CleftGeneDB-Search

Gene: Ptch1

Basic information

Tag	Content
Uniprot ID	Q61115
Entrez ID	19206
Genbank protein ID	AAC98798.1
Genbank nucleotide ID	NM_008957.3; XM_006517159.3;
Ensembl protein ID	ENSMUSP00000021921
Ensembl nucleotide ID	ENSMUSG00000021466
Gene name	Protein patched homolog 1
Gene symbol	Ptch1
Organism	Mus musculus
NCBI taxa ID	10090
Cleft type	CPO,CLP,CLO
Developmental stage	E13.0, E13.5, E14.5
Data sources	Manually collected
Reference	23900075; 24590292; 23897749;
Functional description	Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH). Associates with the smoothened protein (SMO) to transduce the hedgehog's proteins signal. Seems to have a tumor suppressor function, as inactivation of this protein is probably a necessary, if not sufficient step for tumorigenesis.
Sequence	MASAGNAAGA LGRQAGGGRR RRTGGPHRAA PDRDYLHRPS YCDAAFALEQ ISKGKATGRK 60 APLWLRAKFQ RLLFKLGCYI QKNCGKFLVV GLLIFGAFAV GLKAANLETN VEELWVEVGG 120 RVSRELNYTR QKIGEEAMFN PQLMIQTPKE EGANVLTTEA LLQHLDSALQ ASRVHVYMYN 180 RQWKLEHLCY KSGELITETG YMDQIIEYLY PCLIITPLDC FWEGAKLQSG TAYLLGKPPL 240 RWTNFDPLEF LEELKKINYQ VDSWEEMLNK AEVGHGYMDR PCLNPADPDC PATAPNKNST 300 KPLDVALVLN GGCQGLSRKY MHWQEELIVG GTVKNATGKL VSAHALQTMF QLMTPKQMYE 360 HFRGYDYVSH INWNEDRAAA ILEAWQRTYV EVVHQSVAPN STQKVLPFTT TTLDDILKSF 420 SDVSVIRVAS GYLLMLAYAC LTMLRWDCSK SQGAVGLAGV LLVALSVAAG LGLCSLIGIS 480 FNAATTQVLP FLALGVGVDD VFLLAHAFSE TGQNKRIPFE DRTGECLKRT GASVALTSIS 540 NVTAFFMAAL IPIPALRAFS LQAAVVVVFN FAMVLLIFPA ILSMDLYRRE DRRLDIFCCF 600 TSPCVSRVIQ VEPQAYTEPH SNTRYSPPPP YTSHSFAHET HITMQSTVQL RTEYDPHTHV 660 YYTTAEPRSE ISVQPVTVTQ DNLSCQSPES TSSTRDLLSQ FSDSSLHCLE PPCTKWTLSS 720 FAEKHYAPFL LKPKAKVVVI LLFLGLLGVS LYGTTRVRDG LDLTDIVPRE TREYDFIAAQ 780 FKYFSFYNMY IVTQKADYPN IQHLLYDLHK SFSNVKYVML EENKQLPQMW LHYFRDWLQG 840 LQDAFDSDWE TGRIMPNNYK NGSDDGVLAY KLLVQTGSRD KPIDISQLTK QRLVDADGII 900 NPSAFYIYLT AWVSNDPVAY AASQANIRPH RPEWVHDKAD YMPETRLRIP AAEPIEYAQF 960 PFYLNGLRDT SDFVEAIEKV RVICNNYTSL GLSSYPNGYP FLFWEQYISL RHWLLLSISV 1020 VLACTFLVCA VFLLNPWTAG IIVMVLALMT VELFGMMGLI GIKLSAVPVV ILIASVGIGV 1080 EFTVHVALAF LTAIGDKNHR AMLALEHMFA PVLDGAVSTL LGVLMLAGSE FDFIVRYFFA 1140 VLAILTVLGV LNGLVLLPVL LSFFGPCPEV SPANGLNRLP TPSPEPPPSV VRFAVPPGHT 1200 NNGSDSSDSE YSSQTTVSGI SEELRQYEAQ QGAGGPAHQV IVEATENPVF ARSTVVHPDS 1260 RHQPPLTPRQ QPHLDSGSLS PGRQGQQPRR DPPREGLRPP PYRPRRDAFE ISTEGHSGPS 1320 NRDRSGPRGA RSHNPRNPTS TAMGSSVPSY CQPITTVTAS ASVTVAVHPP PGPGRNPRGG 1380 PCPGYESYPE TDHGVFEDPH VPFHVRCERR DSKVEVIELQ DVECEERPWG SSSN 1434

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

Protein structural annotations

3D structure in PDB database

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Cleft type	Developmental stage	Species	Evidence	Details
1:1 ortholog	PTCH1		A0A452EIX7			Capra hircus	Prediction	More>>
1:1 ortholog	PTCH1	5727	Q13635			Homo sapiens	Publication	More>>
1:1 ortholog	Ptch1	19206	Q61115	CPO,CLP,CLO	E13.0, E13.5, E14.5	Mus musculus	Publication	More>>
1:1 ortholog	PTCH1	465254	A0A2J8JHA7			Pan troglodytes	Prediction	More>>
1:1 ortholog	Ptch1	89830	Q6UY90			Rattus norvegicus	Prediction	More>>
1:1 ortholog	ptch1		F8W5M6			Danio rerio	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
PTCH1	rs10512248	HI-SNP	30172247
PTCH1	c.1175C>T; p.Ala392Val (heterozygous)	WES and Sanger sequencing	29908092
PTCH1	rs10512248A>C	GWAS	28232668
PTCH1	c.1111C>T; p.A371* (heterozygous)	Sequencing	30962945

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs254395942	p.Gln131Glu	missense variant	-	NC_000079.6:g.63548147G>C	UniProt
rs51816556	p.Asn814Ser	missense variant	-	NC_000079.6:g.63532614T>C	UniProt
rs265667150	p.His930Pro	missense variant	-	NC_000079.6:g.63525001T>G	UniProt
rs228723531	p.Ala1233Thr	missense variant	-	NC_000079.6:g.63513626C>T	UniProt
rs244883163	p.Pro1264Leu	missense variant	-	NC_000079.6:g.63512047G>A	UniProt
rs46960049	p.Thr1267Asn	missense variant	-	NC_000079.6:g.63512038G>T	UniProt
rs239668604	p.Asp1275Glu	missense variant	-	NC_000079.6:g.63512013G>T	UniProt
rs225556581	p.Pro1292Ser	missense variant	-	NC_000079.6:g.63511964G>A	UniProt
rs49370129	p.Thr1339Met	missense variant	-	NC_000079.6:g.63511822G>A	UniProt

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0005113	patched binding	IDA
GO:0005119	smoothened binding	ISO
GO:0005119	smoothened binding	IBA
GO:0005515	protein binding	IPI
GO:0008158	hedgehog receptor activity	TAS
GO:0008158	hedgehog receptor activity	IBA
GO:0008201	heparin binding	IDA
GO:0008270	zinc ion binding	NAS
GO:0015485	cholesterol binding	ISO
GO:0015485	cholesterol binding	TAS
GO:0030332	cyclin binding	ISO
GO:0030332	cyclin binding	IPI
GO:0044877	protein-containing complex binding	IDA
GO:0097108	hedgehog family protein binding	ISO
GO:0097108	hedgehog family protein binding	IBA

GO:Biological Process

GO ID	GO Term	Evidence
GO:0000122	negative regulation of transcription by RNA polymerase II	ISO
GO:0001658	branching involved in ureteric bud morphogenesis	IMP
GO:0001701	in utero embryonic development	IGI
GO:0001709	cell fate determination	IGI
GO:0001841	neural tube formation	IDA
GO:0001843	neural tube closure	IMP
GO:0003007	heart morphogenesis	IMP
GO:0007165	signal transduction	IDA
GO:0007224	smoothened signaling pathway	IDA
GO:0007224	smoothened signaling pathway	IMP
GO:0007224	smoothened signaling pathway	IGI
GO:0007224	smoothened signaling pathway	IBA
GO:0007346	regulation of mitotic cell cycle	IMP
GO:0007389	pattern specification process	IMP
GO:0007420	brain development	IMP
GO:0008285	negative regulation of cell population proliferation	IMP
GO:0008544	epidermis development	IMP
GO:0009612	response to mechanical stimulus	IEA
GO:0009887	animal organ morphogenesis	IMP
GO:0009953	dorsal/ventral pattern formation	IGI
GO:0009957	epidermal cell fate specification	IGI
GO:0010157	response to chlorate	IDA
GO:0010875	positive regulation of cholesterol efflux	ISO
GO:0016485	protein processing	IMP
GO:0021522	spinal cord motor neuron differentiation	IGI
GO:0021532	neural tube patterning	ISO
GO:0021904	dorsal/ventral neural tube patterning	IMP
GO:0021997	neural plate axis specification	IMP
GO:0030326	embryonic limb morphogenesis	IGI
GO:0030326	embryonic limb morphogenesis	IMP
GO:0030850	prostate gland development	IEA
GO:0030879	mammary gland development	IMP
GO:0032355	response to estradiol	IEA
GO:0032526	response to retinoic acid	IEA
GO:0032880	regulation of protein localization	IDA
GO:0032880	regulation of protein localization	IMP
GO:0035108	limb morphogenesis	ISO
GO:0035137	hindlimb morphogenesis	IMP
GO:0040008	regulation of growth	IMP
GO:0040015	negative regulation of multicellular organism growth	IMP
GO:0042127	regulation of cell population proliferation	IMP
GO:0042493	response to drug	IEA
GO:0042593	glucose homeostasis	IMP
GO:0043433	negative regulation of DNA-binding transcription factor activity	ISO
GO:0043616	keratinocyte proliferation	IMP
GO:0045606	positive regulation of epidermal cell differentiation	IGI
GO:0045668	negative regulation of osteoblast differentiation	ISO
GO:0045879	negative regulation of smoothened signaling pathway	NAS
GO:0045879	negative regulation of smoothened signaling pathway	IGI
GO:0045892	negative regulation of transcription, DNA-templated	IMP
GO:0045893	positive regulation of transcription, DNA-templated	IMP
GO:0048568	embryonic organ development	IGI
GO:0048745	smooth muscle tissue development	IEA
GO:0050680	negative regulation of epithelial cell proliferation	IMP
GO:0051782	negative regulation of cell division	IMP
GO:0060037	pharyngeal system development	ISO
GO:0060603	mammary gland duct morphogenesis	IMP
GO:0060644	mammary gland epithelial cell differentiation	IMP
GO:0060831	smoothened signaling pathway involved in dorsal/ventral neural tube patterning	IMP
GO:0061005	cell differentiation involved in kidney development	IGI
GO:0061053	somite development	ISO
GO:0061053	somite development	IMP
GO:0071397	cellular response to cholesterol	ISO
GO:0071397	cellular response to cholesterol	IEP
GO:0071679	commissural neuron axon guidance	ISO
GO:0072203	cell proliferation involved in metanephros development	IMP
GO:0072205	metanephric collecting duct development	IEA
GO:0072659	protein localization to plasma membrane	ISO
GO:0097421	liver regeneration	IEA

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0005576	extracellular region	TAS
GO:0005634	nucleus	ISO
GO:0005886	plasma membrane	ISO
GO:0005886	plasma membrane	IDA
GO:0005886	plasma membrane	IBA
GO:0005886	plasma membrane	TAS
GO:0005887	integral component of plasma membrane	TAS
GO:0005901	caveola	ISO
GO:0005929	cilium	IDA
GO:0014069	postsynaptic density	ISO
GO:0030496	midbody	IDA
GO:0043231	intracellular membrane-bounded organelle	ISO
GO:0044294	dendritic growth cone	ISO
GO:0044295	axonal growth cone	ISO
GO:0048471	perinuclear region of cytoplasm	ISO
GO:0005794	Golgi apparatus	ISO

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-MMU-162582	Signal Transduction	IEA
R-MMU-5358351	Signaling by Hedgehog	IEA
R-MMU-5610787	Hedgehog 'off' state	IEA
R-MMU-5632681	Ligand-receptor interactions	IEA
R-MMU-5632684	Hedgehog 'on' state	IEA
R-MMU-5635838	Activation of SMO	IEA

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0002	3D-structure
KW-1003	Cell membrane
KW-0325	Glycoprotein
KW-1017	Isopeptide bond
KW-0472	Membrane
KW-0597	Phosphoprotein
KW-0675	Receptor
KW-1185	Reference proteome
KW-0812	Transmembrane
KW-1133	Transmembrane helix
KW-0832	Ubl conjugation

Interpro

InterPro ID	InterPro Term
IPR003392	Ptc/Disp
IPR000731	SSD
IPR004766	TM_rcpt_patched

PROSITE

PROSITE ID	PROSITE Term
PS50156	SSD

Pfam

Pfam ID	Pfam Term
PF02460	Patched
PF12349	Sterol-sensing

Gene: Ptch1

Basic information

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

Protein structural annotations

3D structure in PDB database

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction