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Gene

SHH

sonic hedgehog signaling molecule

Summary

Cytogenetic location
7q36.3
Coordinates
Chromosome 7: 155,799,980–155,812,463 (GRCh38)
Exons
3 exons across 12.5 kb
Protein
462 amino acids
Also known as
HHG1, SMMCI, TPT, TPTPS, MCOPCB5
Previous symbols
HPE3, HLP3
MANE Select transcript
ENST00000297261.7NM_000193.4
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

  • Microphthalmia, Anophthalmia & Coloboma

    • Isolated Anophthalmia, Microphthalmia & Coloboma

      Eye malformations without other features, including nanophthalmos, caused by changes in genes such as VSX2, RAX, MFRP, PRSS56 and others.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      People with nanophthalmos (often MFRP or PRSS56) have a raised risk of angle-closure glaucoma and need regular eye checks; a genetic diagnosis also informs recurrence risk.

  • 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.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

How SHH is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 7, with a bracket where SHH sits. SHH and 5 genes near it on chromosome 7, from 155,306,222 to 156,306,221.Chromosome 77q36.3p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.3155.4 Mb155.6 Mb155.8 Mb156 Mb156.2 MbINSIG1: 155,296,731–155,311,963, forward strandINSIG1EN2: 155,457,555–155,464,831, forward strandEN2CNPY1: 155,474,206–155,555,450, reverse strandCNPY1: 155,474,256–155,644,406, reverse strandRBM33: 155,644,426–155,781,485, forward strandRBM33SHH: 155,799,980–155,812,463, reverse strandSHHDiagram of SHH: 3 exons on the reverse strand of chromosome 7Exon 3: 41 known disease-causing sitesExon 2: 21 known disease-causing sitesExon 1: 18 known disease-causing sitesExon 3: 155,799,980–155,803,726, 3,747 basesExon 2: 155,806,296–155,806,557, 262 basesExon 1: 155,811,823–155,812,463, 641 bases3215′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 4.7 kb of the gene's 12.5 kb; 1,389 of those bases code for the protein.

How a genome test reads SHH

83

positions in SHH 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 12.5 kb of SHH, introns included, not only the 4.7 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.). SHH gene: sonic hedgehog signaling molecule. Retrieved 17 October 2026, from https://dantelabs.com/genes/shh

Vancouver

Dante Labs. SHH gene: sonic hedgehog signaling molecule [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/shh

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