ClinVar Miner

Submissions for variant NM_000343.4(SLC5A1):c.1673G>A (p.Arg558His)

gnomAD frequency: 0.00001  dbSNP: rs201799893
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726922 SCV000704180 pathogenic not provided 2016-12-09 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000114940 SCV001304883 uncertain significance Congenital glucose-galactose malabsorption 2017-04-28 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000114940 SCV001412898 pathogenic Congenital glucose-galactose malabsorption 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 558 of the SLC5A1 protein (p.Arg558His). This variant is present in population databases (rs201799893, gnomAD 0.02%). This missense change has been observed in individual(s) with glucose-galactose malabsorption (PMID: 20486940). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 127077). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SLC5A1 protein function. This variant disrupts the p.Arg558 amino acid residue in SLC5A1. Other variant(s) that disrupt this residue have been observed in individuals with SLC5A1-related conditions (Invitae), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000114940 SCV003835382 uncertain significance Congenital glucose-galactose malabsorption 2022-11-04 criteria provided, single submitter clinical testing
OMIM RCV000114940 SCV000148842 pathogenic Congenital glucose-galactose malabsorption 2011-01-01 no assertion criteria provided literature only

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.