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Gene

HESX1

HESX homeobox 1

Summary

Cytogenetic location
3p14.3
Coordinates
Chromosome 3: 57,197,838–57,199,978 (GRCh38)
Exons
4 exons across 2.1 kb
Protein
185 amino acids
Also known as
RPX, ANF
MANE Select transcript
ENST00000295934.8NM_003865.3
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

  • Hypogonadotropic Hypogonadism

    • Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.

      • 4 GenCC submitters rate it definitive or strong

  • Non-Acquired Combined Pituitary Hormone Deficiency

    • Combined pituitary hormone deficiency, genetic form

      Inherited deficiency of several pituitary hormones, including PROP1, POU1F1, HESX1 and related causes.

      • 4 GenCC submitters rate it definitive or strong

How HESX1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 3, with a bracket where HESX1 sits. HESX1 and 9 genes near it on chromosome 3, from 56,698,908 to 57,698,907.Chromosome 33p14.3p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q2956.8 Mb57 Mb57.2 Mb57.4 Mb57.6 MbARHGEF3: 56,727,414–57,079,329, reverse strandARHGEF3SPATA12: 57,060,659–57,075,530, forward strandSPATA12IL17RD: 57,089,982–57,170,306, reverse strandIL17RDHESX1: 57,197,838–57,199,978, reverse strandHESX1APPL1: 57,227,708–57,289,540, forward strandAPPL1ASB14: 57,268,342–57,292,693, reverse strandASB14DNAH12: 57,293,699–57,544,359, reverse strandDNAH12PDE12: 57,556,249–57,656,494, forward strandPDE12ARF4: 57,571,363–57,598,220, reverse strandARF4DENND6A: 57,625,454–57,693,127, reverse strandDENND6ADiagram of HESX1: 4 exons on the reverse strand of chromosome 3Exon 4: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 2: 5 known disease-causing sitesExon 1: 2 known disease-causing sitesExon 4: 57,197,838–57,198,295, 458 basesExon 3: 57,198,391–57,198,492, 102 basesExon 2: 57,198,753–57,198,952, 200 basesExon 1: 57,199,762–57,199,978, 217 bases43215′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 kb of the gene's 2.1 kb; 558 of those bases code for the protein.

How a genome test reads HESX1

11

positions in HESX1 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 2.1 kb of HESX1, introns included, not only the 1 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.). HESX1 gene: HESX homeobox 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/hesx1

Vancouver

Dante Labs. HESX1 gene: HESX homeobox 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/hesx1

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