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Gene

GLDC

glycine decarboxylase

Summary

Cytogenetic location
9p24.1
Coordinates
Chromosome 9: 6,532,467–6,645,729 (GRCh38)
Exons
25 exons across 113.3 kb
Protein
1,020 amino acids
Also known as
GCSP, NKH
MANE Select transcript
ENST00000321612.8NM_000170.3
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Disorders of Glycine & Serine Metabolism

    • Glycine Encephalopathy (Non-Ketotic Hyperglycinemia)Autosomal recessive

      Caused by variants in GLDC, AMT or GCSH (and, in an atypical form, SLC6A9), which cause high glycine in the brain and can lead to seizures, low muscle tone and developmental problems.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      Actionability

      Knowing allows treatment with sodium benzoate and dextromethorphan, which can reduce seizures in some forms.

How GLDC is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 9, with a bracket where GLDC sits. GLDC and 4 genes near it on chromosome 9, from 6,089,098 to 7,089,097.Chromosome 99p24.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.36.2 Mb6.4 Mb6.6 Mb6.8 Mb7 MbIL33: 6,215,136–6,281,596, forward strandIL33TPD52L3: 6,328,375–6,331,891, forward strandTPD52L3UHRF2: 6,413,151–6,507,056, forward strandUHRF2GLDC: 6,532,467–6,645,729, reverse strandGLDCKDM4C: 6,720,863–7,175,648, forward strandKDM4CDiagram of GLDC: 25 exons on the reverse strand of chromosome 9Exon 25: 9 known disease-causing sitesExon 24: 11 known disease-causing sitesExon 23: 21 known disease-causing sitesExon 22: 17 known disease-causing sitesExon 21: 13 known disease-causing sitesExon 20: 18 known disease-causing sitesExon 19: 21 known disease-causing sitesExon 18: 24 known disease-causing sitesExon 17: 12 known disease-causing sitesExon 16: 11 known disease-causing sitesExon 15: 25 known disease-causing sitesExon 14: 6 known disease-causing sitesExon 13: 13 known disease-causing sitesExon 12: 6 known disease-causing sitesExon 11: 5 known disease-causing sitesExon 10: 14 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 8: 17 known disease-causing sitesExon 7: 27 known disease-causing sitesExon 6: 18 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 4: 31 known disease-causing sitesExon 3: 22 known disease-causing sitesExon 2: 8 known disease-causing sitesExon 1: 27 known disease-causing sitesExon 25: 6,532,467–6,533,160, 694 basesExon 24: 6,534,708–6,534,788, 81 basesExon 23: 6,536,064–6,536,236, 173 basesExon 22: 6,540,051–6,540,146, 96 basesExon 21: 6,550,803–6,550,914, 112 basesExon 20: 6,553,368–6,553,509, 142 basesExon 19: 6,554,669–6,554,781, 113 basesExon 18: 6,556,153–6,556,302, 150 basesExon 17: 6,558,559–6,558,684, 126 basesExon 16: 6,565,354–6,565,429, 76 basesExon 15: 6,587,141–6,587,283, 143 basesExon 14: 6,588,401–6,588,442, 42 basesExon 13: 6,588,618–6,588,702, 85 basesExon 12: 6,589,195–6,589,292, 98 basesExon 11: 6,592,143–6,592,223, 81 basesExon 10: 6,592,851–6,592,990, 140 basesExon 9: 6,595,014–6,595,119, 106 basesExon 8: 6,602,109–6,602,205, 97 basesExon 7: 6,604,588–6,604,784, 197 basesExon 6: 6,605,131–6,605,278, 148 basesExon 5: 6,606,592–6,606,669, 78 basesExon 4: 6,610,192–6,610,356, 165 basesExon 3: 6,620,184–6,620,319, 136 basesExon 2: 6,644,614–6,644,692, 79 basesExon 1: 6,645,245–6,645,729, 485 bases25201510515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.8 kb of the gene's 113.3 kb; 3,063 of those bases code for the protein.

Sequencing GLDC

453

positions in GLDC where ClinVar classes a change as pathogenic or likely pathogenic

43 of them (9.5%) fall in regions short reads find hard.

  • Low mappability (43 sites)

A whole genome covers all 113.3 kb of GLDC, introns included, not only the 3.8 kb of exons.

Genes linked to the same conditions

Traits linked to GLDC

The Human Phenotype Ontology lists these as features of the rare conditions GLDC can cause. Each trait's page lists the other genes linked to it.

External links

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.18-e609d43e.

Cite this page

APA

Dante Labs. (n.d.). GLDC gene: glycine decarboxylase. Retrieved 18 October 2026, from https://dantelabs.com/genes/gldc

Vancouver

Dante Labs. GLDC gene: glycine decarboxylase [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/gldc

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