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Gene

HHAT

hedgehog acyltransferase

Summary

Cytogenetic location
1q32.2
Coordinates
Chromosome 1: 210,328,902–210,676,290 (GRCh38)
Exons
12 exons across 347.4 kb
Protein
493 amino acids
Also known as
FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2
MANE Select transcript
ENST00000261458.8NM_018194.6
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

  • 46,XY Differences of Sex Development and Gonadal Dysgenesis

    • 46,XY differences of sex development

      Conditions in people with XY chromosomes in which gonadal or genital development is atypical, caused by variants in genes such as SRD5A2, HSD17B3, NR5A1, MAP3K1, DHH, WT1, CYP11A1 and LHCGR.

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

      Diagnosis informs hormone treatment, fertility counselling and, where dysgenetic gonads carry Y material, assessment of gonadal tumour risk.

How HHAT 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 HHAT sits. HHAT and 3 genes near it on chromosome 1, from 209,981,513 to 211,023,679.Chromosome 11q32.2p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q44210 Mb210.2 Mb210.4 Mb210.6 Mb210.8 Mb211 MbSYT14: 209,900,923–210,171,389, forward strandSYT14SERTAD4: 210,232,572–210,247,734, forward strandSERTAD4HHAT: 210,328,902–210,676,290, forward strandHHATKCNH1: 210,676,823–211,134,183, reverse strandKCNH1Diagram of HHAT: 12 exons on the forward strand of chromosome 1Exon 8: 1 known disease-causing siteExon 1: 210,328,902–210,329,104, 203 basesExon 2: 210,348,933–210,349,066, 134 basesExon 3: 210,362,852–210,362,919, 68 basesExon 4: 210,387,468–210,387,581, 114 basesExon 5: 210,400,468–210,400,662, 195 basesExon 6: 210,404,464–210,404,679, 216 basesExon 7: 210,418,154–210,418,325, 172 basesExon 8: 210,464,505–210,464,655, 151 basesExon 9: 210,513,153–210,513,188, 36 basesExon 10: 210,587,898–210,588,099, 202 basesExon 11: 210,623,526–210,623,670, 145 basesExon 12: 210,674,288–210,676,290, 2,003 bases1246810125′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 3.6 kb of the gene's 347.4 kb; 1,482 of those bases code for the protein.

How a genome test reads HHAT

1

position in HHAT 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 347.4 kb of HHAT, introns included, not only the 3.6 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.). HHAT gene: hedgehog acyltransferase. Retrieved 16 October 2026, from https://dantelabs.com/genes/hhat

Vancouver

Dante Labs. HHAT gene: hedgehog acyltransferase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/hhat

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