Loss of function mutation in glutamic pyruvate transaminase 2 (GPT2) causes developmental encephalopathy

Abstract

Intellectual disability is genetically heterogeneous, and it is likely that many of the responsible genes have not yet been identified. We describe three siblings with isolated, severe developmental encephalopathy. After extensive uninformative genetic and metabolic testing, whole exome sequencing identified a homozygous novel variant in glutamic pyruvate transaminase 2 (GPT2) or alanine transaminase 2 (ALT2), c.459 C > G p.Ser153Arg that segregated with developmental encephalopathy in the family. This variant was predicted to be damaging by all in silico prediction algorithms. GPT2 is the gene encoding ALT2 which is responsible for the reversible transamination of alanine and 2-oxoglutarate to form pyruvate and glutamate. GPT2 is expressed in brain and is in the pathway to generate glutamate, an excitatory neurotransmitter. Functional assays of recombinant wild-type and mutant ALT2 proteins demonstrated the p.Ser153Arg mutation resulted in a severe loss of enzymatic function. We suggest that recessively inherited loss of function GPT2 mutations are a novel cause of intellectual disability.

Fig. 1

Family pedigree. Shaded symbols indicate affected individuals. Electropherograms show the GPT2 c.459C>G genotype

Fig. 2

Affected sister’s brain MRI showing subtle incomplete and abnormal myelination involving the subcortical white matter

Fig. 3

Location and conservation of S153R in ALT2 proteins. Conserved functional domains of human ALT2 are revealed by Blast (www.ncbi.nlm.nih.gov) against GenBank protein database. The mutation is indicated by the arrow. hALT2: human ALT2 (GenBank accession#: NP_597700); mALT2: murine ALT2 (NP_776291); fALT2: zebrafish ALT2 (NP_001092227); hALT1: human ALT1 (NP_005300); mALT1: murine ALT1 (NP_877957) and fALT1: zebrafishALT1 (NP_001136246

Fig. 4

Expression and functional analyses of recombinant wild type and mutant ALT2 proteins a) Upper panel: ALT activities were measured in lysates of bacteria transformed with vector expressing none (control), the 153S wild-type (WT) or 153R mutant (MUT) protein; lower panel: representative Western blot of bacteria lysates (15 µg protein/lane) blotted with anti-ALT2 antibody. (b) Upper panel: ALT activities were measured in lysates of 293HEK cells transfected with vector expressing (GFP), the 153S wild-type (WT) or 153R mutant (MUT) protein; lower panel: representative Western blot of 293HEK lysates (50 µg protein/lane) blotted with anti-ALT2 antibody. Data are expressed as mean+SD, n=3