ClinVar Miner

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

dbSNP: rs199592185
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Total submissions: 4
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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].
Invitae RCV001417838 SCV001620044 likely benign Fanconi anemia 2023-11-24 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.

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