ClinVar Miner

Submissions for variant NM_006416.5(SLC35A1):c.133A>G (p.Thr45Ala)

gnomAD frequency: 0.00306  dbSNP: rs145006535
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000514694 SCV000609544 uncertain significance not provided 2017-06-22 criteria provided, single submitter clinical testing
Invitae RCV001084562 SCV001014998 likely benign SLC35A1-congenital disorder of glycosylation 2024-01-22 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000514694 SCV001747474 likely benign not provided 2023-11-01 criteria provided, single submitter clinical testing SLC35A1: BS2
GeneDx RCV000514694 SCV001781556 likely benign not provided 2019-08-15 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001358153 SCV001553816 benign not specified no assertion criteria provided clinical testing The SLC35A1 p.Thr45Ala variant was not identified in the literature but was identified in dbSNP (ID: rs145006535), LOVD 3.0 and ClinVar (classified as uncertain significance by Illumina and Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, and as likely benign by Invitae). The variant was identified in control databases in 785 of 282850 chromosomes (3 homozygous) at a frequency of 0.002775 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 542 of 129166 chromosomes (freq: 0.004196), Other in 30 of 7228 chromosomes (freq: 0.004151), European (Finnish) in 104 of 25124 chromosomes (freq: 0.004139), South Asian in 52 of 30612 chromosomes (freq: 0.001699), Latino in 37 of 35440 chromosomes (freq: 0.001044), Ashkenazi Jewish in 9 of 10370 chromosomes (freq: 0.000868) and African in 11 of 24960 chromosomes (freq: 0.000441), but was not observed in the East Asian population. The p.Thr45 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000514694 SCV001743398 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000514694 SCV001974178 likely benign not provided no assertion criteria provided clinical testing

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.