PTCH1 patched 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTCH1provided by HGNC
Official Full Name: patched 1provided by HGNC
Primary source: HGNC:HGNC:9585
See related: Ensembl:ENSG00000185920 MIM:601309; AllianceGenome:HGNC:9585
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; BCNS1; 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: mouse all
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Genomic context

Location:: 9q22.32

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (95442980..95516971, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (107612621..107686610, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (98205262..98279253, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PTCH1-mutant human cerebellar organoids exhibit altered neural development and recapitulate early medulloblastoma tumorigenesis.
Title: PTCH1-mutant human cerebellar organoids exhibit altered neural development and recapitulate early medulloblastoma tumorigenesis.
PTCH1 gene variants rs357564, rs2236405, rs2297086 and rs41313327, mRNA and tissue expression in basal cell carcinoma patients from Western Mexico.
Title: PTCH1 gene variants rs357564, rs2236405, rs2297086 and rs41313327, mRNA and tissue expression in basal cell carcinoma patients from Western Mexico.
Mutations of PTCH1 gene in two pedigrees with bifid rib-basal cell nevus-jaw cyst syndrome.
Title: Mutations of PTCH1 gene in two pedigrees with bifid rib-basal cell nevus-jaw cyst syndrome.
Rs28446116 in PTCH1 is associated with non-syndromic cleft lip with or without palate in the Ningxia population, China.
Title: Rs28446116 in PTCH1 is associated with non-syndromic cleft lip with or without palate in the Ningxia population, China.
New insight into the role of PTCH1 protein in serous ovarian carcinomas.
Title: New insight into the role of PTCH1 protein in serous ovarian carcinomas.
Orthokeratinized odontogenic cysts: A clinicopathologic study of 159 cases and molecular evidence for the absence of PTCH1 mutations.
Title: Orthokeratinized odontogenic cysts: A clinicopathologic study of 159 cases and molecular evidence for the absence of PTCH1 mutations.
Impaired Wnt/beta-catenin and protein patched homolog 1 signaling in extraocular sebaceous carcinoma: A clinical and histopathological study.
Title: Impaired Wnt/beta-catenin and protein patched homolog 1 signaling in extraocular sebaceous carcinoma: A clinical and histopathological study.
Novel PTCH1 and concurrent TP53 mutations in four patients with numerous non-syndromic basal cell carcinomas: The paradigm of oncogenic synergy.
Title: Novel PTCH1 and concurrent TP53 mutations in four patients with numerous non-syndromic basal cell carcinomas: The paradigm of oncogenic synergy.
Differential promoter usages of PTCH1 and down regulation of HHIP are associated with HNSCC progression.
Title: Differential promoter usages of PTCH1 and down regulation of HHIP are associated with HNSCC progression.
Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers.
Title: Inherited rare and common variants in PTCH1 and PTCH2 contributing to the predisposition to reproductive cancers.

Submit: New GeneRIF Correction See all GeneRIFs (241)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Basal cell carcinoma, susceptibility to, 1 MedGen: C2751544 OMIM: 605462 GeneReviews: Not available	Compare labs
Basal cell nevus syndrome 1 MedGen: CN376810 OMIM: 109400 GeneReviews: Nevoid Basal Cell Carcinoma Syndrome	not available
Holoprosencephaly 7 MedGen: C1835820 OMIM: 610828 GeneReviews: Holoprosencephaly Overview	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-07-01) ClinGen Genome Curation PagePubMed Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-07-01) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

hmPTCH1 (e-PCR)
- UniSTS:525569

SHGC-8725 (e-PCR)
- UniSTS:34581

D9S1816 (e-PCR)
- UniSTS:67624

MARC_17597-17598:1030546407:1 (e-PCR)
- UniSTS:268350

G67937 (e-PCR)
- UniSTS:225601

G67931 (e-PCR)
- UniSTS:225602

G67934 (e-PCR)
- UniSTS:225603

G67936 (e-PCR)
- UniSTS:225604

G67932 (e-PCR)
- UniSTS:225605

G67933 (e-PCR)
- UniSTS:225606

G67935 (e-PCR)
- UniSTS:225607

PTCH_1064 (e-PCR)
- UniSTS:277620

RH92918 (e-PCR)
- UniSTS:89474

csnpptch-pcr11-1 (e-PCR)
- UniSTS:243109

csnpptch-pcr22-1 (e-PCR)
- UniSTS:243110

SHGC-156297 (e-PCR)
- UniSTS:185010

Ptch1 (e-PCR), detects polymorphism
- UniSTS:516585

SHGC-83001 (e-PCR)
- UniSTS:101878

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cholesterol binding	IDA Inferred from Direct Assay more info	PubMed
enables cyclin binding	IPI Inferred from Physical Interaction more info	PubMed
enables hedgehog family protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables hedgehog family protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables hedgehog receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IEA Inferred from Electronic Annotation more info
enables patched binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables smoothened binding	IBA Inferred from Biological aspect of Ancestor more info
enables smoothened binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in branching involved in ureteric bud morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation involved in kidney development	IEA Inferred from Electronic Annotation more info
involved_in cell fate determination	IEA Inferred from Electronic Annotation more info
involved_in cell proliferation involved in metanephros development	IEA Inferred from Electronic Annotation more info
involved_in cellular response to cholesterol	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to cholesterol	ISS Inferred from Sequence or Structural Similarity more info
involved_in commissural neuron axon guidance	IEA Inferred from Electronic Annotation more info
involved_in dorsal/ventral neural tube patterning	IEA Inferred from Electronic Annotation more info
involved_in dorsal/ventral pattern formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic limb morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic organ development	IEA Inferred from Electronic Annotation more info
involved_in epidermal cell fate specification	IEA Inferred from Electronic Annotation more info
involved_in glucose homeostasis	IEA Inferred from Electronic Annotation more info
involved_in heart morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in limb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in liver regeneration	IEA Inferred from Electronic Annotation more info
involved_in mammary gland duct morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in mammary gland epithelial cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in metanephric collecting duct development	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell division	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of keratinocyte proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of multicellular organism growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of smoothened signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of smoothened signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of smoothened signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of stem cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neural plate axis specification	ISS Inferred from Sequence or Structural Similarity more info
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
involved_in neural tube patterning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pharyngeal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cholesterol efflux	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of epidermal cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in prostate gland development	IEA Inferred from Electronic Annotation more info
involved_in protein localization to plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in protein processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein localization	IEA Inferred from Electronic Annotation more info
involved_in regulation of smoothened signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to chlorate	IEA Inferred from Electronic Annotation more info
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to mechanical stimulus	IEA Inferred from Electronic Annotation more info
involved_in response to retinoic acid	IEA Inferred from Electronic Annotation more info
involved_in response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in smooth muscle tissue development	IEP Inferred from Expression Pattern more info	PubMed
involved_in smoothened signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in somite development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatid development	IEA Inferred from Electronic Annotation more info
involved_in spinal cord motor neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in stem cell proliferation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
colocalizes_with Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in apical part of cell	IDA Inferred from Direct Assay more info	PubMed
located_in axonal growth cone	IEA Inferred from Electronic Annotation more info
located_in caveola	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary membrane	TAS Traceable Author Statement more info
located_in dendritic growth cone	IEA Inferred from Electronic Annotation more info
located_in endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info	PubMed
located_in midbody	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protein patched homolog 1

NCBI Reference Sequences (RefSeq)

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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

NG_007664.1 RefSeqGene

Range

5001..78984

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_515

mRNA and Protein(s)

NM_000264.5 → NP_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

A3KBI9, E9PEJ8, Q13463, Q13635, Q5R1U7, Q5R1U9, Q5R1V0, Q5VZC0, Q5VZC2, Q86XG7

Related

ENSP00000332353.6, ENST00000331920.11

Conserved Domains (2) summary

PHA03377
Location:1253 → 1369

PHA03377; EBNA-3C; Provisional

TIGR00918
Location:43 → 1206

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family
NM_001083602.3 → NP_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

ENSP00000518556.1, ENST00000711046.1

Conserved Domains (3) summary

TIGR00918
Location:2 → 1140

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

pfam07698
Location:949 → 1095

7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase

pfam12349
Location:396 → 550

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
NM_001083603.3 → NP_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

ENSP00000389744.2, ENST00000437951.6

Conserved Domains (3) summary

TIGR00918
Location:65 → 1205

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

pfam07698
Location:1014 → 1160

7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase

pfam12349
Location:461 → 615

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
NM_001083604.3 → NP_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

Conserved Domains (3) summary

TIGR00918
Location:1 → 1055

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

pfam07698
Location:864 → 1010

7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase

pfam12349
Location:311 → 465

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
NM_001083605.3 → NP_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

Related

ENSP00000510238.1, ENST00000692981.1

Conserved Domains (3) summary

TIGR00918
Location:1 → 1055

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

pfam07698
Location:864 → 1010

7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase

pfam12349
Location:311 → 465

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
NM_001083606.3 → NP_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:1 → 1055

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

pfam07698
Location:864 → 1010

7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase

pfam12349
Location:311 → 465

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
NM_001083607.3 → NP_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

Conserved Domains (3) summary

TIGR00918
Location:1 → 1055

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

pfam07698
Location:864 → 1010

7TM-7TMR_HD; 7TM receptor with intracellular HD hydrolase

pfam12349
Location:311 → 465

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation
NM_001354918.2 → NP_001341847.1 protein patched homolog 1 isoform 8

Status: REVIEWED

Source sequence(s)

AL161729

UniProtKB/TrEMBL

A0A1W5YLI7

Conserved Domains (2) summary

TIGR00918
Location:43 → 1154

2A060602; The Eukaryotic (Putative) Sterol Transporter (EST) Family

cl27975
Location:1201 → 1317

EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)
NM_001354919.2 → NP_001341848.1 protein patched homolog 1 isoform 9

Status: REVIEWED

Source sequence(s)

AL161729, BC043542

Consensus CDS

CCDS87661.1

UniProtKB/TrEMBL

A0A0C4DGJ5

Related

ENSP00000449745.1, ENST00000468211.6

Conserved Domains (1) summary

cl25655
Location:2 → 183

Patched; Patched family