ClinVar Miner

Submissions for variant NM_022166.4(XYLT1):c.421C>T (p.Arg141Trp)

gnomAD frequency: 0.00273  dbSNP: rs74993523
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000413146 SCV000492041 uncertain significance not specified 2016-12-06 criteria provided, single submitter clinical testing The R141W variant in the XYLT1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The NHLBI ESP Exome Sequencing Project reports R141W was observed in 40/4394 (0.91%) alleles from individuals of African American background; however, this variant was not observed in the homozygous state in any individual within this population. The R141W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R141W as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV000888814 SCV001032467 likely benign Desbuquois dysplasia 1 2024-12-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002523958 SCV003628719 likely benign Inborn genetic diseases 2022-09-14 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV003932534 SCV004750886 benign XYLT1-related disorder 2019-06-06 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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