Chapter 139. Disorders of Glycine, Serine, and Proline Metabolism

Glycine and serine are nonessential amino acids that feed into many synthetic pathways. Both are involved in transfer of one-carbon units. Proline is a nonessential amino acid that has unique biochemical properties. While most disorders of amino acid metabolism disrupt catabolic pathways, only a few affect the synthesis of amino acids. Three of them compromise the production of serine or proline. Formation and elimination of glycine occurs through many pathways. One precursor of glycine is choline, which can be oxidized to betaine and sequentially demethylated to dimethylglycine, sarcosine, and glycine, which is finally degraded to CO2 and NH3. Four known defects in glycine metabolism lead to distinct biochemical or clinical phenotypes.

Glycine encephalopathy (GCE) is an inherited metabolic disorder in which large amounts of glycine are found in body fluids, without further metabolic abnormalities.

Clinical Presentation

GCE typically presents with severe neonatal epileptic encephalopathy. Neonates appear normal at birth but develop myoclonic seizures, hiccough, apnea, muscular hypotonia, and unresponsiveness within the first 2 days of life. Their EEG shows a typical burst-suppression pattern. Many affected individuals die early, and survivors are severely retarded or developmentally arrested.1 Rarely, neonatal transient variants and late-onset forms have been described. These can present after an apparently asymptomatic period of months or even years with various symptoms such as mental retardation, episodes of chorea, vertical gaze palsy and delirium, or progressive spastic diplegia and optic atrophy.2,3

Metabolic Derangement, Including Pathophysiology

GCE is caused by defects in the mitochondrial glycine cleavage system (GCS) a multiprotein complex that catalyzes the degradation of glycine to CO2 and NH3, thereby transferring a one-carbon unit onto tetrahydrofolate to form 5,10-methylenetetrahydrofolate (MeTHF). A block in the GCS leads to accumulation of glycine and a lack of MeTHF, which promotes further production of glycine from serine. The latter reaction is catalyzed by serine hydroxymethyl transferase and yields the required MeTHF (see Chapter 153, Fig. 153-1). Glycine modulates N-methyl-D-aspartate (NMDA)–mediated neurotransmission. The accumulation of glycine in GCE is most pronounced in the cerebral compartment, where its increased concentration is thought to be directly responsible for the observed neurological symptoms.

Genetics

All forms of GCE (OMIM no. 605809) are inherited as autosomal recessive traits. The enzyme is multimeric with four distinct protein components. P protein (a pyridoxal phosphate–dependent glycine decarboxylase, 9p22), H protein (a lipoic acid–containing protein, 16q24), T protein (a tetrahydrofolate-requiring aminomethyltransferase, 3p21.2-p21.1), and L protein (a dihydrolipoamide dehydrogenase, 7q31-q32). Several mutations in the P and T genes and one in the H gene have been found, with the T protein being most commonly affected.4,5 A single mutation is responsible for most cases in Finland.6 Prenatal diagnosis can be performed by biochemical analysis of chorionic villus sample biopsies, but false negatives have been reported.7 Once a mutation is known, genetic testing is more reliable.8

Diagnostic Tests, Differential Diagnoses

Hyperglycinemia on plasma amino acid analysis in the absence of ketoacidosis makes GCE likely. Analysis of organic acids in urine helps to differentiate it from hyperglycinemia secondary to organic acidemia (see Chapter 137). In GCE, glycine is especially raised in CSF, and the ratio of its concentration in CSF to that in plasma is usually above 0.08, whereas it will be at least above 0.04 in most atypical cases.2,5 The diagnosis can be confirmed by enzyme assay in transformed lymphocytes9 or by liver biopsy.

Treatment, Prognosis, and Long-Term Outcome

There is no effective treatment for early onset GCE, and affected children have a very poor prognosis, with a shortened life span.1 In late-onset variants, there has been modest success with large doses of sodium benzoate, which is conjugated with glycine to form hippurate that can be excreted with urine. Benzoate can normalize plasma glycine and reduce CSF glycine concentrations and thus can decrease seizure activity.10 Ketamine, strychnine, or dextrorphan are antagonists at the N-methyl-D-aspartate (NMDA) receptor and could partly counteract glycine toxicity in some patients.11

Clinical Presentation

A “fishy” body odor and myopathy with muscular fatigue and elevated CK levels have been reported in an adult with dimethylglycine dehydrogenase (DMGDH) deficiency.12

Metabolic Derangement, Including Pathophysiology

Dimethylglycine dehydrogenase (DMGDH) is involved in the metabolism of choline, converting dimethylglycine to sarcosine. Sarcosine dehydrogenase then transforms sarcosine to glycine. Both enzymes use flavin adenine dinucleotide and yield 5,10-methylenetetrahydrofolate in their reaction mechanisms. DMGDH deficiency leads to accumulation of dimethylglycine in plasma and urine.

Genetics

DMGDH deficiency (OMIM no. 605850) is caused by mutations in the DMGDH gene, which is located on chromosome 5q12.2-q12.3 and is believed to be transmitted in an autosomal recessive manner. A homozygous missense mutation has been identified in the one affected individual.13

Diagnostic Tests, Including Differential Diagnoses

Grossly increased DMG concentrations in body fluids suggest this diagnosis. Milder increases can be seen in folate deficiency or in hyperhomocysteinemia patients on betaine treatment. A “fish-odor” syndrome is more frequently caused by trimethylaminuria (see Chapter 163).

Treatment, Prognosis, and Long-Term Outcome

No treatment has been established yet.

Clinical Presentation

Sarcosinemia has been found in individuals with mental retardation, congenital malformation, or growth failure,14,15 but a causal relationship has not been established, because it was also identified in many otherwise apparently healthy persons. It has been cited as a classical example for an ascertainment bias.16

Metabolic Derangement, Including Pathophysiology

Succinate dehydrogenase (SDH) is a key component in the glycine-sarcosine cycle that regulates the ratio of SAM to SAH and thereby regulates the activity of many transmethylases that use SAM as a methyl donor. SDH deficiency leads to excessive accumulation of sarcosine in body fluids and may stimulate NMDA receptors.17 Sarcosine also accumulates in extreme folate deficiency, but not to the same extent.

Genetics

SDH deficiency (OMIM no. 268900) is inherited as an autosomal recessive trait. The SDH gene has been mapped to chromosome 9q34,18 but no mutations have been reported.

Diagnostic Tests, Including Differential Diagnoses

Sarcosine is normally present in blood or urine in only very small amounts. If plasma amino acid analysis reveals severe hypersarcosinemia, measurement of folate levels in blood and analysis of organic acids in urine should be done to exclude multiple acyl-CoA-dehydrogenase deficiency. SDH deficiency can be confirmed by enzyme assay in liver tissue only. However, this is rarely justified.

Treatment, Prognosis, and Long-Term Outcome

There is no treatment available.

Clinical Presentation

Recently, the first individuals with glycine N-methyltransferase (GNMT) deficiency were identified whose only clinical abnormalities were mild hepatomegaly and chronic elevation of serum transaminases not attributable to conventional causes of liver disease.19,20 These were the first reported cases of an inborn error affecting the activity of GNMT.

Metabolic Derangement, Including Pathophysiology

GNMT together with SDH forms the glycine-sarcosine cycle that regulates the ratio of SAM to SAH and thereby the flux through transmethylation reactions that use SAM as methyl donor. SAM and methionine accumulate, whereas sarcosine is not elevated. Homocysteine is normal.

Genetics

Three different mutations in three patients with GNMT deficiency (OMIM no. 606664) have been reported in the GNMT gene, which is located on chromosome 6p12.20,21

Diagnostic Tests, Including Differential Diagnoses

Isolated hypermethioninemia and increased SAM concentrations without elevation of sarcosine are pathognomonic for this disorder.

Treatment, Prognosis, and Long-Term Outcome

There is no known treatment. The potential usefulness of methionine restriction has not been sufficiently explored.

Three defects have been demonstrated in the synthesis of serine. They are extremely rare but potentially treatable and easy to diagnose.

Clinical Presentation

Deficiency of 3-phosphoglycerate dehydrogenase (3-PGDH) is a very rare disorder of L-serine biosynthesis that is characterized by congenital microcephaly, psychomotor retardation, and intractable seizures. Brain MRI can show severe hypomyelination. Intrauterine growth retardation, failure to thrive, cataracts, and hypogonadism have also been observed.22-24

Metabolic Derangement, Including Pathophysiology

Three-PGDH is needed to synthesize serine, the most important endogenous one-carbon donor, from glucose.

Genetics

Mutations in the PHDGH gene on chromosome 1q12 are responsible for 3-PGDH deficiency (OMIM no. 601815).25

Diagnostic Tests, Including Differential Diagnoses

Amino acid analysis in preprandial plasma or CSF reveals decreased serine and moderately low glycine concentrations in plasma and CSF. In addition, 5-methylfolate in CSF is decreased. Postprandial amino acids may be normal. The diagnosis can be confirmed by enzyme assay in fibroblasts or by mutation analysis.25

Treatment, Prognosis, and Long-Term Outcome

Early supplementation with high doses of L-serine and possibly glycine can have a dramatic effect on seizures and psychomotor development. Antenatal treatment has been attempted to avoid prenatal damage and seems to be promising.26,27

Clinical Presentation

Only one patient has been identified who presented with pre- and postnatal growth retardation, moderate psychomotor retardation, and facial dysmorphism suggestive of Williams syndrome.28 He indeed had a 7q11.23 deletion, including a deficiency of phosphoserine phosphatase and lowered serine plasma and CSF concentrations.

Metabolic Derangement, Including Pathophysiology

Phosphoserine phosphatase (PSPH) catalyzes the last step in the biosynthesis of serine from carbohydrates—the hydrolysis of O-phosphoserine—and therefore leads to decreased production of serine.

Genetics

PSPH deficiency (OMIM no. 172480) is caused by mutations in the PSPH gene, which is located on chromosome 7q15.2-q15.1. The inheritance is autosomal recessive. A mutation could be identified in the one patient known so far.29

Diagnostic Tests, Including Differential Diagnoses

Plasma and CSF amino acid analysis demonstrates moderately decreased serine concentrations. PSPH activity can be measured in fibroblasts and lymphocytes.

Treatment, Prognosis, and Long-Term Outcome

Oral serine supplementation normalized plasma and CSF serine concentrations and may be beneficial.

This enzyme catalyses 3-hydroxy-pyruvate transformation to 3-P-serine. A patient with this defect has been recently described.

While a number of disorders in the metabolism of proline and hydroxyproline have been described, only three may be associated with clinical disease. In hyperprolinemia, a defect in the catabolism of proline leads to its accumulation alone (type 1) or together with the metabolite pyrroline-5-carboxylate (type 2). Delta-1-pyrroline 5-carboxylate synthetase deficiency is another example of an amino acid synthesis disorder.

Clinical Presentation

Hyperprolinemia type 1 is asymptomatic in most affected individuals but can be associated with cognitive impairment, epilepsy, and psychiatric features in a subset of patients. This has long been thought to represent another ascertainment bias, but newer studies in patients with microdeletion 22q11 syndromes and case reports suggest a causal relationship.30,32,32

Metabolic Derangement, Including Pathophysiology

This disorder is caused by a deficiency of proline dehydrogenase (PRODH), which catalyzes the oxidation of proline to pyrroline-5-carboxylate. Proline hence accumulates in all body fluids. Residual activity of PRODH in the 0% to 30% range results in hyperprolinemia type 1, whereas residual activity in the 30% to 50% range (such as in individuals who are hemizygous or heterozygous for an inactivating mutation) is associated either with normal plasma proline levels or with mild-to-moderate hyperprolinemia.31

Genetics

Hyperprolinemia type 1 (OMIM no. 239500) is caused by mutations in the PRODH gene, which is located on chromosome 22q11.2. The inheritance is autosomal recessive. Several mutations or microdeletions have been identified.31,33,34

Diagnostic Tests, Including Differential Diagnoses

Plasma or urinary amino acid analysis reveals grossly elevated proline concentrations in the range of 500 to 2000 μmol/L. Urinary excretion of hydroxyproline and glycine is increased. Secondary hyperprolinemia has been observed in hyperlactic acidemia. Enzyme assay requires a liver biopsy, but diagnosis can be confirmed by mutation analysis.

Treatment, Prognosis, and Long-Term Outcome

Most cases are asymptomatic, and there is no treatment available.

Clinical Presentation

Hyperprolinemia type 2 is usually associated with epilepsy and often with developmental retardation and cognitive impairment.

Metabolic Derangement, Including Pathophysiology

This disorder is caused by a deficiency of delta-1-pyrroline 5-carboxylate dehydrogenase (P5CDH), which catalyzes the conversion of proline into glutamate. Consequently, proline accumulates grossly in all body fluids, and increased concentrations of pyrroline-5-carboxylate (P5C) and 3-OH-pyrroline-5-carboxylate are found. Inactivation of pyridoxal phosphate and other aldehyde toxicity has been hypothesized to explain the neurotoxicity of P5C.35,36

Genetics

Hyperprolinemia type 2 (OMIM no. 239510) is caused by mutations in the P5CDH gene, which is located on chromosome 1p36. The inheritance is autosomal recessive. Several mutations have been identified.37

Diagnostic Tests, Including Differential Diagnoses

Plasma or urinary amino acid analysis reveals grossly elevated proline concentrations of over 2000 μmol/L. As in hyperprolinemia type 1, the urinary excretion of hydroxyproline and glycine is increased. The presence of P5C differentiates hyperprolinemia 2 from hyperprolinemia type 1. The diagnosis can be confirmed by enzyme assay in fibroblasts or leukocytes or by mutation analysis.

Treatment, Prognosis, and Long-Term Outcome

There is no treatment available.

Clinical Presentation

Two children who presented with neurodegeneration, cataracts, joint hypermobility, and skin laxity were confirmed to suffer from PCS deficiency.38

Metabolic Derangement, Including Pathophysiology

PCS deficiency causes an insufficient synthesis of proline and ornithine. A relative deficiency of the urea cycle intermediates ornithine, citrulline, and arginine leads to hyperammonemia, which is aggravated by fasting.39,40

Genetics

PCS deficiency (OMIM no. 138250) is inherited in an autosomal recessive manner. The gene is located on chromosome 10q24.3, and at least one mutation has been described.38,39

Diagnostic Tests, Including Differential Diagnoses

Plasma amino acid analysis detects low levels of proline and ornithine as well as a secondary hypocitrullinemia. Direct enzyme assay is not possible. The diagnosis can be confirmed by mutation analysis.

Treatment, Prognosis, and Long-Term Outcome

Treatment aims at supplementing the lack of L-proline and L-ornithine.

Clinical Presentation

Hydroxyprolinemia is a benign biochemical abnormality.

Metabolic Derangement, Including Pathophysiology

This disorder is caused by a deficiency of 4-OH-L-proline oxidase, which catalyzes the first step in the catabolism of hydroxyproline. Consequently, hydroxyproline accumulates in body fluids. Elevated serum hydroxyproline appears not to cause any significant clinical symptoms.41

Genetics

No genetic analyses in hydroxyprolinemia (OMIM no. 237000) have been described.

Diagnostic Tests, Including Differential Diagnoses

Plasma or urinary amino acid analysis reveals five- to tenfold elevated hydroxyproline concentrations. The absence of delta-1-pyrroline-3-hydroxy-5-carboxylic acid and enzyme assay in a liver biopsy or mutation analysis confirm this disorder.

Treatment, Prognosis, and Long-Term Outcome

There is no treatment available. See Table 139-1 for other rare disorders of glycine, proline and serine metabolism.