Human Gene PTCH2 (ENST00000447098.6) from GENCODE V44
  Description: Homo sapiens patched 2 (PTCH2), transcript variant 2, mRNA. (from RefSeq NM_001166292)
RefSeq Summary (NM_001166292): This gene encodes a transmembrane receptor of the patched gene family. The encoded protein may function as a tumor suppressor in the hedgehog signaling pathway. Alterations in this gene have been associated with nevoid basal cell carcinoma syndrome, basal cell carcinoma, medulloblastoma, and susceptibility to congenital macrostomia. Alternatively spliced transcript variants have been described.[provided by RefSeq, Oct 2009].
Gencode Transcript: ENST00000447098.6
Gencode Gene: ENSG00000117425.14
Transcript (Including UTRs)
   Position: hg38 chr1:44,819,844-44,842,944 Size: 23,101 Total Exon Count: 23 Strand: -
Coding Region
   Position: hg38 chr1:44,820,689-44,842,932 Size: 22,244 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:44,819,844-44,842,944)mRNA (may differ from genome)Protein (1146 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTC2_HUMAN
DESCRIPTION: RecName: Full=Protein patched homolog 2; Short=PTC2;
FUNCTION: May have a role in epidermal development. May act as a receptor for Sonic hedgehog (SHH).
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
DISEASE: Defects in PTCH2 are a cause of medulloblastoma (MDB) [MIM:155255]. MDB is a malignant, invasive embryonal tumor of the cerebellum with a preferential manifestation in children. Although the majority of medulloblastomas occur sporadically, some manifest within familial cancer syndromes such as Turcot syndrome and basal cell nevus syndrome (Gorlin syndrome).
DISEASE: Defects in PTCH2 are a cause of sporadic basal cell carcinoma (BCC) [MIM:605462].
SIMILARITY: Belongs to the patched family.
SIMILARITY: Contains 1 SSD (sterol-sensing) domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org//Genes/PTCH2ID41892ch1p34.html";
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ptch2/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PTCH2
Diseases sorted by gene-association score: basal cell nevus syndrome* (544), basal cell carcinoma 1* (450), medulloblastoma* (276), macrostomia, isolated* (247), medulloblastoma, ptch2-related* (100), basal cell carcinoma (33), breast papillary carcinoma (9), intravenous leiomyomatosis (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 20.38 RPKM in Testis
Total median expression: 160.04 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -290.50845-0.344 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003392 - Patched
IPR000731 - SSD
IPR004766 - TM_rcpt_patched

Pfam Domains:
PF02460 - Patched family

ModBase Predicted Comparative 3D Structure on Q9Y6C5
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserNo orthologNo orthologGenome BrowserGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGI  EnsemblWormBase 
Protein Sequence  Protein SequenceProtein Sequence 
Alignment  AlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005119 smoothened binding
GO:0008158 hedgehog receptor activity
GO:0097108 hedgehog family protein binding

Biological Process:
GO:0001709 cell fate determination
GO:0007165 signal transduction
GO:0008544 epidermis development
GO:0009957 epidermal cell fate specification
GO:0042633 hair cycle
GO:0043588 skin development
GO:0045606 positive regulation of epidermal cell differentiation
GO:0045879 negative regulation of smoothened signaling pathway

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF119569 - Homo sapiens patched 2 (PTCH2) mRNA, complete cds.
LF206570 - JP 2014500723-A/14073: Polycomb-Associated Non-Coding RNAs.
MA442147 - JP 2018138019-A/14073: Polycomb-Associated Non-Coding RNAs.
AY359016 - Homo sapiens clone DNA67654 Patched 2 (UNQ560) mRNA, complete cds.
BC143712 - Homo sapiens cDNA clone IMAGE:9052226.
AF087651 - Homo sapiens patched 2 (PTCH2) mRNA, complete cds.
AF091501 - Homo sapiens receptor protein patched 2 (PTCH2) mRNA, complete cds.
BC152911 - Synthetic construct Homo sapiens clone IMAGE:100016143, MGC:184152 patched homolog 2 (Drosophila) (PTCH2) mRNA, encodes complete protein.
AY358555 - Homo sapiens clone DNA35621 Patched 2 (UNQ560) mRNA, complete cds.
AB527344 - Synthetic construct DNA, clone: pF1KE0077, Homo sapiens PTCH2 gene for patched homolog 2, without stop codon, in Flexi system.
LF213882 - JP 2014500723-A/21385: Polycomb-Associated Non-Coding RNAs.
MA449459 - JP 2018138019-A/21385: Polycomb-Associated Non-Coding RNAs.
LF356288 - JP 2014500723-A/163791: Polycomb-Associated Non-Coding RNAs.
MA591865 - JP 2018138019-A/163791: Polycomb-Associated Non-Coding RNAs.
LF356287 - JP 2014500723-A/163790: Polycomb-Associated Non-Coding RNAs.
MA591864 - JP 2018138019-A/163790: Polycomb-Associated Non-Coding RNAs.
LF356286 - JP 2014500723-A/163789: Polycomb-Associated Non-Coding RNAs.
MA591863 - JP 2018138019-A/163789: Polycomb-Associated Non-Coding RNAs.
LF356285 - JP 2014500723-A/163788: Polycomb-Associated Non-Coding RNAs.
MA591862 - JP 2018138019-A/163788: Polycomb-Associated Non-Coding RNAs.
AK307168 - Homo sapiens cDNA, FLJ97116.
LF356284 - JP 2014500723-A/163787: Polycomb-Associated Non-Coding RNAs.
MA591861 - JP 2018138019-A/163787: Polycomb-Associated Non-Coding RNAs.
LF356283 - JP 2014500723-A/163786: Polycomb-Associated Non-Coding RNAs.
MA591860 - JP 2018138019-A/163786: Polycomb-Associated Non-Coding RNAs.
LF356282 - JP 2014500723-A/163785: Polycomb-Associated Non-Coding RNAs.
MA591859 - JP 2018138019-A/163785: Polycomb-Associated Non-Coding RNAs.
LF356279 - JP 2014500723-A/163782: Polycomb-Associated Non-Coding RNAs.
MA591856 - JP 2018138019-A/163782: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04340 - Hedgehog signaling pathway
hsa05200 - Pathways in cancer
hsa05217 - Basal cell carcinoma

Reactome (by CSHL, EBI, and GO)

Protein Q9Y6C5 (Reactome details) participates in the following event(s):

R-HSA-445124 Patched binds Smoothened
R-HSA-373080 Class B/2 (Secretin family receptors)
R-HSA-500792 GPCR ligand binding
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000447098.1, ENST00000447098.2, ENST00000447098.3, ENST00000447098.4, ENST00000447098.5, NM_001166292, O95341, O95856, PTC2_HUMAN, Q53Z57, Q5QP87, Q6UX14, Q9Y6C5, uc021omv.1, UNQ560/PRO1121/PRO57079
UCSC ID: ENST00000447098.6
RefSeq Accession: NM_001166292
Protein: Q9Y6C5 (aka PTC2_HUMAN)
CCDS: CCDS53312.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.