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

dbSNP: rs876661296

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000951080	SCV001097443	benign	not provided	2024-01-31	criteria provided, single submitter	clinical testing
GeneDx	RCV000951080	SCV001908150	benign	not provided	2019-02-01	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 26047794, 29959532, 25296721, 16688119, 27378183, 28470390)
Fulgent Genetics, Fulgent Genetics	RCV002503877	SCV002812474	likely benign	Hypophosphatemic nephrolithiasis/osteoporosis 1; Fanconi renotubular syndrome 2; Hypercalcemia, infantile, 2	2021-10-27	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000951080	SCV004011644	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	SLC34A1: BS1, BS2
Mayo Clinic Laboratories, Mayo Clinic	RCV000951080	SCV004227159	uncertain significance	not provided	2023-01-11	criteria provided, single submitter	clinical testing	BS2, PM3, PM4, PS3_supporting, PS4_moderate
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.
MK Azim Lab, Mohammad Ali Jinnah University	RCV000223670	SCV001478333	uncertain significance	Hypercalcemia, infantile, 2	2021-01-31	no assertion criteria provided	clinical testing
Molecular Genetics Laboratory, Biocruces Bizkaia Health Research Institute	RCV000223670	SCV004708193	likely pathogenic	Hypercalcemia, infantile, 2	2024-03-08	no assertion criteria provided	clinical testing