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Gene

SIX3

SIX homeobox 3

Summary

Cytogenetic location
2p21
Coordinates
Chromosome 2: 44,941,702–44,946,071 (GRCh38)
Exons
2 exons across 4.4 kb
Protein
332 amino acids
Previous symbols
HPE2
MANE Select transcript
ENST00000260653.5NM_005413.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Curated report relevant to this gene

  • Non-Acquired Combined Pituitary Hormone Deficiency

    • Congenital hypopituitarism is characterized by multiple pituitary hormone deficiency, including somatotroph, thyrotroph, lactotroph, corticotroph or gonadotroph deficiencies, due to mutations of pituitary transcription factors involved in pituitary ontogenesis.

      • 4 GenCC submitters rate it definitive or strong

How SIX3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 2, with a bracket where SIX3 sits. SIX3 and 3 genes near it on chromosome 2, from 44,443,887 to 45,443,886.Chromosome 22p21p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.344.6 Mb44.8 Mb45 Mb45.2 Mb45.4 MbCAMKMT: 44,361,874–44,776,433, forward strandCAMKMTSIX3: 44,941,702–44,946,071, forward strandSIX3SIX2: 45,005,182–45,009,520, reverse strandSIX2SRBD1: 45,384,544–45,612,165, reverse strandSRBD1Diagram of SIX3: 2 exons on the forward strand of chromosome 2Exon 1: 13 known disease-causing sitesExon 1: 44,941,702–44,942,910, 1,209 basesExon 2: 44,944,568–44,946,071, 1,504 bases125′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 2.7 kb of the gene's 4.4 kb; 999 of those bases code for the protein.

How a genome test reads SIX3

13

positions in SIX3 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 4.4 kb of SIX3, introns included, not only the 2.7 kb of exons.

Genes linked to the same conditions

Traits linked to SIX3

The Human Phenotype Ontology lists these as features of the rare conditions SIX3 can cause. Each trait's page lists the other genes linked to it.

Abnormality of the nervous system

Show 33 more traits

External links

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.). SIX3 gene: SIX homeobox 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/six3

Vancouver

Dante Labs. SIX3 gene: SIX homeobox 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/six3

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