ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.2154C>T (p.Phe718=)

gnomAD frequency: 0.00001  dbSNP: rs558637226
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000248754 SCV000316262 likely benign not specified criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000726409 SCV000344450 uncertain significance not provided 2016-08-02 criteria provided, single submitter clinical testing
Invitae RCV001079754 SCV001009497 pathogenic Nephronophthisis 2023-06-13 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 262696). This variant has been observed in individual(s) with clinical features of nephronophthisis (PMID: 30002499; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs558637226, gnomAD 0.005%). This sequence change affects codon 718 of the NPHP3 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the NPHP3 protein.
3billion RCV001775105 SCV002012328 likely pathogenic Nephronophthisis 3 2021-10-02 criteria provided, single submitter clinical testing Functional studies provide supportting evidence of the variant having a damaging effect on the gene or gene product (PMID: 30002499, PS3_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.00001061, PM2). The variant was observed in trans with a pathogenic variant (NM_153240.4:c.2694-2_2694-1del) as compound heterozygous (3billion dataset, PM3). In addition, It has been reported to co-segregate with the disease in at least one similarly affected relative/individual in the same family or similarly affected unrelated family (PMID: 30002499). The variant has been reported as pathogenic (ClinVar ID: VCV000262696.4).Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
CeGaT Center for Human Genetics Tuebingen RCV000726409 SCV004155567 likely benign not provided 2023-03-01 criteria provided, single submitter clinical testing NPHP3: BP4, BP7

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