ClinVar Miner

Submissions for variant NM_000478.6(ALPL):c.1505C>T (p.Ser502Leu)

gnomAD frequency: 0.00029  dbSNP: rs550358395
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000710511 SCV000840749 uncertain significance not provided 2017-11-14 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000710511 SCV002050016 uncertain significance not provided 2021-07-08 criteria provided, single submitter clinical testing The ALPL c.1505C>T; p.Ser502Leu variant (rs550358395), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 585385). This variant is found in the general population with an overall allele frequency of 0.012% (33/269432 alleles) in the Genome Aggregation Database. The serine at codon 502 is weakly conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.186). Due to limited information, the clinical significance of the p.Ser502Leu variant is uncertain at this time.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002279495 SCV002565143 likely benign Osteogenesis imperfecta 2021-02-09 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002507242 SCV002814248 uncertain significance Adult hypophosphatasia; Childhood hypophosphatasia; Infantile hypophosphatasia 2021-12-20 criteria provided, single submitter clinical testing
Invitae RCV000710511 SCV003294950 uncertain significance not provided 2022-09-08 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 502 of the ALPL protein (p.Ser502Leu). This variant is present in population databases (rs550358395, gnomAD 0.08%). This missense change has been observed in individual(s) with hypophosphatasia (Invitae). ClinVar contains an entry for this variant (Variation ID: 585385). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Natera, Inc. RCV001825412 SCV002094095 uncertain significance Hypophosphatasia 2019-10-28 no assertion criteria provided clinical testing

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