SHH

Chr 7

sonic hedgehog signaling molecule

Also known as: HHG1, HLP3, HPE3, MCOPCB5, SMMCI, ShhNC, TPT, TPTPS

This gene encodes a protein that is instrumental in patterning the early embryo. It has been implicated as the key inductive signal in patterning of the ventral neural tube, the anterior-posterior limb axis, and the ventral somites. Of three human proteins showing sequence and functional similarity to the sonic hedgehog protein of Drosophila, this protein is the most similar. The protein is made as a precursor that is autocatalytically cleaved; the N-terminal portion is soluble and contains the signalling activity while the C-terminal portion is involved in precursor processing. More importantly, the C-terminal product covalently attaches a cholesterol moiety to the N-terminal product, restricting the N-terminal product to the cell surface and preventing it from freely diffusing throughout the developing embryo. Defects in this protein or in its signalling pathway are a cause of holoprosencephaly (HPE), a disorder in which the developing forebrain fails to correctly separate into right and left hemispheres. HPE is manifested by facial deformities. It is also thought that mutations in this gene or in its signalling pathway may be responsible for VACTERL syndrome, which is characterized by vertebral defects, anal atresia, tracheoesophageal fistula with esophageal atresia, radial and renal dysplasia, cardiac anomalies, and limb abnormalities. Additionally, mutations in a long range enhancer located approximately 1 megabase upstream of this gene disrupt limb patterning and can result in preaxial polydactyly. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtMicrophthalmia/Coloboma 5
UniProtHoloprosencephaly 3
UniProtSolitary median maxillary central incisor
UniProtTriphalangeal thumb with polysyndactyly

Clinical highlights

Gene-disease validity (ClinGen)
holoprosencephaly 3 · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
8
Active trials
685
Pubs (1 yr)
P/LP submissions
P/LP missense
0.24
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — SHH
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.24LOEUF
pLI 0.983
Z-score 3.25
OE 0.00 (0.000.24)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.95Z-score
OE missense 0.46 (0.390.54)
106 obs / 232.5 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.00 (0.000.24)
00.351.4
Missense OE?0.46 (0.390.54)
00.61.4
Synonymous OE?1.14
01.21.6
LoF obs/exp: 0 / 12.3Missense obs/exp: 106 / 232.5Syn Z: -1.15

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SHH · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

Atypical Teratoid/Rhabdoid Tumors (AT/RTs)Central Nervous System (CNS) Tumors

Feasibility of Using Bortezomib With or Without Chemotherapy in Patients With Atypical Teratoid/Rhabdoid Tumors

ACTIVE NOT RECRUITING
NCT06853080Phase PHASE2Taipei Medical UniversityStarted 2020-12-02
Bortezomib
Medulloblastoma RecurrentMedulloblastoma, Childhood, RecurrentMedulloblastoma, SHH-activated and TP53 Mutant

Relapsed and Progressive Sonic Hedgehog Medulloblastoma With U1 Mutation Registry Study

RECRUITING
NCT07242963Mohammad H. Abu ArjaStarted 2025-09-30
Pitt Hopkins Syndrome

An Exploratory Evaluation of the Safety and Efficacy of Vorinostat in Pitt Hopkins Syndrome

RECRUITING
NCT07150026Phase PHASE1Unravel Biosciences, Inc.Started 2026-03-15
Vorinostat (SAHA)Placebo
Advanced Non-small Cell Lung CancerEGFR MutationHER2 Mutation

First in Human Study of BAY2927088 in Participants Who Have Advanced Non-small Cell Lung Cancer (NSCLC) With Mutations in the Genes of Epidermal Growth Factor Receptor (EGFR) and/or Human Epidermal Growth Factor Receptor 2 (HER2)

RECRUITING
NCT05099172Phase PHASE1, PHASE2BayerStarted 2021-10-25
BAY2927088_formulation ABAY2927088_formulation B_1BAY2927088_formulation B_2
Medulloblastoma, Childhood

Novel Molecular Targets and Innovative Therapeutic Perspective in Medulloblastoma

RECRUITING
NCT06959979Phase EARLY_PHASE1Fondazione Policlinico Universitario Agostino Gemelli IRCCSStarted 2024-11-25
CDK4/6 Inhibitor (Palbociclib, Ribociclib, Abemaciclib)
Brain Arteriovenous Malformations (AVMs)

Shh Signaling in Brain AVMs: Novel Player & Therapeutic Target

NOT YET RECRUITING
NCT07676721Fondazione Policlinico Universitario Agostino Gemelli IRCCSStarted 2026-08-01
Breast Cancer

Carboplatin and Nab-Paclitaxel With or Without Vorinostat in Treating Women With Newly Diagnosed Operable Breast Cancer

ACTIVE NOT RECRUITING
NCT00616967Phase PHASE2Sidney Kimmel Comprehensive Cancer Center at Johns HopkinsStarted 2008-05
carboplatinpaclitaxel albumin-stabilized nanoparticle formulationvorinostat
Rett Syndrome

Rett REVOLUTION Trial: An Exploratory Evaluation of the Safety and Efficacy of Vorinostat in Rett Syndrome

RECRUITING
NCT07150013Phase PHASE1Unravel Biosciences, Inc.Started 2026-03-15
Vorinostat (SAHA)Placebo