Submissions for variant NM_000290.4(PGAM2):c.310G>A (p.Ala104Thr)

gnomAD frequency: 0.00132  dbSNP: rs150570281

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000726387	SCV000344277	uncertain significance	not provided	2016-09-06	criteria provided, single submitter	clinical testing
GeneDx	RCV000726387	SCV000618214	uncertain significance	not provided	2018-01-25	criteria provided, single submitter	clinical testing	The A104T variant in the PGAM2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. While not present in the homozygous state, this variant is observed in 42/10362 (0.41%) alleles from individuals of African background in the ExAC dataset (Lek et al., 2016). The A104T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret A104T as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001503664	SCV001708520	likely benign	Glycogen storage disease type X	2025-01-29	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV001503664	SCV003836340	uncertain significance	Glycogen storage disease type X	2022-04-14	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003940073	SCV004756701	likely benign	PGAM2-related disorder	2023-05-22	no assertion criteria provided	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).