ClinVar Miner

Submissions for variant NM_145199.3(LIPT1):c.488C>T (p.Ser163Leu)

dbSNP: rs1553515438
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 2
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000657854 SCV000779611 likely pathogenic not provided 2018-05-16 criteria provided, single submitter clinical testing The S163L variant in the LIPT1 gene has been reported previously in an individual with abnormalities of the nervous system (Retterer et al., 2016). This variant is not observed in large population cohorts (Lek et al., 2016). The S163L 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. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. We interpret S163L as a likely pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000657854 SCV002158898 uncertain significance not provided 2022-07-18 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 163 of the LIPT1 protein (p.Ser163Leu). This missense change has been observed in individual(s) with nervous system abnormalities (PMID: 26633542). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 546073).

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.