ClinVar Miner

Submissions for variant NM_000478.6(ALPL):c.1327G>T (p.Ala443Ser)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
JKU Lab, Dept of Paediatrics, Johannes Kepler University RCV004586481 SCV005073979 likely pathogenic Hypophosphatasia 2024-06-11 criteria provided, single submitter clinical testing The variant is absent from GnomAD. The ACMG criteria applied can be looked up in the ALPL gene variant database. https://alplmutationdatabase.jku.at
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004690511 SCV005185026 uncertain significance not specified 2024-05-23 criteria provided, single submitter clinical testing Variant summary: ALPL c.1327G>T (p.Ala443Ser) results in a conservative amino acid change located in the Alk_phosphatase domain (IPR001952) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 245870 control chromosomes. c.1327G>T has been reported in the literature in the presumed compound heterozygous state in at least 1 individual affected with autosomal recessive Hypophosphatasia (example, Pierpont_2021). These data do not allow any conclusion about variant significance. A different variant affecting the same codon has been classified as pathogenic by our lab (c.1328C>T, p.Ala443Val), supporting the critical relevance of codon 443 to ALPL protein function. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 33579333). No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005015203 SCV005644701 likely pathogenic Adult hypophosphatasia; Childhood hypophosphatasia; Infantile hypophosphatasia 2024-05-24 criteria provided, single submitter clinical testing

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