ClinVar Miner

Submissions for variant NM_000278.5(PAX2):c.529G>A (p.Ala177Thr)

gnomAD frequency: 0.00007  dbSNP: rs749684940
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002031580 SCV002309179 uncertain significance Renal coloboma syndrome; Focal segmental glomerulosclerosis 7 2024-12-06 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 177 of the PAX2 protein (p.Ala177Thr). This variant is present in population databases (rs749684940, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of PAX2-related conditions (PMID: 34059960, 34696790, 36549658). ClinVar contains an entry for this variant (Variation ID: 1524244). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Possibly Damaging". 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 RCV002031580 SCV002775825 uncertain significance Renal coloboma syndrome; Focal segmental glomerulosclerosis 7 2022-04-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002550488 SCV003706295 uncertain significance Inborn genetic diseases 2021-07-06 criteria provided, single submitter clinical testing The c.529G>A (p.A177T) alteration is located in exon 5 (coding exon 5) of the PAX2 gene. This alteration results from a G to A substitution at nucleotide position 529, causing the alanine (A) at amino acid position 177 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV005057942 SCV005690061 uncertain significance not provided 2024-08-06 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34059960, 34696790, 36549658)

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