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Gene

OTC

ornithine transcarbamylase

Summary

Cytogenetic location
Xp11.4
Coordinates
Chromosome X: 38,352,604–38,421,446 (GRCh38)
Exons
10 exons across 68.8 kb
Protein
354 amino acids
Also known as
OTCase, OTCD, OTC1
MANE Select transcript
ENST00000039007.5NM_000531.6
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

  • Urea Cycle Disorder

    • A genetic inborn error of metabolism characterized by the deficiency of one of the enzymes necessary for the urea cycle. It results in accumulation of ammonia in the body.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      • On the ACMG secondary findings list
      What knowing changes

      Nitrogen scavenger therapy (sodium benzoate, glycerol phenylbutyrate/Ravicti); protein-restricted diet with essential amino acid supplementation; emergency hyperammonemia protocols; liver transplantation (curative); mRNA therapy trials for OTC; carglumic acid for NAGS deficiency

How OTC is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome X, with a bracket where OTC sits. OTC and 8 genes near it on chromosome X, from 37,887,025 to 38,887,024.Chromosome XXp11.4p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2838 Mb38.2 Mb38.4 Mb38.6 Mb38.8 Mb: 37,349,330–38,687,674, forward strandH2AP: 37,990,779–37,991,314, forward strandH2APH2AL3: 37,994,272–37,994,904, forward strandH2AL3SYTL5: 38,006,515–38,128,964, forward strandSYTL5SRPX: 38,149,336–38,220,941, reverse strandSRPXRPGR: 38,269,115–38,327,573, reverse strandRPGROTC: 38,352,604–38,421,446, forward strandOTCTSPAN7: 38,561,498–38,689,249, forward strandTSPAN7MID1IP1: 38,801,417–38,806,555, forward strandMID1IP1Diagram of OTC: 10 exons on the forward strand of chromosome XExon 1: 7 known disease-causing sitesExon 2: 17 known disease-causing sitesExon 3: 9 known disease-causing sitesExon 4: 7 known disease-causing sitesExon 5: 33 known disease-causing sitesExon 6: 31 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 8: 25 known disease-causing sitesExon 9: 16 known disease-causing sitesExon 10: 7 known disease-causing sitesExon 1: 38,352,604–38,352,773, 170 bases. 3 variants with a page in exon 1. List themExon 2: 38,367,291–38,367,429, 139 bases. 4 variants with a page in exon 2. List themExon 3: 38,369,796–38,369,877, 82 bases. 2 variants with a page in exon 3. List themExon 4: 38,381,342–38,381,429, 88 bases. 2 variants with a page in exon 4. List themExon 5: 38,401,275–38,401,428, 154 bases. 7 variants with a page in exon 5. List themExon 6: 38,403,618–38,403,740, 123 bases. 9 variants with a page in exon 6. List themExon 7: 38,408,742–38,408,795, 54 bases. 3 variants with a page in exon 7. List themExon 8: 38,408,876–38,409,025, 150 bases. 4 variants with a page in exon 8. List themExon 9: 38,411,862–38,411,999, 138 bases. 6 variants with a page in exon 9. List themExon 10: 38,421,023–38,421,446, 424 bases. 1 variant with a page in exon 10. List them12468105′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 1.5 kb of the gene's 68.8 kb; 1,065 of those bases code for the protein.

How a genome test reads OTC

182

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

None of them falls in a region short reads find hard.

A whole genome covers all 68.8 kb of OTC, introns included, not only the 1.5 kb of exons.

Variants with a page (49)

The OTC variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A208Tc.622G>AExon 638,403,699Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
A209Vc.626C>TExon 638,403,703Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
A233Vc.698C>TExon 738,408,776Likely pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.3G>AExon 138,352,699Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.77+1G>AIntron 138,352,774Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.298+2T>GIntron 338,369,879Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.540+1G>AIntron 538,401,429Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.540+265G>AIntron 538,401,693Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.663+1G>TIntron 638,403,741Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts
c.663+2T>CIntron 638,403,742Pathogenic2 stars out of 4 criteria provided, multiple submitters, no conflicts

See all 49 OTC variants →

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.). OTC gene: ornithine transcarbamylase. Retrieved 16 October 2026, from https://dantelabs.com/genes/otc

Vancouver

Dante Labs. OTC gene: ornithine transcarbamylase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/otc

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