ClinVar Miner

Submissions for variant NM_003052.5(SLC34A1):c.1724C>T (p.Thr575Ile)

gnomAD frequency: 0.00003  dbSNP: rs201331677
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001362628 SCV001558658 uncertain significance not provided 2024-12-18 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 575 of the SLC34A1 protein (p.Thr575Ile). This variant is present in population databases (rs201331677, gnomAD 0.007%). This missense change has been observed in individuals with SLC34A1-related conditions (PMID: 28893421; internal data). ClinVar contains an entry for this variant (Variation ID: 548679). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SLC34A1 protein function with a negative predictive value of 80%. 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.
Revvity Omics, Revvity RCV001362628 SCV003825679 uncertain significance not provided 2020-12-10 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004533454 SCV004118455 uncertain significance SLC34A1-related disorder 2023-07-20 criteria provided, single submitter clinical testing The SLC34A1 c.1724C>T variant is predicted to result in the amino acid substitution p.Thr575Ile. This variant was reported in the homozygous state in an individual with nephrocalcinosis and hypercalcemia (Daga et al 2018. PubMed ID: 28893421). It was also reported in the heterozygous state in two additional patients from a large exome sequencing cohort; however, clinical information was not provided (Supp. Table 1 in Capalbo A et al 2019. PubMed ID: 31589614). This variant is reported in 0.0070% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/5-176825091-C-T). Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Fulgent Genetics, Fulgent Genetics RCV005034229 SCV005671584 likely pathogenic Hypophosphatemic nephrolithiasis/osteoporosis 1; Fanconi renotubular syndrome 2; Hypercalcemia, infantile, 2 2024-06-12 criteria provided, single submitter clinical testing
Yale Center for Mendelian Genomics, Yale University RCV000662329 SCV000784661 likely pathogenic Nephrocalcinosis; Nephrolithiasis 2017-09-08 no assertion criteria provided literature only

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