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PTCH1 patched 1 [ Homo sapiens (human) ]

Gene ID: 5727, updated on 1-Jun-2020

Summary

Official Symbol
PTCH1provided by HGNC
Official Full Name
patched 1provided by HGNC
Primary source
HGNC:HGNC:9585
See related
Ensembl:ENSG00000185920 MIM:601309
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PTC; BCNS; PTC1; PTCH; NBCCS
Summary
This gene encodes a member of the patched family of proteins and a component of the hedgehog signaling pathway. Hedgehog signaling is important in embryonic development and tumorigenesis. The encoded protein is the receptor for the secreted hedgehog ligands, which include sonic hedgehog, indian hedgehog and desert hedgehog. Following binding by one of the hedgehog ligands, the encoded protein is trafficked away from the primary cilium, relieving inhibition of the G-protein-coupled receptor smoothened, which results in activation of downstream signaling. Mutations of this gene have been associated with basal cell nevus syndrome and holoprosencephaly. [provided by RefSeq, Aug 2017]
Expression
Broad expression in endometrium (RPKM 11.5), testis (RPKM 8.7) and 24 other tissues See more
Orthologs

Genomic context

See PTCH1 in Genome Data Viewer
Location:
9q22.32
Exon count:
28
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (95442980..95516971, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (98205264..98279247, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376155 Neighboring gene uncharacterized LOC105376156 Neighboring gene metallothionein 1 pseudogene 1 Neighboring gene uncharacterized LOC100507346 Neighboring gene VISTA enhancer hs1258 Neighboring gene VISTA enhancer hs1417 Neighboring gene uncharacterized LOC105376157 Neighboring gene uncharacterized LOC105376158

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
BCC1
MedGen: C2751544 OMIM: 605462 GeneReviews: Not available
Compare labs
Gorlin syndrome Compare labs
Holoprosencephaly 7
MedGen: C1835820 OMIM: 610828 GeneReviews: Holoprosencephaly Overview
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

Little evidence for dosage pathogenicity (Last evaluated (2011-12-01)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2011-12-01)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
NHGRI GWA Catalog
Chemerin, a novel adipokine in the regulation of angiogenesis.
NHGRI GWA Catalog
Genome-wide association analysis identifies 20 loci that influence adult height.
NHGRI GWA Catalog
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ26746, FLJ42602

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cholesterol binding IDA
Inferred from Direct Assay
more info
PubMed 
cyclin binding IPI
Inferred from Physical Interaction
more info
PubMed 
hedgehog family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hedgehog family protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
hedgehog receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heparin binding IEA
Inferred from Electronic Annotation
more info
 
patched binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
smoothened binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
smoothened binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
animal organ morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
branching involved in ureteric bud morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cell differentiation involved in kidney development IEA
Inferred from Electronic Annotation
more info
 
cell fate determination IEA
Inferred from Electronic Annotation
more info
 
cell proliferation involved in metanephros development IEA
Inferred from Electronic Annotation
more info
 
cellular response to cholesterol IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to cholesterol ISS
Inferred from Sequence or Structural Similarity
more info
 
commissural neuron axon guidance IEA
Inferred from Electronic Annotation
more info
 
dorsal/ventral pattern formation ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic limb morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
embryonic organ development IEA
Inferred from Electronic Annotation
more info
 
epidermal cell fate specification IEA
Inferred from Electronic Annotation
more info
 
glucose homeostasis IEA
Inferred from Electronic Annotation
more info
 
heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
keratinocyte proliferation IEA
Inferred from Electronic Annotation
more info
 
limb morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
liver regeneration IEA
Inferred from Electronic Annotation
more info
 
mammary gland duct morphogenesis IEA
Inferred from Electronic Annotation
more info
 
mammary gland epithelial cell differentiation IEA
Inferred from Electronic Annotation
more info
 
metanephric collecting duct development IEP
Inferred from Expression Pattern
more info
PubMed 
negative regulation of DNA-binding transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell division IEA
Inferred from Electronic Annotation
more info
 
negative regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of multicellular organism growth ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of smoothened signaling pathway TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural plate axis specification ISS
Inferred from Sequence or Structural Similarity
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
neural tube patterning IMP
Inferred from Mutant Phenotype
more info
PubMed 
pharyngeal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cholesterol efflux IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of epidermal cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
prostate gland development IEA
Inferred from Electronic Annotation
more info
 
protein localization to plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
protein processing ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
regulation of protein localization IEA
Inferred from Electronic Annotation
more info
 
regulation of smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
response to chlorate IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to mechanical stimulus IEA
Inferred from Electronic Annotation
more info
 
response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
smooth muscle tissue development IEP
Inferred from Expression Pattern
more info
PubMed 
smoothened signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
smoothened signaling pathway IEP
Inferred from Expression Pattern
more info
PubMed 
smoothened signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
smoothened signaling pathway involved in dorsal/ventral neural tube patterning IEA
Inferred from Electronic Annotation
more info
 
somite development IMP
Inferred from Mutant Phenotype
more info
PubMed 
spinal cord motor neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
axonal growth cone IEA
Inferred from Electronic Annotation
more info
 
caveola IDA
Inferred from Direct Assay
more info
PubMed 
ciliary membrane TAS
Traceable Author Statement
more info
 
dendritic growth cone IEA
Inferred from Electronic Annotation
more info
 
endocytic vesicle membrane TAS
Traceable Author Statement
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
PubMed 
midbody IEA
Inferred from Electronic Annotation
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007664.1 RefSeqGene

    Range
    5001..78984
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_515

mRNA and Protein(s)

  1. NM_000264.5NP_000255.2  protein patched homolog 1 isoform L

    See identical proteins and their annotated locations for NP_000255.2

    Status: REVIEWED

    Source sequence(s)
    AL161729
    Consensus CDS
    CCDS6714.1
    UniProtKB/Swiss-Prot
    Q13635
    Related
    ENSP00000332353.6, ENST00000331920.11
    Conserved Domains (2) summary
    PHA03377
    Location:12531369
    PHA03377; EBNA-3C; Provisional
    TIGR00918
    Location:431206
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
  2. NM_001083602.3NP_001077071.1  protein patched homolog 1 isoform M

    Status: REVIEWED

    Source sequence(s)
    AB189436, AB209495, AI417736, BC043542, BX117041, CR744004, U59464
    Consensus CDS
    CCDS47996.1
    UniProtKB/Swiss-Prot
    Q13635
    Related
    ENSP00000389744.1, ENST00000437951.5
    Conserved Domains (3) summary
    TIGR00918
    Location:21140
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam07698
    Location:9491095
    7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase
    pfam12349
    Location:396550
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
  3. NM_001083603.3NP_001077072.1  protein patched homolog 1 isoform L'

    Status: REVIEWED

    Source sequence(s)
    AB189437, AB209495, AI417736, AL161729, BX117041, CR744004, U59464
    Consensus CDS
    CCDS47995.1
    UniProtKB/Swiss-Prot
    Q13635
    Related
    ENSP00000364423.2, ENST00000375274.6
    Conserved Domains (3) summary
    TIGR00918
    Location:651205
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam07698
    Location:10141160
    7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase
    pfam12349
    Location:461615
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
  4. NM_001083604.2NP_001077073.1  protein patched homolog 1 isoform S

    See identical proteins and their annotated locations for NP_001077073.1

    Status: REVIEWED

    Source sequence(s)
    AB189438, AB209495, AI417736, BX117041, CR744004, U59464
    Consensus CDS
    CCDS43851.1
    UniProtKB/Swiss-Prot
    Q13635
    Related
    ENSP00000399981.1, ENST00000421141.5
    Conserved Domains (3) summary
    TIGR00918
    Location:11055
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam07698
    Location:8641010
    7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase
    pfam12349
    Location:311465
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
  5. NM_001083605.2NP_001077074.1  protein patched homolog 1 isoform S

    See identical proteins and their annotated locations for NP_001077074.1

    Status: REVIEWED

    Source sequence(s)
    AB189439, AB209495, AI417736, BX117041, CR744004, U59464
    Consensus CDS
    CCDS43851.1
    UniProtKB/Swiss-Prot
    Q13635
    Conserved Domains (3) summary
    TIGR00918
    Location:11055
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam07698
    Location:8641010
    7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase
    pfam12349
    Location:311465
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
  6. NM_001083606.3NP_001077075.1  protein patched homolog 1 isoform S

    See identical proteins and their annotated locations for NP_001077075.1

    Status: REVIEWED

    Source sequence(s)
    AB209495, AI358880, AI417736, AL161729, BX117041, CR744004, U43148
    Consensus CDS
    CCDS43851.1
    UniProtKB/Swiss-Prot
    Q13635
    Related
    ENSP00000414823.2, ENST00000429896.6
    Conserved Domains (3) summary
    TIGR00918
    Location:11055
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam07698
    Location:8641010
    7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase
    pfam12349
    Location:311465
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
  7. NM_001083607.2NP_001077076.1  protein patched homolog 1 isoform S

    See identical proteins and their annotated locations for NP_001077076.1

    Status: REVIEWED

    Source sequence(s)
    AB189440, AB209495, AI417736, BF195352, BX117041, CR744004, U59464
    Consensus CDS
    CCDS43851.1
    UniProtKB/Swiss-Prot
    Q13635
    Related
    ENSP00000396135.1, ENST00000418258.5
    Conserved Domains (3) summary
    TIGR00918
    Location:11055
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    pfam07698
    Location:8641010
    7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase
    pfam12349
    Location:311465
    Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
  8. NM_001354918.2NP_001341847.1  protein patched homolog 1 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL161729
    Conserved Domains (2) summary
    TIGR00918
    Location:431154
    2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
    cl27975
    Location:12011317
    EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
  9. NM_001354919.2NP_001341848.1  protein patched homolog 1 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AL161729, BC043542
    Consensus CDS
    CCDS87661.1
    Related
    ENSP00000449745.1, ENST00000468211.6
    Conserved Domains (1) summary
    cl25655
    Location:2183
    Patched; Patched family

RNA

  1. NR_149061.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL161729

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    95442980..95516971 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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