ClinVar Miner

Submissions for variant NM_002637.4(PHKA1):c.2916C>T (p.Ser972=)

gnomAD frequency: 0.00002  dbSNP: rs782102345
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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 RCV001169831 SCV001332610 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV001760118 SCV001999681 likely benign not provided 2022-02-18 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Nucleotide substitution has no predicted effect on splicing and is not conserved across species
Invitae RCV001169831 SCV003447386 uncertain significance Glycogen storage disease IXd 2023-05-22 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 915259). This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. This variant is present in population databases (rs782102345, gnomAD 0.01%). This sequence change affects codon 972 of the PHKA1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the PHKA1 protein. It affects a nucleotide within the consensus splice site. 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.

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