Submissions for variant NM_000290.4(PGAM2):c.455C>T (p.Thr152Ile)

dbSNP: rs199869174

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV001163807	SCV001325884	uncertain significance	Glycogen storage disease type X	2018-01-12	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae	RCV001163807	SCV001646570	likely benign	Glycogen storage disease type X	2024-01-13	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002558576	SCV003710929	uncertain significance	Inborn genetic diseases	2022-03-16	criteria provided, single submitter	clinical testing	The c.455C>T (p.T152I) alteration is located in exon 2 (coding exon 2) of the PGAM2 gene. This alteration results from a C to T substitution at nucleotide position 455, causing the threonine (T) at amino acid position 152 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences	RCV003953550	SCV004769345	likely benign	PGAM2-related condition	2020-12-16	criteria provided, single submitter	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).