ClinVar Miner

Submissions for variant NM_003041.4(SLC5A2):c.1961A>G (p.Asn654Ser)

gnomAD frequency: 0.00531  dbSNP: rs61742739
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000013768 SCV001274153 uncertain significance Familial renal glucosuria 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Invitae RCV001512825 SCV001720312 benign not provided 2023-12-15 criteria provided, single submitter clinical testing
Mendelics RCV002247333 SCV002519376 uncertain significance not specified 2022-05-04 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003914837 SCV004734676 likely benign SLC5A2-related condition 2021-12-06 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
OMIM RCV000013768 SCV000034015 pathogenic Familial renal glucosuria 2004-02-01 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000013768 SCV001142463 uncertain significance Familial renal glucosuria 2020-01-06 no assertion criteria provided curation NM_003041.3:c.1961A>G in the SLC5A2 gene has an allele frequency of 0.03 in Ashkenazi Jewish subpopulation in the gnomAD database. Although 10 homozygous occurrences are observed in the gnomAD database, renal glucosuria is not lethal in young age. Therefore we did not count this as a strong benign evidence. One individual with renal glucosuria, was a compound heterozygote for this variant and p.Q167fsX186 mutation (PMID: 14614622). We interpret it as variant of uncertain significance (VUS). ACMG/AMP criteria applied: BS1; PM3.

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