ClinVar Miner

Submissions for variant NM_002637.4(PHKA1):c.3511G>A (p.Ala1171Thr)

gnomAD frequency: 0.00034  dbSNP: rs144813238
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000385052 SCV000482733 benign Glycogen storage disease IXd 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000385052 SCV001494049 uncertain significance Glycogen storage disease IXd 2023-12-04 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1171 of the PHKA1 protein (p.Ala1171Thr). This variant is present in population databases (rs144813238, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 368644). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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 RCV002523835 SCV003681453 uncertain significance Inborn genetic diseases 2022-10-26 criteria provided, single submitter clinical testing The c.3511G>A (p.A1171T) alteration is located in exon 32 (coding exon 32) of the PHKA1 gene. This alteration results from a G to A substitution at nucleotide position 3511, causing the alanine (A) at amino acid position 1171 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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