ClinVar Miner

Submissions for variant NM_000278.5(PAX2):c.506C>T (p.Thr169Met)

gnomAD frequency: 0.00001  dbSNP: rs758091898
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001910183 SCV002185253 uncertain significance Renal coloboma syndrome; Focal segmental glomerulosclerosis 7 2023-05-08 criteria provided, single submitter clinical testing 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 169 of the PAX2 protein (p.Thr169Met). This variant is present in population databases (rs758091898, gnomAD 0.02%). 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: 1408870).
Ambry Genetics RCV004955809 SCV005463401 likely benign Inborn genetic diseases 2024-09-04 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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