The GLDC gene on chromosome 9p24.1 provides instructions for making an enzyme called Glycine Dehydrogenase. This protein consists of 1,020 amino acids and weighs about 113 kDa. Glycine dehydrogenase enzyme is one of four mitochondrial proteins (P, H, T, and L) that make a large complex called glycine cleavage enzyme that catalyzes the degradation of glycine. Degradation of excess glycine is necessary for the normal development and function of nerve cells in the brain and spinal cord.

Defects in the glycine dehydrogenase enzyme result in building up of excess amounts of glycine in the brain and spinal cord. Glycine build up causes intellectual disability, seizures, and breathing difficulties characteristic of glycine encephalopathy disease.

The GLDC gene consists of 25 coding exons and its length is approximately 113 kb. More than 40 mutations have been identified in this gene in patients with glycine encephalopathy disease. These mutations account for 80% of all cases of the disease. The most common mutations are caused by single amino acid substitutions. Also, insertion, deletion and splice site mutations have been reported to cause the disease. These mutations result in either production of a nonfunctional version of glycine dehydrogenase, or reduce but do not eliminate the enzyme's activity.