ClinVar Miner

Submissions for variant NM_000293.3(PHKB):c.1546C>T (p.Gln516Ter)

gnomAD frequency: 0.00002  dbSNP: rs758004953
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000393619 SCV000343865 pathogenic not provided 2016-07-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000778463 SCV000914718 uncertain significance Glycogen storage disease IXb 2018-11-12 criteria provided, single submitter clinical testing The PHKB c.1546C>T (p.Gln516Ter) variant is a stop-gained variant, which was observed by ICSL 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 for this variant, it 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. No publications were found based on this search. Due to the potential impact of stop-gained variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for phosphorylase kinase deficiency.
Labcorp Genetics (formerly Invitae), Labcorp RCV000778463 SCV003022048 pathogenic Glycogen storage disease IXb 2023-03-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln516*) in the PHKB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHKB are known to be pathogenic (PMID: 9215682, 9326319). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 289493). This variant has not been reported in the literature in individuals affected with PHKB-related conditions. This variant is present in population databases (rs758004953, gnomAD 0.002%).

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