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Gene

HCCS

holocytochrome c synthase

Summary

Cytogenetic location
Xp22.2
Coordinates
Chromosome X: 11,111,332–11,123,086 (GRCh38)
Exons
7 exons across 11.8 kb
Protein
268 amino acids
Also known as
CCHL
Previous symbols
MLS
MANE Select transcript
ENST00000380762.5NM_005333.5
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

  • Microphthalmia, Anophthalmia & Coloboma

    • Syndromic Microphthalmia

      Microphthalmia occurring with features outside the eye, caused by changes in genes such as SOX2, OTX2, BCOR, STRA6 and BMP4.

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

      A genetic diagnosis guides checks for associated features, such as pituitary hormone problems with SOX2 or OTX2, and informs recurrence risk.

How HCCS is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome X, with a bracket where HCCS sits. HCCS and 3 genes near it on chromosome X, from 10,617,209 to 11,617,208.Chromosome XXp22.2p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2810.8 Mb11 Mb11.2 Mb11.4 Mb11.6 MbMID1: 10,445,310–10,833,730, reverse strandMID1HCCS: 11,111,332–11,123,086, forward strandHCCSARHGAP6: 11,117,651–11,665,931, reverse strandARHGAP6AMELX: 11,293,413–11,300,761, forward strandAMELXDiagram of HCCS: 7 exons on the forward strand of chromosome XExon 2: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 7: 2 known disease-causing sitesExon 1: 11,111,332–11,111,518, 187 basesExon 2: 11,112,019–11,112,160, 142 basesExon 3: 11,114,835–11,114,986, 152 basesExon 4: 11,117,267–11,117,415, 149 basesExon 5: 11,118,501–11,118,620, 120 basesExon 6: 11,120,907–11,120,993, 87 basesExon 7: 11,121,612–11,123,086, 1,475 bases12345675′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 2.3 kb of the gene's 11.8 kb; 807 of those bases code for the protein.

How a genome test reads HCCS

7

positions in HCCS 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 11.8 kb of HCCS, introns included, not only the 2.3 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.). HCCS gene: holocytochrome c synthase. Retrieved 17 October 2026, from https://dantelabs.com/genes/hccs

Vancouver

Dante Labs. HCCS gene: holocytochrome c synthase [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/hccs

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