ClinVar Miner

Submissions for variant NM_001177316.2(SLC34A3):c.846G>A (p.Pro282=)

gnomAD frequency: 0.00004  dbSNP: rs121918236
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute Of Human Genetics Munich, Klinikum Rechts Der Isar, Tu München RCV000001494 SCV000608393 pathogenic Autosomal recessive hypophosphatemic bone disease 2017-09-30 criteria provided, single submitter clinical testing
Hadassah Hebrew University Medical Center RCV000001494 SCV001430588 likely pathogenic Autosomal recessive hypophosphatemic bone disease 2019-06-20 criteria provided, single submitter clinical testing
Laboratory of Functional Genomics, Research Centre for Medical Genetics RCV000001494 SCV001781032 likely pathogenic Autosomal recessive hypophosphatemic bone disease 2021-08-11 criteria provided, single submitter clinical testing Synonymous variant c.846G>A in SLC34A3 could be classified as likely pathogenic variant according to ACMG criteria (PM2, PS3, PM3). The variant vas observed in 12 y.o. female patient with hypophosphatemic rickets with hypercalciuria in compound heterozygous state with c.1304delG variant in SLC34A3 gene.
Invitae RCV002512648 SCV003441512 likely pathogenic not provided 2024-01-11 criteria provided, single submitter clinical testing This sequence change affects codon 282 of the SLC34A3 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SLC34A3 protein. This variant also falls at the last nucleotide of exon 8, which is part of the consensus splice site for this exon. This variant is present in population databases (rs121918236, gnomAD 0.005%). This variant has been observed in individual(s) with hypophosphatemic rickets with hypercalciuria (PMID: 16358215, 31672324, 33223529, 34805638). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1429). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Revvity Omics, Revvity RCV000001494 SCV003825681 uncertain significance Autosomal recessive hypophosphatemic bone disease 2020-07-21 criteria provided, single submitter clinical testing
OMIM RCV000001494 SCV000021649 pathogenic Autosomal recessive hypophosphatemic bone disease 2006-02-01 no assertion criteria provided literature only

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