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Gene

GCSH

glycine cleavage system protein H

Summary

Cytogenetic location
16q23.2
Coordinates
Chromosome 16: 81,081,945–81,096,395 (GRCh38)
Exons
5 exons across 14.5 kb
Protein
173 amino acids
Inheritance
Autosomal recessive
MANE Select transcript
ENST00000315467.9NM_004483.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

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
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

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

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How GCSH is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where GCSH sits. GCSH and 12 genes near it on chromosome 16, from 80,589,170 to 81,589,169.Chromosome 1616q23.2p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.380.6 Mb80.8 Mb81 Mb81.2 Mb81.4 MbCDYL2: 80,597,907–80,804,611, reverse strandCDYL2: 80,828,736–81,006,894, reverse strandCMC2: 80,966,448–81,020,270, reverse strandCMC2CENPN: 81,006,506–81,033,558, forward strandCENPN: 81,022,316–81,096,284, reverse strandATMIN: 81,035,809–81,047,350, forward strandC16orf46: 81,053,195–81,077,267, reverse strandC16orf46: 81,053,587–81,096,296, reverse strandGCSH: 81,081,945–81,096,395, reverse strandGCSHPKD1L2: 81,100,875–81,220,370, reverse strandBCO1: 81,238,576–81,291,226, forward strandBCO1GAN: 81,314,932–81,390,884, forward strandGANCMIP: 81,444,800–81,711,762, forward strandCMIPDiagram of GCSH: 5 exons on the reverse strand of chromosome 16Exon 4: 3 known disease-causing sitesExon 2: 1 known disease-causing siteExon 1: 3 known disease-causing sitesExon 5: 81,081,945–81,082,963, 1,019 basesExon 4: 81,084,463–81,084,594, 132 basesExon 3: 81,087,601–81,087,664, 64 basesExon 2: 81,090,601–81,090,680, 80 basesExon 1: 81,096,131–81,096,395, 265 bases543215′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 1.6 kb of the gene's 14.5 kb; 522 of those bases code for the protein.

How a genome test reads GCSH

8

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

1 of them (13%) falls in a region short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 14.5 kb of GCSH, introns included, not only the 1.6 kb of exons.

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 2026-10-16: 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 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). GCSH gene: glycine cleavage system protein H. Retrieved 17 October 2026, from https://dantelabs.com/genes/gcsh

Vancouver

Dante Labs. GCSH gene: glycine cleavage system protein H [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/gcsh

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