ClinVar Miner

Submissions for variant NM_000293.3(PHKB):c.1631A>G (p.Asn544Ser)

gnomAD frequency: 0.00029  dbSNP: rs139383341
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001116235 SCV001274286 uncertain significance Glycogen storage disease IXb 2018-01-13 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 RCV001116235 SCV002130895 uncertain significance Glycogen storage disease IXb 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 544 of the PHKB protein (p.Asn544Ser). This variant is present in population databases (rs139383341, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with PHKB-related conditions. ClinVar contains an entry for this variant (Variation ID: 884922). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002556290 SCV003715166 uncertain significance Inborn genetic diseases 2021-08-10 criteria provided, single submitter clinical testing The c.1631A>G (p.N544S) alteration is located in exon 17 (coding exon 17) of the PHKB gene. This alteration results from a A to G substitution at nucleotide position 1631, causing the asparagine (N) at amino acid position 544 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV003106121 SCV003761995 uncertain significance not provided 2023-01-17 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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