We recently reported a deletion of exon 2 of the trimethyllysine hydroxylase epsilon (
TMLHE) gene in a proband with autism. TMLHEmaps to the X chromosome and encodes the first enzyme in carnitine biosynthesis, 6- N-trimethyllysine dioxygenase. Deletion of exon 2 of TMLHEcauses enzyme deficiency, resulting in increased substrate concentration (6- N-trimethyllysine) and decreased product levels (3-hydroxy-6- N-trimethyllysine and γ-butyrobetaine) in plasma and urine. TMLHEdeficiency is common in control males (24 in 8,787 or 1 in 366) and was not significantly increased in frequency in probands from simplex autism families (9 in 2,904 or 1 in 323). However, it was 2.82-fold more frequent in probands from male-male multiplex autism families compared with controls (7 in 909 or 1 in 130; P= 0.023). Additionally, six of seven autistic male siblings of probands in male-male multiplex families had the deletion, suggesting that TMLHEdeficiency is a risk factor for autism (metaanalysis Z-score = 2.90 and P= 0.0037), although with low penetrance (2–4%). These data suggest that dysregulation of carnitine metabolism may be important in nondysmorphic autism; that abnormalities of carnitine intake, loss, transport, or synthesis may be important in a larger fraction of nondysmorphic autism cases; and that the carnitine pathway may provide a novel target for therapy or prevention of autism.