ClinVar Miner

Submissions for variant NM_145207.3(AFG2A):c.1505C>T (p.Pro502Leu)

gnomAD frequency: 0.00001  dbSNP: rs759111245
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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 RCV001304887 SCV001494192 uncertain significance Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome 2022-09-07 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 502 of the SPATA5 protein (p.Pro502Leu). This variant is present in population databases (rs759111245, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SPATA5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1007666). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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.
PreventionGenetics, part of Exact Sciences RCV003433105 SCV004116875 uncertain significance AFG2A-related disorder 2022-11-15 criteria provided, single submitter clinical testing The AFG2A c.1505C>T variant is predicted to result in the amino acid substitution p.Pro502Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0099% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/4-123868434-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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