ClinVar Miner

Submissions for variant NM_145207.3(AFG2A):c.1151T>C (p.Ile384Thr)

dbSNP: rs780025409
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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 RCV000687469 SCV000815034 uncertain significance Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome 2018-07-05 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with threonine at codon 384 of the SPATA5 protein (p.Ile384Thr). The isoleucine residue is highly conserved and there is a moderate physicochemical difference between isoleucine and threonine. This variant is present in population databases (rs780025409, ExAC 0.002%). This variant has not been reported in the literature in individuals with SPATA5-related disease. 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, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
GeneDx RCV004760703 SCV005371548 uncertain significance not provided 2023-07-05 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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