ClinVar Miner

Submissions for variant NM_003052.5(SLC34A1):c.272_292del (p.Val91_Ala97del) (rs876661296)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000951080 SCV001097443 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
OMIM RCV000223670 SCV000280020 pathogenic Hypercalcemia, infantile, 2 2016-10-06 no assertion criteria provided literature only
Reproductive Health Research and Development,BGI Genomics RCV000223670 SCV001142351 likely pathogenic Hypercalcemia, infantile, 2 2020-01-06 no assertion criteria provided curation NM_003052.4:c.272_292del in the SLC34A1 gene has an allele frequency of 0.025 in European (non-Finnish) subpopulation in the gnomAD database, including 41 homozygous occurrences. However, considering the prevalence of hypercalcemia in the general population is approximately 1% to 2% (NCBI Bookshelf, Hypercalcemia), and it is not lethal, we decided not to take the allele frequency as a strong benign evidence. This variant was identified in homozygous state in a girl who presented with incidental nephrocalcinosis and polyuria (PMID: 26047794). Functional analyses confirmed the impaired trafficking of NaPi-IIa-91del7 in HEK293 cells while phosphate uptake in the Xenopus oocyte system was largely preserved (PMID: 26047794). We interpret it as Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PS3, PM3, PM4.

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