 SCV000152099 benign not specified 2017-04-27 criteria provided, single submitter clinical testing
Eurofins NTD LLC (GA) RCV000117830 SCV000203131 benign not specified 2014-02-04 criteria provided, single submitter clinical testing
Invitae RCV000205933 SCV000260349 benign Nephronophthisis 2021-12-15 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000117830 SCV000303399 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001094569 SCV000415935 likely benign Nephronophthisis 1 2017-04-28 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Laboratory Services,Illumina RCV000307224 SCV000415936 likely benign Senior-Loken syndrome 1 2017-04-28 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Laboratory Services,Illumina RCV000345710 SCV000415937 likely benign Joubert syndrome with renal defect 2017-04-28 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Mendelics RCV000986793 SCV001135924 benign Joubert syndrome 1 2019-05-28 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001258231 SCV001435137 benign Intellectual disability, X-linked 102 criteria provided, single submitter research The heterozygous p.Arg5Leu variant in NPHP1 has been identified in at least 5 individuals with Bardet-Biedl syndrome (PMID: 24746959), and has been identified in >5% of Latino chromosomes and 20 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In vitro functional studies provide some evidence that the p.Arg5Leu variant may slightly impact protein function (PMID: 24746959). However, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as benign for autosomal recessive Bardet-Biedl syndrome.
GeneDx RCV001705849 SCV001847244 benign not provided 2018-09-18 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 27535533, 24746959)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000117830 SCV002547954 likely benign not specified 2022-05-03 criteria provided, single submitter clinical testing

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