HGNC Approved Gene Symbol: GCSH
Cytogenetic location: 16q23.2 Genomic coordinates (GRCh38) : 16:81,081,945-81,096,395 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16q23.2 | Multiple mitochondrial dysfunctions syndrome 7 | 620423 | Autosomal recessive | 3 |
The enzyme system for cleavage of glycine (glycine cleavage system; EC 2.1.2.10), which is confined to the mitochondria, is composed of 4 protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase; 238300), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme; 238310), and L protein (a lipoamide dehydrogenase; 238331).
Hiraga et al. (1988) cloned a cDNA encoding H protein from a human liver cDNA library. Koyata and Hiraga (1991) isolated a 1,192-bp cDNA that encodes the entire precursor of human H protein. Fujiwara et al. (1991) isolated a full-length GCSH cDNA encoding a precursor protein of 173 amino acids and a mature protein of 125 amino acids. By dot-blot analysis, Kure et al. (2001) found that GCSH was expressed in all 29 tissues examined.
Kure et al. (2001) isolated and characterized a human PAC clone encoding GCSH. They found that GCSH spans 13.5 kb and contains 5 exons.
Sakata et al. (2001) reported the structure and expression of the glycine cleavage system in rat central nervous system.
By fluorescence in situ hybridization, Kure et al. (2001) mapped the GCSH gene to chromosome 16q24.
Multiple Mitochondrial Dysfunctions Syndrome 7
In 3 patients from 2 Indian families with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423) Majethia et al. (2021) identified a homozygous mutation (c.1A-G; 238330.0002) in the GCSH gene predicted to disrupt the methionine start site. Homozygosity mapping demonstrated a shared 490-kb region of homozygosity on chromosome 16 shared by the 2 families.
In 5 unrelated patients with MMDS7, Arribas-Carreira et al. (2023) identified biallelic mutations in the GCSH gene (238330.0002-238330.0008). Analysis of the mutations in patient cells, COS7 cells, and/or yeast cells showed that the mutations had variable effects in glycine exchange and protein lipoylation. Most of the mutations resulted in hypomorphic effects on both glycine exchange and lipoylation, whereas some mutations affected only 1 function. Patient phenotypes showed some correlation to the enzyme defect in either of the 2 GCSH enzyme functions (glycine exchange or lipoylation).
Reclassified Variants
The complex rearrangement (238330.0001) identified in a patient with glycine encephalopathy by Koyata and Hiraga (1991) has been reclassified as a variant of unknown significance. Hiraga et al. (1981) found low activity for both P protein and H protein and a structural abnormality of H protein in the liver and brain of a patient with glycine encephalopathy. This patient was also reported to have progressive degeneration of the central nervous system (Trauner et al., 1981). By Southern analysis using an H protein cDNA probe, Koyata and Hiraga (1991) found a deletion of one SacI fragment in the GCSH gene (238330.0001) in this patient. The same fragment was deleted in 1 of 7 patients with GCE resulting from deficiency of glycine decarboxylase (GCE1; 605899).
Polymorphisms
By direct sequencing analysis, Kure et al. (2001) identified 5 single-nucleotide polymorphisms in the GCSH gene.
Leung et al. (2021) found that Gcsh homozygous null genotype resulted in embryonic death prior to gestational day 10.5. Maternal formate supplementation did not rescue the embryonic lethality, suggesting that the lethality did not result from defective 1-carbon metabolism.
This variant, formerly titled GLYCINE ENCEPHALOPATHY, has been reclassified as a variant of unknown significance because its contribution to the disorder has not been confirmed.
By Southern analysis using an H protein cDNA probe, Koyata and Hiraga (1991) found a deletion of one SacI fragment in a patient with glycine encephalopathy (see 605899) reported by Hiraga et al. (1981). The same fragment was deleted in 1 of 7 patients with glycine encephalopathy resulting from deficiency of glycine decarboxylase (GLDC; 238300).
In 3 patients, including a sib pair, from 2 Indian families with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423), Majethia et al. (2021) identified homozygosity for a c.1A-G transition (c.1A-G, NM_004483.5) in the GCSH gene, predicted to disrupt the methionine initiation site. The mutations were identified by whole-exome sequencing and confirmed by Sanger sequencing, and the parents were shown to be mutation carriers. The variant was present in gnomAD in 2 individuals in heterozygosity only.
In 2 unrelated patients (patients 2 and 3) with MMDS7 Arribas-Carreira et al. (2023) identified compound heterozygosity for the c.1A-G mutation and a 1-bp insertion (c.293-2_293-1insT, 238330.0003) or a nonsense mutation (Q76X; 238330.0004), respectively. The mutations were identified by whole-exome sequencing. Expression of GCSH with the c.1A-G mutation in COS7 cells resulted in near absence of normal-sized H protein and lipoylated H protein, with decreased mitochondrial localization. Functional studies showed decreased glycine exchange activity and decreased lipoylation activity. RNA analysis of the c.293-2_293-1insT mutation, carried by the father of patient 2, showed that it resulted in skipping of exon 4 and in-frame deletion of 44 amino acids (Asp98_Asp141del). Western blot analysis in chorionic villus cells (CVS) cells from patient 2 demonstrated reduced H protein expression and near absence of lipoylated proteins in the mitochondria. Both patients 2 and 3 had a severe presentation, and died at ages 7 days and 11 months.
For discussion of the c.293-2_293-1insT (c.293-2_293-1insT, NM_004483.5) mutation in the GCSH gene, resulting in skipping of exon 4, that was identified in patient 2 with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423) by Arribas-Carreira et al. (2023), see 238330.0002.
For discussion of the c.226C-T transition (c.226C-T, NM_004483.5) in the GCSH gene, resulting in a gln76-to-ter (Q76X) substitution, that was identified in patient 3 with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423) by Arribas-Carreira et al. (2023), see 238330.0002.
In a patient (patient 1) with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423), Arribas-Carreira et al. (2023) identified compound heterozygosity for 2 mutations in the GCSH gene: a c.170A-G transition (c.170A-G, NM_004483.5), resulting in a his57-to-arg (H57R) substitution, and a deletion of exon 2 (238330.0006). The mutations were identified by sequencing of a custom exome panel and multiplex ligation-dependent probe amplification. Expression of GCSH with the H57R mutation in COS7 cells resulted in increased levels of H protein and mitochondrial colocalization. Functional studies showed increased glycine exchange activity and decreased lipoylation activity. A yeast model of the mutation demonstrated impaired mitochondrial respiration and cell growth. The patient had a severe presentation and died at age 18 days.
For discussion of the deletion of exon 2 in the GCSH gene that was identified in patient 1 with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423) by Arribas-Carreira et al. (2023), see 238330.0005.
In a patient (patient 5) with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423), Arribas-Carreira et al. (2023) identified homozygosity for a duplication of exons 4 and 5 (c.292+1_293-1_*919_?dup, NM_004483.5) of the GCSH gene. The genomic coordinates of the deletion were given as chr16:81,116,399-81,118,259. The mutation was identified by whole-exome sequencing. Western blot analysis of patient fibroblasts demonstrated reduced H protein expression and decreased lipoylated proteins in the mitochondria. The patient had an attenuated phenotype and was 20 months of age at the time of the report.
In a patient (patient 6) with multiple mitochondrial dysfunctions syndrome-7 (MMDS7; 620423), Arribas-Carreira et al. (2023) identified homozygosity for a c.344C-T transition (c.344C-T, NM_004483.5) in the GCSH gene, resulting in a pro115-to-leu (P115L) substitution. The mutation was identified by sequencing of a custom exome panel. Western blot analysis of patient fibroblasts demonstrated reduced H protein expression and decreased lipoylated proteins in the mitochondria. Expression of the mutant protein in COS7 cells resulted in almost normal amounts of H protein correctly localized to mitochondria, decreased glycine exchange activity, and decreased lipoylation activity. This patient had an attenuated phenotype with severe global developmental delays at age 4.5 years.
Arribas-Carreira, L., Dallabona, C., Swanson, M. A., Farris, J., Ostergaard, E., Tsiakas, K., Hempel, M., Aquaviva-Bourdain, C., Koutsoukos, S., Stence, N. V., Magistrati, M., Spector, E. B., and 19 others. Pathogenic variants in GCSH encoding the moonlighting H-protein cause combined nonketotic hyperglycinemia and lipoate deficiency. Hum. Molec. Genet. 32: 917-933, 2023. [PubMed: 36190515] [Full Text: https://doi.org/10.1093/hmg/ddac246]
Fujiwara, K., Okamura-Ikeda, K., Hayasaka, K., Motokawa, Y. The primary structure of human H-protein of the glycine cleavage system deduced by cDNA cloning. Biochem. Biophys. Res. Commun. 176: 711-716, 1991. [PubMed: 2025283] [Full Text: https://doi.org/10.1016/s0006-291x(05)80242-6]
Hiraga, K., Kochi, H., Hayasaka, K., Kikuchi, G., Nyhan, W. L. Defective glycine cleavage system in non-ketotic hyperglycinemia: occurrence of a less active glycine decarboxylase and an abnormal aminomethyl carrier protein. J. Clin. Invest. 68: 525-534, 1981. [PubMed: 6790577] [Full Text: https://doi.org/10.1172/jci110284]
Hiraga, K., Kure, S., Yamamoto, M., Ishiguro, Y., Suzuki, T. Cloning of cDNA encoding human H-protein, a constituent of the glycine cleavage system. Biochem. Biophys. Res. Commun. 151: 758-762, 1988. [PubMed: 3348809] [Full Text: https://doi.org/10.1016/s0006-291x(88)80345-0]
Koyata, H., Hiraga, K. The glycine cleavage system: structure of a cDNA encoding human H-protein, and partial characterization of its gene in patients with hyperglycinemias. Am. J. Hum. Genet. 48: 351-361, 1991. [PubMed: 1671321]
Kure, S., Kojima, K., Kudo, T., Kanno, K., Aoki, Y., Suzuki, Y., Shinka, T., Sakata, Y., Narisawa, K., Matsubara, Y. Chromosomal localization, structure, single-nucleotide polymorphisms, and expression of the human H-protein gene of the glycine cleavage system (GCSH), a candidate gene for nonketotic hyperglycinemia. J. Hum. Genet. 46: 378-384, 2001. [PubMed: 11450847] [Full Text: https://doi.org/10.1007/s100380170057]
Leung, K.-Y., De Castro, S. C. P., Galea, G. L., Copp, A. J., Greene, N. D. E. Glycine cleavage system H protein is essential for embryonic viability, implying additional function beyond the glycine cleavage system. Front. Genet. 12: 625120, 2021. [PubMed: 33569080] [Full Text: https://doi.org/10.3389/fgene.2021.625120]
Majethia, P., Somashekar, P. H., Hebbar, M., Kadavigere, R., Praveen, B. K., Girisha, K. M., Shukla, A. Biallelic start loss variant, c.1A > G in GCSH is associated with variant nonketotic hyperglycinemia. Clin. Genet. 100: 201-205, 2021. [PubMed: 33890291] [Full Text: https://doi.org/10.1111/cge.13970]
Sakata, Y., Owada, Y., Sato, K., Kojima, K., Hisanaga, K., Shinka, T., Suzuki, Y., Aoki, Y., Satoh, J., Kondo, H., Matsubara, Y., Kure, S. Structure and expression of the glycine cleavage system in rat central nervous system. Molec. Brain Res. 94: 119-130, 2001. [PubMed: 11597772] [Full Text: https://doi.org/10.1016/s0169-328x(01)00225-x]
Trauner, D. A., Page, T., Greco, C., Sweetman, L., Kulovich, S., Nyhan, W. L. Progressive neurodegenerative disorder in a patient with nonketotic hyperglycinemia. J. Pediat. 98: 272-275, 1981. [PubMed: 6780675] [Full Text: https://doi.org/10.1016/s0022-3476(81)80659-2]