SHH

Chr 7AD

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]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Holoprosencephaly 3MIM #142945
AD
Microphthalmia/coloboma 5MIM #611638
AD
Single median maxillary central incisorMIM #147250
AD
UniProtSolitary median maxillary central incisor
UniProtTriphalangeal thumb with polysyndactyly
UniProtPreaxial polydactyly 2
UniProtHypoplasia or aplasia of tibia with polydactyly

Clinical highlights

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.
4
Active trials
714
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
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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 (0.00–0.24)
Highly constrained

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

Missense Constraint?
2.95Z-score
OE missense 0.46 (0.39–0.54)
106 obs / 232.5 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.24)
0≤0.351.4
Missense OE?0.46 (0.39–0.54)
0≤0.61.4
Synonymous OE?1.14
0≤1.21.6
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.