ClinVar Miner

Submissions for variant NM_003052.5(SLC34A1):c.745C>T (p.Arg249Ter)

gnomAD frequency: 0.00001  dbSNP: rs1426432774
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV001195304 SCV001365626 likely pathogenic Autosomal recessive infantile hypercalcemia 2019-05-08 criteria provided, single submitter clinical testing The p.Arg249X variant in SLC34A1 has not been previously reported in individuals with infantile hypercalcemia but has been identified in 1/18384 East Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). This nonsense variant leads to a premature termination codon at position 249, which is predicted to lead to a truncated or absent protein. Loss of function of the SLC34A1 gene is strongly associated to autosomal recessive infantile hypercalcemia. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal recessive infantile hypercalcemia. ACMG/AMP Criteria applied: PVS1, PM2.
Fulgent Genetics, Fulgent Genetics RCV002484062 SCV002780169 likely pathogenic Hypophosphatemic nephrolithiasis/osteoporosis 1; Fanconi renotubular syndrome 2; Hypercalcemia, infantile, 2 2021-08-25 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV005094043 SCV005848081 pathogenic not provided 2024-09-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg249*) in the SLC34A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC34A1 are known to be pathogenic (PMID: 26047794). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with SLC34A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 929955). For these reasons, this variant has been classified as Pathogenic.

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