ClinVar Miner

Submissions for variant NM_145199.3(LIPT1):c.292C>G (p.Arg98Gly)

gnomAD frequency: 0.00019  dbSNP: rs137973334
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001560053 SCV001782387 pathogenic not provided 2022-08-12 criteria provided, single submitter clinical testing Published functional studies in patient fibroblasts demonstrate that transfection of wildtype LIPT1 enzyme rescued PDHC complex activity, whereas transfection of R98G LIPT1 enzyme did not (Tort et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24256811, 29681092, 27247813, 26740555, 28719003, 26633542)
Labcorp Genetics (formerly Invitae), Labcorp RCV001560053 SCV002251518 uncertain significance not provided 2024-12-16 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 98 of the LIPT1 protein (p.Arg98Gly). This variant is present in population databases (rs137973334, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of lipoyltransferase 1 deficiency (PMID: 24256811). ClinVar contains an entry for this variant (Variation ID: 189836). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt LIPT1 protein function with a positive predictive value of 80%. 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.
Illumina Laboratory Services, Illumina RCV001560053 SCV003802784 likely pathogenic not provided 2022-08-05 criteria provided, single submitter clinical testing The LIPT1 c.292C>G (p.Arg98Gly) missense variant results in the substitution of arginine at amino acid position 98 with glycine.The c.292C>G variant is reported in a compound heterozygous state in two affected individuals in the literature, in both instances, in trans with the p.Ser71Phe variant (PMID: 24256811; PMID: 34440436). Normal LIPT1 protein levels are reported in patient liver cells, but transfection of patient fibroblasts with the c.292C>G variant did not restore lipoylation of mitochondrial proteins, PDHC activity, or increase the oxidation rate of pyruvate or leucine, suggesting a loss of function consequence. Additionally, the Arg98 residue is conserved and structural modelling suggests that it is involved in lipoic acid binding (PMID: 24256811; PMID: 17570395). The c.292C>G variant is reported at a frequency of 0.000241 in the European (non-Finnish) population of the Genome Aggregation Database (version 2.1.1). Based on the available evidence, c.292C>G (p.Arg98Gly) variant is classified as likely pathogenic for lipoyltransferase 1 deficiency.
OMIM RCV000170327 SCV000222738 pathogenic Lipoyl transferase 1 deficiency 2014-04-01 no assertion criteria provided literature only

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