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Gene

EGLN1

egl-9 family hypoxia inducible factor 1

Summary

Cytogenetic location
1q42.2
Coordinates
Chromosome 1: 231,363,756–231,422,287 (GRCh38)
Exons
5 exons across 58.5 kb
Protein
426 amino acids
Inheritance
Autosomal dominant
Also known as
SM-20, PHD2, ZMYND6, HIFPH2
Previous symbols
C1orf12
MANE Select transcript
ENST00000366641.4NM_022051.3
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 reports relevant to this gene

  • Hereditary Pheochromocytoma and Paraganglioma

    • EGLN1-related erythrocytosis and pheochromocytoma/paraganglioma predispositionAutosomal dominant

      Variants in EGLN1 that cause a raised red-cell count and an increased risk of pheochromocytoma and paraganglioma.

      • ClinGen rates the link definitive
      • 1 GenCC submitter rates it definitive or strong

  • Polycythemia

    • Familial Erythrocytosis 3 (EGLN1)Autosomal dominant

      A dominant form of inherited erythrocytosis caused by changes in EGLN1 that disturb the body's oxygen-sensing pathway and increase red cell production.

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

      Knowing the inherited cause avoids it being mistaken for polycythaemia vera or other acquired causes, and spares unnecessary investigations.

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How EGLN1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where EGLN1 sits. EGLN1 and 12 genes near it on chromosome 1, from 230,893,022 to 231,893,021.Chromosome 11q42.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44231 Mb231.2 Mb231.4 Mb231.6 Mb231.8 MbTTC13: 230,902,936–230,978,893, reverse strandTTC13ARV1: 230,978,981–231,000,735, forward strandARV1FAM89A: 230,999,826–231,040,270, reverse strandFAM89ATRIM67: 231,162,058–231,221,565, forward strandTRIM67FSAF1: 231,223,763–231,241,187, reverse strandFSAF1GNPAT: 231,241,184–231,277,973, forward strandGNPATEXOC8: 231,332,753–231,337,852, reverse strandEXOC8SPRTN: 231,337,104–231,375,416, forward strandSPRTNEGLN1: 231,363,756–231,422,287, reverse strandEGLN1: 231,363,797–231,528,603, reverse strandTSNAX: 231,528,541–231,566,524, forward strandTSNAXTSNAX-DISC1: 231,528,653–231,819,244, forward strandTSNAX-DISC1DISC1: 231,626,663–232,041,272, forward strandDISC1Diagram of EGLN1: 5 exons on the reverse strand of chromosome 1Exon 4: 1 known disease-causing siteExon 3: 3 known disease-causing sitesExon 2: 2 known disease-causing sitesExon 1: 8 known disease-causing sitesExon 5: 231,363,756–231,366,475, 2,720 basesExon 4: 231,367,569–231,367,636, 68 basesExon 3: 231,370,562–231,370,698, 137 basesExon 2: 231,373,980–231,374,099, 120 basesExon 1: 231,420,998–231,422,287, 1,290 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 4.3 kb of the gene's 58.5 kb; 1,281 of those bases code for the protein.

How a genome test reads EGLN1

14

positions in EGLN1 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 58.5 kb of EGLN1, introns included, not only the 4.3 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.). EGLN1 gene: egl-9 family hypoxia inducible factor 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/egln1

Vancouver

Dante Labs. EGLN1 gene: egl-9 family hypoxia inducible factor 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/egln1

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