ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.3341C>T (p.Thr1114Ile)

dbSNP: rs137852293
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000548701 SCV000626793 likely pathogenic Glycogen storage disease IXa1 2020-09-15 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This sequence change replaces threonine with isoleucine at codon 1114 of the PHKA2 protein (p.Thr1114Ile). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has been reported to segregate with X-linked liver glycogenosis in a single family (PMID: 8733133, 7959740) and has been found in an individual affected with a glycogen storage disease and hepatomegaly (Invitae). ClinVar contains an entry for this variant (Variation ID: 10533). 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.
OMIM RCV000011279 SCV000031507 pathogenic Glycogen storage disease IXa2 1996-05-01 no assertion criteria provided literature only

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