A mutation creating an upstream translation initiation codon in SLC22A5 5'UTR is a frequent cause of primary carnitine deficiency.

Sacha Ferdinandusse,Wendy Oostheim,Hans R Waterham,Merel S Ebberink,Lodewijk Ijlst,Henk Lenthe,Frédéric M Vaz,Ronald J.A Wanders,Heleen Te Brinke,Jos P.N Ruiter,Janet Haasjes

doi:10.1002/humu.23839

Abstract

Primary carnitine deficiency is caused by a defect in the active cellular uptake of carnitine by Na+‐dependent organic cation transporter novel 2 (OCTN2). Genetic diagnostic yield for this metabolic disorder has been relatively low, suggesting that disease‐causing variants are missed. We Sanger sequenced the 5′ untranslated region (UTR) of SLC22A5 in individuals with possible primary carnitine deficiency in whom no or only one mutant allele had been found. We identified a novel 5′‐UTR c.‐149G>A variant which we characterized by expression studies with reporter constructs in HeLa cells and by carnitine‐transport measurements in fibroblasts using a newly developed sensitive assay based on tandem mass spectrometry. This variant, which we identified in 57 of 236 individuals of our cohort, introduces a functional upstream out‐of‐frame translation initiation codon. We show that the codon suppresses translation from the wild‐type ATG of SLC22A5, resulting in reduced OCTN2 protein levels and concomitantly lower transport activity. With an allele frequency of 24.2% the c.‐149G>A variant is the most frequent cause of primary carnitine deficiency in our cohort and may explain other reported cases with an incomplete genetic diagnosis. Individuals carrying this variant should be clinically re‐evaluated and monitored to determine if this variant has clinical consequences.

Highlights

Primary carnitine deficiency (MIM# 212140) is caused by a defect in the active cellular uptake of carnitine by the Na+‐dependent organic cation transporter novel 2 (OCTN2; Nezu et al, 1999; Tang et al, 1999)
Because carnitine is essential for the transport of long‐chain fatty acids into the mitochondrion for β‐oxidation, the lack of carnitine results in impaired fatty acid oxidation which affects in particular organs that rely on energy production by fatty acid oxidation such as the heart, skeletal muscle and liver
The first individuals identified with primary carnitine deficiency all presented with severe clinical symptoms, including acute metabolic decompensation or cardiomyopathy, but because the disorder has been included in many neonatal screening programs worldwide, an increasing number of individuals with milder or no clinical symptoms have been identified

Summary

| INTRODUCTION

Primary (or systemic) carnitine deficiency (MIM# 212140) is caused by a defect in the active cellular uptake of carnitine by the Na+‐dependent organic cation transporter novel 2 (OCTN2; Nezu et al, 1999; Tang et al, 1999). We report the identification and characterization of a 5′ untranslated region (UTR) variant in SLC22A5, c.‐149G>A, which introduces a functional upstream out‐of‐frame translation initiation codon We show that this codon suppresses translation from the wild‐ type AUG of SLC22A5, resulting in reduced OCTN2 protein levels and concomitantly lower OCTN2 transport activity explaining the carnitine deficiency in patients harboring this variant. We identified this variant in 57 individuals in whom we previously identified only one or no mutation in the coding region of SLC22A5

| METHODS

| RESULTS

Findings

| DISCUSSION