SHH Gene (Protein Coding)

Sonic Hedgehog Signaling Molecule

GC07M155799
GIFtS:
50
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. T... See more...

Aliases for SHH Gene

Aliases for SHH Gene

  • Sonic Hedgehog Signaling Molecule 2 3 5
  • Shh Unprocessed N-Terminal Signaling And C-Terminal Autoprocessing Domains 3 4
  • Sonic Hedgehog Protein 3 4
  • MCOPCB5 2 3
  • SMMCI 2 3
  • ShhNC 3 4
  • TPTPS 2 3
  • HHG1 2 3
  • TPT 2 3
  • Sonic Hedgehog (Drosophila) Homolog 2
  • Sonic Hedgehog Homolog 3
  • HHG-1 4
  • HLP3 3
  • HPE3 3
  • SHH 5

External Ids for SHH Gene

Previous HGNC Symbols for SHH Gene

  • HPE3
  • HLP3

Previous GeneCards Identifiers for SHH Gene

  • GC07M153825
  • GC07M154898
  • GC07M155013
  • GC07M155014
  • GC07M155095
  • GC07M155288
  • GC07M155592
  • GC07M149327

Summaries for SHH Gene

Entrez Gene Summary for SHH Gene

  • 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]

GeneCards Summary for SHH Gene

SHH (Sonic Hedgehog Signaling Molecule) is a Protein Coding gene. Diseases associated with SHH include Solitary Median Maxillary Central Incisor and Holoprosencephaly 3. Among its related pathways are Development_Hedgehog and PTH signaling pathways in bone and cartilage development and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is IHH.

UniProtKB/Swiss-Prot Summary for SHH Gene

  • [Sonic hedgehog protein]: The C-terminal part of the sonic hedgehog protein precursor displays an autoproteolysis and a cholesterol transferase activity (By similarity). Both activities result in the cleavage of the full-length protein into two parts (ShhN and ShhC) followed by the covalent attachment of a cholesterol moiety to the C-terminal of the newly generated ShhN (By similarity). Both activities occur in the reticulum endoplasmic (By similarity). Once cleaved, ShhC is degraded in the endoplasmic reticulum (By similarity).
  • [Sonic hedgehog protein N-product]: The dually lipidated sonic hedgehog protein N-product (ShhNp) is a morphogen which is essential for a variety of patterning events during development. Induces ventral cell fate in the neural tube and somites (PubMed:24863049). Involved in the patterning of the anterior-posterior axis of the developing limb bud (By similarity). Essential for axon guidance (By similarity). Binds to the patched (PTCH1) receptor, which functions in association with smoothened (SMO), to activate the transcription of target genes (PubMed:10753901). In the absence of SHH, PTCH1 represses the constitutive signaling activity of SMO (PubMed:10753901).

Tocris Summary for SHH Gene

  • The Hedgehog (Hh) signaling pathway is crucial in the development of all animals. In the embryo, it regulates morphogenesis of a variety of tissues and organs; in the adult, it controls stem cell proliferation. There are three known human Hh proteins: Shh, Dhh and Ihh.

Gene Wiki entry for SHH Gene

Additional gene information for SHH Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHH Gene

Genomics for SHH Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SHH Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH07J155806 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 600.7 +3.9 3900 3.3 HNRNPL GATAD2A ATF7 REST TFE3 KDM1A ZIC2 RBFOX2 RXRB SP1 SHH lnc-CNPY1-12 RBM33
GH07J155813 Promoter/Enhancer 1.3 EPDnew Ensembl dbSUPER 600.7 +0.2 162 0.6 PRDM10 PRDM1 POLR2A EZH2 GTF2F1 ZNF341 ATF7 RAD21 ZBTB10 ZBTB26 SHH lnc-CNPY1-12 RBM33
GH07J155811 Enhancer 0.5 ENCODE 600.7 +1.4 1381 0.2 EZH2 ZNF341 CEBPB ATF4 GLIS1 ZNF398 KLF1 HLF SHH lnc-CNPY1-12 RBM33
GH07J155814 Enhancer 0.5 ENCODE 600.7 +0.7 741 0.2 EZH2 ZBTB26 ZFHX2 KLF17 GLIS1 KLF1 SHH lnc-CNPY1-12 RBM33
GH07J155203 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 5.9 +605.6 605605 5.8 RNF2 ARHGAP35 SP1 CREB1 HNRNPL ATF7 PRDM10 ZNF629 LEF1 IKZF1 PAXIP1-AS2 PAXIP1 RBM33 PAXIP1-DT ENSG00000273183 ENSG00000228521 INSIG1 SHH ENSG00000287865 lnc-PAXIP1-23
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHH on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHH

Top Transcription factor binding sites by QIAGEN in the SHH gene promoter:
  • NF-1
  • NF-kappaB1
  • Oct-B1
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU3F2

Genomic Locations for SHH Gene

Genomic Locations for SHH Gene
chr7:155,799,980-155,812,463
(GRCh38/hg38)
Size:
12,484 bases
Orientation:
Minus strand
chr7:155,592,680-155,604,967
(GRCh37/hg19)
Size:
12,288 bases
Orientation:
Minus strand

Genomic View for SHH Gene

Genes around SHH on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHH Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHH Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SHH Gene

Proteins for SHH Gene

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  • Protein details for SHH Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15465-SHH_HUMAN
    Recommended name:
    Sonic hedgehog protein
    Protein Accession:
    Q15465
    Secondary Accessions:
    • A4D247
    • Q75MC9

    Protein attributes for SHH Gene

    Size:
    462 amino acids
    Molecular mass:
    49607 Da
    Quaternary structure:
    • Interacts with HHATL/GUP1 which negatively regulates HHAT-mediated palmitoylation of the SHH N-terminus (By similarity). ShhNp is active as a multimer (PubMed:24522195). Interacts with BOC and CDON (By similarity). Interacts with HHIP (PubMed:19561609). Interacts with DISP1 via its cholesterol anchor (PubMed:22902404, PubMed:22677548). Interacts with SCUBE2 (PubMed:24522195, PubMed:22677548). Interacts with glypican GPC3 (By similarity).

    Three dimensional structures from OCA and Proteopedia for SHH Gene

neXtProt entry for SHH Gene

Protein Expression for SHH Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SHH Gene

  • [Sonic hedgehog protein]: The C-terminal domain displays an autoproteolysis activity and a cholesterol transferase activity (By similarity). Both activities result in the cleavage of the full-length protein and covalent attachment of a cholesterol moiety to the C-terminal of the newly generated N-terminal fragment (ShhN) (By similarity). Cholesterylation is required for the sonic hedgehog protein N-product targeting to lipid rafts and multimerization (PubMed:24522195, PubMed:26875496). ShhN is the active species in both local and long-range signaling, whereas the C-product (ShhC) is degraded in the reticulum endoplasmic (By similarity).
  • [Sonic hedgehog protein N-product]: N-palmitoylation by HHAT of ShhN is required for sonic hedgehog protein N-product multimerization and full activity (By similarity). It is a prerequisite for the membrane-proximal positioning and the subsequent shedding of this N-terminal peptide (PubMed:24522195).
  • [Sonic hedgehog protein N-product]: The lipidated N- and C-terminal peptides of ShhNp can be cleaved (shedding)(PubMed:24522195). The N-terminal palmitoylated peptide is cleaved at the Cardin-Weintraub (CW) motif site (PubMed:24522195). The cleavage reduced the interactions with heparan sulfate. The cleavage is enhanced by SCUBE2 (PubMed:24522195, PubMed:23118222).
  • Glycosylation at Asn278
  • Modification sites at PhosphoSitePlus

Other Protein References for SHH Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SHH Gene

Domains & Families for SHH Gene

Gene Families for SHH Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SHH Gene

InterPro:
Blocks:
  • Hedgehog amino-terminal signaling domain
  • Sonic hedgehog protein signature
  • Hedgehog protein, hint region
  • Hedgehog/Intein hint domain, C-terminal
  • Hedgehog/DD-peptidase, zinc-binding motif
ProtoNet:

Suggested Antigen Peptide Sequences for SHH Gene

GenScript: Design optimal peptide antigens:
  • Sonic hedgehog homolog (Drosophila) (D9ZGF9_HUMAN)
  • HHG-1 (SHH_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15465

UniProtKB/Swiss-Prot:

SHH_HUMAN :
  • [Sonic hedgehog protein N-product]: Binds calcium and zinc ions; this stabilizes the protein fold and is essential for protein-protein interactions mediated by this domain.
  • Belongs to the hedgehog family.
Domain:
  • [Sonic hedgehog protein N-product]: Binds calcium and zinc ions; this stabilizes the protein fold and is essential for protein-protein interactions mediated by this domain.
  • [Sonic hedgehog protein N-product]: The Cardin-Weintraub (CW) motif is required for heparan sulfate binding of the solubilized ShhNp (PubMed:23118222). The N-terminal palmitoylated peptide is cleaved at the heparan sulfate-binding Cardin-Weintraub (CW) motif site (PubMed:24522195). The cleavage reduced the interactions with heparan sulfate. The cleavage is enhanced by SCUBE2 (PubMed:24522195).
Family:
  • Belongs to the hedgehog family.
genes like me logo Genes that share domains with SHH: view

Function for SHH Gene

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  2. CRISPR
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Molecular function for SHH Gene

UniProtKB/Swiss-Prot Function:
[Sonic hedgehog protein]: The C-terminal part of the sonic hedgehog protein precursor displays an autoproteolysis and a cholesterol transferase activity (By similarity). Both activities result in the cleavage of the full-length protein into two parts (ShhN and ShhC) followed by the covalent attachment of a cholesterol moiety to the C-terminal of the newly generated ShhN (By similarity). Both activities occur in the reticulum endoplasmic (By similarity). Once cleaved, ShhC is degraded in the endoplasmic reticulum (By similarity).
UniProtKB/Swiss-Prot Function:
[Sonic hedgehog protein N-product]: The dually lipidated sonic hedgehog protein N-product (ShhNp) is a morphogen which is essential for a variety of patterning events during development. Induces ventral cell fate in the neural tube and somites (PubMed:24863049). Involved in the patterning of the anterior-posterior axis of the developing limb bud (By similarity). Essential for axon guidance (By similarity). Binds to the patched (PTCH1) receptor, which functions in association with smoothened (SMO), to activate the transcription of target genes (PubMed:10753901). In the absence of SHH, PTCH1 represses the constitutive signaling activity of SMO (PubMed:10753901).
GENATLAS Biochemistry:
embryonic patterning gene,Drosophila segment polarity gene Sonic hedgehog homolog,general ventralizing signal,expressed in the notochord and floor plate cells,gut endoderm,posterior limb buds,inductive signal for somite differentiation and limb development at the anteroposterior axis,targetting BMP2 and HOXD genes through a FGF4 positive feedback loop,also expressed in fetal liver,lung and kidney and in hair follicle,involved in signal transduction,SHH pathway

LifeMap Function Summary for SHH Gene

During embryonic development, SHH as signaling molecule is secreted from the following cells
It affects the following cells:
SHH as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:

Phenotypes From GWAS Catalog for SHH Gene

Gene Ontology (GO) - Molecular Function for SHH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005113 patched binding IEA,IDA 8906787
GO:0005509 calcium ion binding IBA,IDA 19561609
GO:0005515 protein binding IPI 19561609
GO:0005539 glycosaminoglycan binding IEA --
GO:0008233 peptidase activity IEA --
genes like me logo Genes that share ontologies with SHH: view
genes like me logo Genes that share phenotypes with SHH: view

Human Phenotype Ontology for SHH Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SHH Gene

MGI Knock Outs for SHH:
  • Shh Shh<tm1Amc>
  • Shh Shh<tm1Chg>
  • Shh Shh<tm1(EGFP/cre)Cjt>
  • Shh Shh<tm3Amc>
  • Shh Shh<tm6Amc>
  • Shh Shh<tm1b(EUCOMM)Wtsi>
  • Shh Shh<tm2.1Amc>
  • Shh Shh<tm1Tmj>
  • Shh Shh<tm1Tshir>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHH

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SHH Gene

Localization for SHH Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHH Gene

[Sonic hedgehog protein N-product]: Cell membrane. Lipid-anchor. Note=The dual-lipidated sonic hedgehog protein N-product (ShhNp) is firmly tethered to the cell membrane where it forms multimers (PubMed:24522195). Further solubilization and release from the cell surface seem to be achieved through different mechanisms, including the interaction with DISP1 and SCUBE2, movement by lipoprotein particles, transport by cellular extensions called cytonemes or by the proteolytic removal of both terminal lipidated peptides (PubMed:26875496, PubMed:24522195). {ECO:0000305 PubMed:24522195, ECO:0000305 PubMed:26875496}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SHH gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 4
cytosol 4
cytoskeleton 3
nucleus 3
mitochondrion 2
endosome 2
lysosome 2
golgi apparatus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for SHH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA,ISS --
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with SHH: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SHH Gene

Pathways & Interactions for SHH Gene

genes like me logo Genes that share pathways with SHH: view

Pathways by source for SHH Gene

1 GeneGo (Thomson Reuters) pathway for SHH Gene
  • Development_Hedgehog and PTH signaling pathways in bone and cartilage development
1 Cell Signaling Technology pathway for SHH Gene

SIGNOR curated interactions for SHH Gene

Activates:
Inactivates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SHH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA,ISS --
GO:0001525 angiogenesis IEA --
GO:0001569 branching involved in blood vessel morphogenesis IEA,ISS --
GO:0001570 vasculogenesis IEA,ISS --
GO:0001656 metanephros development IEA,ISS --
genes like me logo Genes that share ontologies with SHH: view

Drugs & Compounds for SHH Gene

Products:

  1. Drug

(40) Drugs for SHH Gene - From: ClinicalTrials, ApexBio, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cisplatin Approved Pharma Inhibits DNA synthesis,chemotherapy drug, Potent pro-apoptotic anticancer agent; activates caspase-3, Platinum 3412
Cyclophosphamide Approved, Investigational Pharma Nitrogen mustard alkylating agent and prodrug. 3670
Epinephrine Approved, Vet_approved Pharma 1364
Gemcitabine Approved Pharma Ribonucleotide reductase and DNA synthesis inhibitor, Nucleoside Analogs 2451
leucovorin Approved Pharma 3692,1548

(5) Tocris Compounds for SHH Gene

Compound Action Cas Number
20(S)-Hydroxycholesterol Allosteric activator of Hedgehog (Hh) signaling; induces Smo accumulation 516-72-3
Cyclopamine Inhibitor of Hedgehog (Hh) signaling 4449-51-8
Jervine Inhibitor of Hedgehog (Hh) signaling; binds directly to Smo 469-59-0
SANT-1 Inhibitor of hedgehog (Hh) signaling; antagonizes smoothened activity 304909-07-7
SANT-2 Inhibitor of Hedgehog (Hh) signaling; antagonizes smoothened activity 329196-48-7

(16) ApexBio Compounds for SHH Gene

Compound Action Cas Number
20(S)-Hydroxycholesterol 516-72-3
AY 9944 dihydrochloride Hedgehog Inhibitor 366-93-8
Ciliobrevin A Hh pathway antagonist 302803-72-1
Cyclopamine Hedgehog (Hh) signaling Inhibitor 4449-51-8
GANT61 GLI antagonist 500579-04-4
GDC-0449 (Vismodegib) Hedgehog antagonist,potent and selective 879085-55-9
HPI 1 Hh signaling inhibitor 599150-20-6
Jervine Hedgehog signaling Inhibitor 469-59-0
JK 184 Hh signaling inhibitor 315703-52-7
LY2940680 Hedgehog/SMO antagonist,inhibits Hh signaling 1258861-20-9
PF-5274857 Smo antagonist,potent and selective 1373615-35-0
Purmorphamine Hedgehog agonist 483367-10-8
SAG Hh and Smo agonist 912545-86-9
SANT-1 Shh inhibitor,potent and cell-permeable 304909-07-7
SANT-2 329196-48-7
U 18666A inhibitor of cholesterol transport and synthesis 3039-71-2
genes like me logo Genes that share compounds with SHH: view

Transcripts for SHH Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SHH Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHH

Alternative Splicing Database (ASD) splice patterns (SP) for SHH Gene

No ASD Table

Relevant External Links for SHH Gene

GeneLoc Exon Structure for
SHH

Expression for SHH Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SHH Gene

mRNA expression in normal human tissues for SHH Gene
mRNA expression by BioGPS for SHH GenemRNA expression by GTEx for SHH Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SHH Gene

This gene is overexpressed in Liver (x9.8), Bladder (x8.4), Nerve - Tibial (x6.5), and Adrenal Gland (x6.3).

Protein differential expression in normal tissues from HIPED for SHH Gene

This gene is overexpressed in Fetal Liver (26.4), Placenta (24.3), and Peripheral blood mononuclear cells (12.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SHH Gene



Protein tissue co-expression partners for SHH Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHH

SOURCE GeneReport for Unigene cluster for SHH Gene:

Hs.164537

Evidence on tissue expression from TISSUES for SHH Gene

  • Lung(4.5)
  • Bone marrow(4.5)
  • Nervous system(3.7)
  • Kidney(3.1)
  • Intestine(3.1)
  • Skin(3)
  • Muscle(2.8)
  • Pancreas(2.8)
  • Stomach(2.8)
  • Heart(2.7)
  • Bone(2.7)
  • Eye(2.7)
  • Liver(2.7)
  • Blood(2.7)
  • Thyroid gland(2.5)
  • Adrenal gland(2.4)
  • Lymph node(2.3)
  • Gall bladder(2.2)
  • Spleen(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SHH Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • pharynx
  • pituitary gland
  • skull
  • tooth
Thorax:
  • aorta
  • clavicle
  • diaphragm
  • heart
  • heart valve
  • lung
Abdomen:
  • abdominal wall
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
  • stomach
Pelvis:
  • testicle
  • ureter
  • uterus
Limb:
  • arm
  • digit
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with SHH: view

No data available for mRNA Expression by UniProt/SwissProt for SHH Gene

Orthologs for SHH Gene

This gene was present in the common ancestor of animals.

Orthologs for SHH Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SHH 30
  • 99.71 (n)
-- 31
  • 75 (a)
 ManyToMany
Dog
(Canis familiaris)
 Mammalia SHH 30 31
  • 89.15 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Shh 30 17 31
  • 87.9 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Shh 30
  • 87.02 (n)
Oppossum
(Monodelphis domestica)
 Mammalia SHH 31
  • 83 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SHH 30 31
  • 82.68 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 72 (a)
 ManyToMany
Chicken
(Gallus gallus)
 Aves SHH 30 31
  • 81.17 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SHH 31
  • 79 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia shh 30
  • 67.53 (n)
African clawed frog
(Xenopus laevis)
 Amphibia LOC398047 30
Zebrafish
(Danio rerio)
 Actinopterygii shha 31
  • 71 (a)
 OneToMany
shhb 30 31
  • 65.3 (n)
 OneToMany
shh 30
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP001412 30
  • 60 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta hh 30 31 32
  • 58.71 (n)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 43 (a)
 ManyToMany
-- 31
  • 31 (a)
 ManyToMany
Species where no ortholog for SHH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SHH Gene

ENSEMBL:
Gene Tree for SHH (if available)
TreeFam:
Gene Tree for SHH (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SHH: view image

Paralogs for SHH Gene

Paralogs for SHH Gene

(2) SIMAP similar genes for SHH Gene using alignment to 5 proteins:

  • SHH_HUMAN
  • C9JC48_HUMAN
  • D9ZGF9_HUMAN
  • F8WB84_HUMAN
  • F8WEH4_HUMAN
genes like me logo Genes that share paralogs with SHH: view

Variants for SHH Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHH Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
646865 Pathogenic: Holoprosencephaly 3 155,806,434(-) C/CGTAGT FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
651974 Likely Pathogenic: Holoprosencephaly 3 155,811,821(-) A/G SPLICE_DONOR_VARIANT
666320 Likely Pathogenic: Microphthalmia, isolated, with coloboma 5 155,803,187(-) C/A NONSENSE,INTRON_VARIANT
667597 Benign: not provided 155,805,972(-) T/C INTRON_VARIANT
669009 Benign/Likely Benign: not provided 156,791,369(-) G/C INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for SHH Gene

Structural Variations from Database of Genomic Variants (DGV) for SHH Gene

Variant ID Type Subtype PubMed ID
esv2663062 CNV deletion 23128226
nsv1075489 CNV deletion 25765185
nsv509227 CNV insertion 20534489
nsv951662 CNV deletion 24416366

Variation tolerance for SHH Gene

Residual Variation Intolerance Score: 23.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.69; 14.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHH Gene

Human Gene Mutation Database (HGMD)
SHH
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHH

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHH Gene

Disorders for SHH Gene

MalaCards: The human disease database

(142) MalaCards diseases for SHH Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SHH in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SHH_HUMAN
  • Microphthalmia, isolated, with coloboma, 5 (MCOPCB5) [MIM:611638]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present. Ocular colobomas are a set of malformations resulting from abnormal morphogenesis of the optic cup and stalk, and the fusion of the fetal fissure (optic fissure). {ECO:0000269 PubMed:12503095}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Holoprosencephaly 3 (HPE3) [MIM:142945]: A structural anomaly of the brain, in which the developing forebrain fails to correctly separate into right and left hemispheres. Holoprosencephaly is genetically heterogeneous and associated with several distinct facies and phenotypic variability. The majority of holoprosencephaly type 3 cases are apparently sporadic, although clear examples of autosomal dominant inheritance have been described. {ECO:0000269 PubMed:10441331, ECO:0000269 PubMed:10556296, ECO:0000269 PubMed:11479728, ECO:0000269 PubMed:15107988, ECO:0000269 PubMed:15221788, ECO:0000269 PubMed:15942952, ECO:0000269 PubMed:15942953, ECO:0000269 PubMed:16282375, ECO:0000269 PubMed:17001669, ECO:0000269 PubMed:19603532, ECO:0000269 PubMed:8896572, ECO:0000269 PubMed:9302262}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Solitary median maxillary central incisor (SMMCI) [MIM:147250]: Rare dental anomaly characterized by the congenital absence of one maxillary central incisor. {ECO:0000269 PubMed:11471164, ECO:0000269 PubMed:15103725}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Triphalangeal thumb-polysyndactyly syndrome (TPTPS) [MIM:174500]: Autosomal dominant syndrome. It is characterized by a wide spectrum of pre- and post-axial abnormalities due to altered SHH expression pattern during limb development. {ECO:0000269 PubMed:12837695, ECO:0000269 PubMed:18417549}. Note=The gene represented in this entry is involved in disease pathogenesis. Mutations located in intron 5 of LMBR1 disrupt a long-range, cis-regulatory element of SHH expression.
  • Preaxial polydactyly 2 (PPD2) [MIM:174500]: Polydactyly consists of duplication of the distal phalanx. The thumb in PPD2 is usually opposable and possesses a normal metacarpal. {ECO:0000269 PubMed:12837695}. Note=The gene represented in this entry is involved in disease pathogenesis. Mutations located in intron 5 of LMBR1 disrupt a long-range, cis-regulatory element of SHH and result in abnormal, ectopic SHH expression with pathological consequences (PubMed:12837695). {ECO:0000269 PubMed:12837695}.
  • Hypoplasia or aplasia of tibia with polydactyly (THYP) [MIM:188740]: An autosomal dominant disease characterized by hypoplastic or absent tibia, and polydactyly. {ECO:0000269 PubMed:19847792, ECO:0000269 PubMed:24965254}. Note=The gene represented in this entry is involved in disease pathogenesis. Mutations located in intron 5 of LMBR1 disrupt a long-range, cis-regulatory element of SHH and result in abnormal, ectopic SHH expression with pathological consequences. {ECO:0000303 PubMed:19847792, ECO:0000303 PubMed:24965254}.
  • Laurin-Sandrow syndrome (LSS) [MIM:135750]: A rare autosomal dominant disorder characterized by polysyndactyly of hands and/or feet, mirror image duplication of the feet, nasal defects, and loss of identity between fibula and tibia. Some patients do not have nasal abnormalities (segmental Laurin-Sandrow syndrome). {ECO:0000269 PubMed:24456159}. Note=The gene represented in this entry is involved in disease pathogenesis. Abnormal SHH limb expression with pathological consequences is caused by duplications (16-75 kb) involving the ZPA regulatory sequence (ZRS), a SHH long-range cis-regulatory element, located in LMBR1 intron 5 (PubMed:24456159).

Additional Disease Information for SHH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SHH: view

No data available for Genatlas for SHH Gene

Publications for SHH Gene

  1. Cloning, expression, and chromosomal location of SHH and IHH: two human homologues of the Drosophila segment polarity gene hedgehog. (PMID: 7590746) Marigo V … Seidman CE (Genomics 1995) 2 3 4 23
  2. The mutational spectrum of holoprosencephaly-associated changes within the SHH gene in humans predicts loss-of-function through either key structural alterations of the ligand or its altered synthesis. (PMID: 19603532) Roessler E … Muenke M (Human mutation 2009) 3 4 23
  3. Molecular mechanisms of Sonic hedgehog mutant effects in holoprosencephaly. (PMID: 16282375) Maity T … Beachy PA (Proceedings of the National Academy of Sciences of the United States of America 2005) 3 4 23
  4. Molecular screening of SHH, ZIC2, SIX3, and TGIF genes in patients with features of holoprosencephaly spectrum: Mutation review and genotype-phenotype correlations. (PMID: 15221788) Dubourg C … David V (Human mutation 2004) 3 4 23
  5. SONIC HEDGEHOG mutations causing human holoprosencephaly impair neural patterning activity. (PMID: 12709790) Schell-Apacik C … Ming JE (Human genetics 2003) 3 23 41

ExternalLinks

View latest publications for SHH gene in Mastermind

Products for SHH Gene

  • Addgene plasmids for SHH

Sources for SHH Gene