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Gene

HMX1

H6 family homeobox 1

Summary

Cytogenetic location
4p16.1
Coordinates
Chromosome 4: 8,867,048–8,871,839 (GRCh38)
Exons
2 exons across 4.8 kb
Protein
348 amino acids
Also known as
H6, NKX5-3
MANE Select transcript
ENST00000400677.5NM_018942.3
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 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.

      • ClinGen rates the link definitive
      • 4 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 HMX1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
Chromosome 4, with a bracket where HMX1 sits. HMX1 and 25 genes near it on chromosome 4, from 8,369,444 to 9,369,443.Chromosome 44p16.1p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.28.4 Mb8.6 Mb8.8 Mb9 Mb9.2 MbACOX3: 8,364,703–8,440,750, reverse strandACOX3TRMT44: 8,436,140–8,496,273, forward strandTRMT44GPR78: 8,558,725–8,619,761, forward strandGPR78CPZ: 8,592,638–8,619,761, forward strandCPZHMX1: 8,867,048–8,871,839, reverse strandHMX1FAM90A26: 9,170,409–9,176,730, forward strandFAM90A26USP17L10: 9,210,657–9,212,249, forward strandUSP17L10USP17L11: 9,215,405–9,216,997, forward strandUSP17L11USP17L12: 9,220,152–9,221,744, forward strandUSP17L12USP17L13: 9,224,896–9,226,488, forward strandUSP17L15: 9,234,385–9,236,046, forward strandUSP17L17: 9,243,879–9,245,471, forward strandUSP17L18: 9,248,630–9,250,222, forward strandUSP17L19: 9,253,378–9,254,970, forward strandUSP17L20: 9,258,124–9,259,716, forward strandUSP17L21: 9,262,872–9,264,464, forward strandUSP17L22: 9,267,619–9,269,211, forward strandUSP17L23: 9,272,364–9,272,914, forward strandUSP17L24: 9,325,165–9,326,757, forward strandUSP17L24USP17L25: 9,329,911–9,331,503, forward strandUSP17L25USP17L26: 9,334,658–9,336,250, forward strandUSP17L26USP17L5: 9,339,403–9,340,995, forward strandUSP17L5USP17L27: 9,344,148–9,345,740, forward strandUSP17L28: 9,348,893–9,350,485, forward strandUSP17L29: 9,353,638–9,355,230, forward strandUSP17L30: 9,363,129–9,364,721, forward strandDiagram of HMX1: 2 exons on the reverse strand of chromosome 4Exon 2: 8,867,048–8,868,345, 1,298 basesExon 1: 8,871,221–8,871,839, 619 bases215′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 1.9 kb of the gene's 4.8 kb; 1,047 of those bases code for the protein.

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.
  • 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.). HMX1 gene: H6 family homeobox 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/hmx1

Vancouver

Dante Labs. HMX1 gene: H6 family homeobox 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hmx1

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