ClinVar Miner

Submissions for variant NM_000278.5(PAX2):c.641A>G (p.Asn214Ser)

gnomAD frequency: 0.00004  dbSNP: rs148402788
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000482076 SCV000573975 uncertain significance not provided 2017-03-22 criteria provided, single submitter clinical testing The N237S variant in the PAX2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The N237S variant is observed in 3/16,512 (0.02%) alleles from individuals of South Asian background in the ExAC dataset (Lek et al., 2016). This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. However, the N237S variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. We interpret N237S as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001865489 SCV002301954 uncertain significance Renal coloboma syndrome; Focal segmental glomerulosclerosis 7 2025-01-29 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 214 of the PAX2 protein (p.Asn214Ser). This variant is present in population databases (rs148402788, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PAX2-related conditions. ClinVar contains an entry for this variant (Variation ID: 424189). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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 RCV001865489 SCV002783265 uncertain significance Renal coloboma syndrome; Focal segmental glomerulosclerosis 7 2021-09-21 criteria provided, single submitter clinical testing
Ambry Genetics RCV003243144 SCV003937768 uncertain significance Inborn genetic diseases 2023-04-07 criteria provided, single submitter clinical testing The c.710A>G (p.N237S) alteration is located in exon 7 (coding exon 7) of the PAX2 gene. This alteration results from a A to G substitution at nucleotide position 710, causing the asparagine (N) at amino acid position 237 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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