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Gene

COL25A1

collagen type XXV alpha 1 chain

Summary

Cytogenetic location
4q25
Coordinates
Chromosome 4: 108,808,725–109,302,658 (GRCh38)
Exons
38 exons across 493.9 kb
Protein
654 amino acids
MANE Select transcript
ENST00000399132.6NM_198721.4
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

  • Congenital Cranial Dysinnervation Disorders

    • Congenital Fibrosis of the Extraocular Muscles

      A group of conditions, caused by changes in genes such as KIF21A, TUBB3 and PHOX2A, in which eye movements are restricted and the eyelids often droop from birth.

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

      A genetic diagnosis explains the condition, can guide planning for eye-muscle and eyelid surgery and informs recurrence risk.

How COL25A1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 4, with a bracket where COL25A1 sits. COL25A1 and 9 genes near it on chromosome 4, from 108,314,791 to 109,796,592.Chromosome 44q25p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.2108.4 Mb108.6 Mb108.8 Mb109 Mb109.2 Mb109.4 Mb109.6 MbRPL34: 108,620,508–108,632,886, forward strandRPL34OSTC: 108,650,577–108,668,418, forward strandOSTCETNPPL: 108,741,969–108,763,228, reverse strandETNPPLCOL25A1: 108,808,725–109,302,658, reverse strandCOL25A1SEC24B: 109,433,602–109,540,896, forward strandSEC24BMCUB: 109,560,209–109,688,799, forward strandMCUBCASP6: 109,685,837–109,703,583, reverse strandCASP6PLA2G12A: 109,709,765–109,730,070, reverse strandPLA2G12A: 109,713,916–109,801,999, reverse strandCFI: 109,730,868–109,802,200, reverse strandCFIDiagram of COL25A1: 38 exons on the reverse strand of chromosome 4Exon 30: 1 known disease-causing siteExon 23: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 38: 108,808,725–108,813,929, 5,205 basesExon 37: 108,817,397–108,817,435, 39 basesExon 36: 108,819,252–108,819,329, 78 basesExon 35: 108,824,174–108,824,227, 54 basesExon 34: 108,825,196–108,825,222, 27 basesExon 33: 108,827,135–108,827,188, 54 basesExon 32: 108,832,380–108,832,433, 54 basesExon 31: 108,841,695–108,841,721, 27 basesExon 30: 108,844,519–108,844,569, 51 basesExon 29: 108,845,189–108,845,251, 63 basesExon 28: 108,846,139–108,846,219, 81 basesExon 27: 108,848,759–108,848,803, 45 basesExon 26: 108,852,236–108,852,280, 45 basesExon 25: 108,852,902–108,852,925, 24 basesExon 24: 108,859,656–108,859,733, 78 basesExon 23: 108,860,927–108,860,971, 45 basesExon 22: 108,862,501–108,862,545, 45 basesExon 21: 108,863,319–108,863,387, 69 basesExon 20: 108,869,088–108,869,150, 63 basesExon 19: 108,884,178–108,884,222, 45 basesExon 18: 108,889,221–108,889,256, 36 basesExon 17: 108,889,701–108,889,733, 33 basesExon 16: 108,896,667–108,896,711, 45 basesExon 15: 108,899,154–108,899,180, 27 basesExon 14: 108,901,119–108,901,172, 54 basesExon 13: 108,918,172–108,918,216, 45 basesExon 12: 108,920,578–108,920,604, 27 basesExon 11: 108,937,808–108,937,843, 36 basesExon 10: 108,940,539–108,940,646, 108 basesExon 9: 108,941,366–108,941,437, 72 basesExon 8: 108,974,367–108,974,393, 27 basesExon 7: 108,974,533–108,974,559, 27 basesExon 6: 109,010,358–109,010,375, 18 basesExon 5: 109,048,168–109,048,175, 8 basesExon 4: 109,050,135–109,050,179, 45 basesExon 3: 109,300,583–109,300,652, 70 basesExon 2: 109,301,723–109,302,075, 353 basesExon 1: 109,302,169–109,302,658, 490 bases3830201015′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 7.7 kb of the gene's 493.9 kb; 1,965 of those bases code for the protein.

How a genome test reads COL25A1

6

positions in COL25A1 where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (17%) falls in a region short reads find hard.

  • Segmental duplications (1 site)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 493.9 kb of COL25A1, introns included, not only the 7.7 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.). COL25A1 gene: collagen type XXV alpha 1 chain. Retrieved 17 October 2026, from https://dantelabs.com/genes/col25a1

Vancouver

Dante Labs. COL25A1 gene: collagen type XXV alpha 1 chain [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/col25a1

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