ClinVar Miner

Submissions for variant NM_032444.4(SLX4):c.5040G>T (p.Arg1680Ser)

dbSNP: rs199592185
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 4
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001292854 SCV001481534 uncertain significance Fanconi anemia complementation group P 2019-09-25 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Labcorp Genetics (formerly Invitae), Labcorp RCV001417838 SCV001620044 likely benign Fanconi anemia 2025-01-21 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV001417838 SCV002529374 uncertain significance Fanconi anemia 2021-12-16 criteria provided, single submitter curation
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV001292854 SCV002768734 uncertain significance Fanconi anemia complementation group P 2020-05-25 criteria provided, single submitter clinical testing A heterozygous missense variant was identified, NM_032444.2(SLX4):c.5040G>T in exon 14 of 15 of the SLX4 gene. This substitution is predicted to create a major amino acid change from arginine to serine at position 1680 of the protein, NP_115820.2(SLX4):p.(Arg1680Ser). The arginine at this position has low conservation (100 vertebrates, UCSC), and is not situated in a known functional domain. In silico software predicts this variant to be benign (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD population database at a frequency of 0.01% (28 heterozygotes, 0 homozygotes). An alternative nucleotide change resulting in the same protein alteration to serine has been reported in the gnomAD database at a frequency of 0.004% (12 heterozygotes, 0 homozygotes). In addition, an alternative residue change at the same location has been reported in the gnomAD database at a frequency of 0.0008%. The alternative nucleotide change resulting in a serine has been previously reported as a VUS (ClinVar), and this variant has been reported in the germline of a patient with head and neck squamous cell carcinoma (Chandrasekharappa, S. et al. (2017)). Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS) with LOW CLINICAL RELEVANCE.

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.