ClinVar

Description

Variant summary: POLG c.3131T>C (p.Val1044Ala) results in a non-conservative amino acid change located in the DNA-directed DNA polymerase, family A, palm domain (IPR001098) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00065 in 251418 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in POLG causing POLG-Related Spectrum Disorders (0.00065 vs 0.0035), allowing no conclusion about variant significance. c.3131T>C has been reported in the literature as a compound heterozygous genotype in an individual with an Alpers-like phenotype (Isohanni_2011), in the heterozygous state together with other POLG variants (phase unspecified) in an individual suspected of an atypical mitochondrial DNA depletion syndrome presenting with liver fibrosis with portal hypertension (Stalke_2018), and as an uninformative genotype (i.e. zygosity not specified) in at least one individual from a cohort of patients with POLG-related disorders (Hkitmat_2020). It has also been reported in a case-control study in two individuals affected with multiple sclerosis, but was also found in one control individual (Traboulsee_2017). These reports do not provide unequivocal conclusions about association of the variant with POLG-Related Spectrum Disorders. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 32391929, 21357833, 28776642, 28337550). Fifteen submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. The majority classified the variant as VUS, and one submitter classified it as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.