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
Labcorp Genetics (formerly Invitae), Labcorp RCV000548701 SCV000626793 pathogenic Glycogen storage disease IXa1 2024-02-23 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 1114 of the PHKA2 protein (p.Thr1114Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with X-linked liver glycogenosis and a glycogen storage disease and hepatomegaly (PMID: 8733133, 33763395; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 10533). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PHKA2 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000011279 SCV000031507 pathogenic Glycogen storage disease IXa2 1996-05-01 no assertion criteria provided literature only

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