ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.3983C>T (p.Pro1328Leu)

gnomAD frequency: 0.00068  dbSNP: rs199583130
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000592208 SCV000704673 uncertain significance not provided 2017-06-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001088286 SCV001001278 likely benign Nephronophthisis 2024-12-11 criteria provided, single submitter clinical testing
Yale Center for Mendelian Genomics, Yale University RCV001849405 SCV002106522 likely pathogenic Congenital anomaly of kidney and urinary tract 2018-08-24 no assertion criteria provided literature only
Genetic Services Laboratory, University of Chicago RCV003151110 SCV003839784 uncertain significance not specified 2022-08-15 no assertion criteria provided clinical testing DNA sequence analysis of the NPHP4 gene demonstrated a sequence change, c.3983C>T, in exon 28 that results in an amino acid change, p.Pro1328Leu. This sequence change has been previously described in the compound heterozygous state in an individual with congenital kidney/urinary tract anomalies (PMID: 30143558). This sequence change has been described in the gnomAD database with a frequency of 0.24% in the African subpopulation and 0.023% in the general population (dbSNP rs199583130). The p.Pro1328Leu change affects a highly conserved amino acid residue. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Pro1328Leu substitution. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Pro1328Leu change remains unknown at this time.

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