ClinVar Genomic variation as it relates to human health

Reported in the homozygous state and in the presence of a second pathogenic variant in individuals with primary carnitine deficiency (Ferdinandusse et al., 2019); Individuals homozygous for this variant had approximately 31% average carnitine transport activity in fibroblasts compared to controls (Ferdinandusse et al., 2019); In vitro functional studies demonstrate that c.-149G>A introduces an upstream out-of-frame translation initiation codon that causes reduced production of OCTN2 protein (Ferdinandusse et al., 2019); This variant is associated with the following publications: (PMID: 31187905, 31864849, 31980526)

This variant occurs in a non-coding region of the SLC22A5 gene. It does not change the encoded amino acid sequence of the SLC22A5 protein. This variant is present in population databases (rs57262206, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individuals with primary carnitine deficiency (PMID: 31187905). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 25340). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects SLC22A5 function (PMID: 31187905). For these reasons, this variant has been classified as Pathogenic.

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

Variant summary: SLC22A5 c.-149G>A is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of 0.0014 in 150938 control chromosomes in the gnomAD v3.1.2 database, including 1 homozygote. This frequency is not higher than expected for a pathogenic variant in SLC22A5 causing Systemic Primary Carnitine Deficiency (0.0014 vs 0.0046), allowing no conclusion about variant significance. c.-149G>A has been reported to segregate with carnitine uptake defect in a large family where several affected members were homozygous for the variant of interest (Verbeeten_2020). The variant has also been reported in several other unrelated individuals (homozygous, compound heterozygous and heterozygous) affected with primary carnitine deficiency (Ferdinandusse_2019). Most of the affected patients showed a mild phenotype. Functional studies conducted in patient derived fibroblasts (from homozygous individuals) showed reduced Carnitine transport activity (Verbeeten_2020, Ferdinandusse_2019). Ferdinandusse et al also report that c.-149G>A introduces a functional upstream out-of-frame translation initiation codon and this codon suppresses translation from the wild-type AUG of SLC22A5, resulting in reduced OCTN2 protein levels and therefore, lower OCTN2 transport activity and carnitine deficiency in patients harboring this variant (Ferdinandusse_2019). Seven ClinVar submitters (evaluation after 2014) cite the variant as pathogenic (n=6) or uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

SLC22A5: PM3:Very Strong, PP1:Moderate, PS3:Moderate, PM2:Supporting

PP1_strong, PS3, PS4

The SLC22A5 c.-149G>A variant is located in the 5' untranslated region. This variant has been reported, in the homozygous or compound heterozygous state, in numerous individuals with primary carnitine deficiency (PCD) (Ferdinandusse et al. 2019. PubMed ID: 31187905; Verbeeten et al. 2020. PubMed ID: 31864849). It was found in in the homozygous and apparently compound heterozogous state in several individuals who were classified as having a likely benign form of PCD who were asymptomatic or only had mild symptoms, regardless of treatment. (Crefcoeur et al. 2023. PubMed ID: 37487700). The c.-149G>A variant was predicted to create a novel translation initiation codon upstream of the canonical AUG start codon, and in a functional assay using a luciferase reporter construct, the c.-149G>A variant was found to reduce luciferase activity to 11% of control (Ferdinandusse et al. 2019. PubMed ID: 31187905). Furthermore, carnitine transport activity was reduced in patient fibroblasts with the c.-149G>A variant (Ferdinandusse et al. 2019. PubMed ID: 31187905; Verbeeten et al. 2020. PubMed ID: 31864849). Based on these observations, we classify this variant as pathogenic.