ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.3268G>A (p.Ala1090Thr)

gnomAD frequency: 0.00003  dbSNP: rs573269001
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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 RCV001957934 SCV002216187 uncertain significance Nephronophthisis 2021-11-26 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1090 of the NPHP4 protein (p.Ala1090Thr). This variant is present in population databases (rs573269001, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Fulgent Genetics, Fulgent Genetics RCV002479520 SCV002789607 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2024-06-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002562169 SCV003596819 uncertain significance Inborn genetic diseases 2022-01-18 criteria provided, single submitter clinical testing The c.3268G>A (p.A1090T) alteration is located in exon 23 (coding exon 22) of the NPHP4 gene. This alteration results from a G to A substitution at nucleotide position 3268, causing the alanine (A) at amino acid position 1090 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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