ClinVar Miner

Submissions for variant NM_058004.4(PI4KA):c.4666G>A (p.Val1556Met)

gnomAD frequency: 0.00013  dbSNP: rs144363917
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) RCV001785414 SCV003920789 pathogenic Spastic paraplegia 84, autosomal recessive 2023-04-27 criteria provided, single submitter research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003479351 SCV004223132 uncertain significance not specified 2023-11-22 criteria provided, single submitter clinical testing Variant summary: PI4KA c.4666G>A (p.Val1556Met) results in a conservative amino acid change located in the phosphoinositide 3-kinase, accessory (PIK) domain (IPR001263) of the encoded protein sequence. Two of four in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00018 in 248792 control chromosomes (gnomAD). c.4666G>A has been reported in the literature in the compound heterozygous state in an individual affected with spastic paraplegia and mild intellectual disability (Verdura_2021). This report does not provide unequivocal conclusions about association of the variant with PI4KA-Related Disorders. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 34415322). No clinical diagnostic laboratories have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.
GeneDx RCV004591566 SCV005079780 uncertain significance not provided 2023-11-22 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34415322)
OMIM RCV001785414 SCV002026469 pathogenic Spastic paraplegia 84, autosomal recessive 2022-09-28 no assertion criteria provided literature only

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