ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.703G>A (p.Gly235Arg)

gnomAD frequency: 0.00008  dbSNP: rs368570508
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001365282 SCV001561547 uncertain significance Nephronophthisis 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 235 of the NPHP3 protein (p.Gly235Arg). This variant is present in population databases (rs368570508, gnomAD 0.02%). This missense change has been observed in individual(s) with nephronophthisis (PMID: 30586318). ClinVar contains an entry for this variant (Variation ID: 562444). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NPHP3 protein function with a negative predictive value of 80%. 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 RCV002485581 SCV002793446 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-10-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV002531426 SCV003718993 uncertain significance Inborn genetic diseases 2021-11-09 criteria provided, single submitter clinical testing The c.703G>A (p.G235R) alteration is located in exon 4 (coding exon 4) of the NPHP3 gene. This alteration results from a G to A substitution at nucleotide position 703, causing the glycine (G) at amino acid position 235 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Gharavi Laboratory, Columbia University RCV000681924 SCV000809407 likely pathogenic not provided 2018-09-16 no assertion criteria provided research

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