ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.87G>T (p.Glu29Asp)

gnomAD frequency: 0.00010  dbSNP: rs951093397
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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) RCV000592381 SCV000702234 uncertain significance not provided 2016-09-27 criteria provided, single submitter clinical testing
Invitae RCV001217627 SCV001389474 uncertain significance Nephronophthisis 2022-11-22 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 497620). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.02%). This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 29 of the NPHP3 protein (p.Glu29Asp). 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. 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 RCV002491177 SCV002783803 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-02-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002530995 SCV003575079 uncertain significance Inborn genetic diseases 2021-08-02 criteria provided, single submitter clinical testing The c.87G>T (p.E29D) alteration is located in exon 1 (coding exon 1) of the NPHP3 gene. This alteration results from a G to T substitution at nucleotide position 87, causing the glutamic acid (E) at amino acid position 29 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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