ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3290A>G (p.Asn1097Ser)

gnomAD frequency: 0.00001  dbSNP: rs1157229330
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001992220 SCV002282435 uncertain significance Nephronophthisis 2022-05-20 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1097 of the NPHP3 protein (p.Asn1097Ser).
Fulgent Genetics, Fulgent Genetics RCV002479712 SCV002779267 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-04-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV003250400 SCV003941655 uncertain significance Inborn genetic diseases 2023-05-24 criteria provided, single submitter clinical testing The c.3290A>G (p.N1097S) alteration is located in exon 23 (coding exon 23) of the NPHP3 gene. This alteration results from a A to G substitution at nucleotide position 3290, causing the asparagine (N) at amino acid position 1097 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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