Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	5097
Gene name	Protocadherin 1
Gene symbol	PCDH1
Synonyms (NCBI Gene)	PC42PCDH42
Chromosome	5
Chromosome location	5q31.3
Summary	This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The prot

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miRTarBase ID	miRNA	Experiments	Reference
MIRT535463	hsa-miR-495-3p	PAR-CLIP	22012620
MIRT535462	hsa-miR-5688	PAR-CLIP	22012620
MIRT738875	hsa-miR-3199	HITS-CLIP	33718276
MIRT738877	hsa-miR-4697-5p	HITS-CLIP	33718276
MIRT535463	hsa-miR-495-3p	PAR-CLIP	22012620
MIRT535462	hsa-miR-5688	PAR-CLIP	22012620
MIRT1216732	hsa-miR-124	CLIP-seq
MIRT1216733	hsa-miR-146a	CLIP-seq
MIRT1216734	hsa-miR-146b-5p	CLIP-seq
MIRT1216735	hsa-miR-155	CLIP-seq
MIRT1216736	hsa-miR-18a	CLIP-seq
MIRT1216737	hsa-miR-18b	CLIP-seq
MIRT1216738	hsa-miR-3121-3p	CLIP-seq
MIRT1216739	hsa-miR-3123	CLIP-seq
MIRT1216740	hsa-miR-329	CLIP-seq
MIRT1216741	hsa-miR-331-3p	CLIP-seq
MIRT1216742	hsa-miR-362-3p	CLIP-seq
MIRT1216743	hsa-miR-3925-5p	CLIP-seq
MIRT1216744	hsa-miR-3941	CLIP-seq
MIRT1216745	hsa-miR-3976	CLIP-seq
MIRT1216746	hsa-miR-4253	CLIP-seq
MIRT1216747	hsa-miR-4290	CLIP-seq
MIRT1216748	hsa-miR-4685-5p	CLIP-seq
MIRT1216749	hsa-miR-4735-3p	CLIP-seq
MIRT1216750	hsa-miR-4747-5p	CLIP-seq
MIRT1216751	hsa-miR-4761-3p	CLIP-seq
MIRT1216752	hsa-miR-506	CLIP-seq
MIRT1216753	hsa-miR-569	CLIP-seq
MIRT1216754	hsa-miR-603	CLIP-seq
MIRT1216755	hsa-miR-1207-5p	CLIP-seq
MIRT1216756	hsa-miR-1275	CLIP-seq
MIRT1216757	hsa-miR-214	CLIP-seq
MIRT1216758	hsa-miR-3619-5p	CLIP-seq
MIRT1216759	hsa-miR-3940-5p	CLIP-seq
MIRT738876	hsa-miR-4488	CLIP-seq
MIRT1216760	hsa-miR-4507	CLIP-seq
MIRT1216761	hsa-miR-4530	CLIP-seq
MIRT1216762	hsa-miR-4665-5p	CLIP-seq
MIRT1216763	hsa-miR-4763-3p	CLIP-seq
MIRT1216764	hsa-miR-634	CLIP-seq
MIRT1216765	hsa-miR-761	CLIP-seq
MIRT738874	hsa-miR-3186-5p	CLIP-seq
MIRT738876	hsa-miR-4488	CLIP-seq
MIRT1216743	hsa-miR-3925-5p	CLIP-seq
MIRT2291000	hsa-miR-217	CLIP-seq
MIRT2291001	hsa-miR-4514	CLIP-seq
MIRT2291002	hsa-miR-4640-5p	CLIP-seq
MIRT2291003	hsa-miR-4692	CLIP-seq
MIRT2291004	hsa-miR-4726-5p	CLIP-seq
MIRT2291005	hsa-miR-4736	CLIP-seq
MIRT2291006	hsa-miR-598	CLIP-seq
MIRT738876	hsa-miR-4488	CLIP-seq
MIRT2588628	hsa-miR-2355-5p	CLIP-seq
MIRT2588629	hsa-miR-3157-5p	CLIP-seq
MIRT2588630	hsa-miR-4283	CLIP-seq
MIRT2588631	hsa-miR-4690-3p	CLIP-seq
MIRT2588628	hsa-miR-2355-5p	CLIP-seq
MIRT2588629	hsa-miR-3157-5p	CLIP-seq
MIRT2588630	hsa-miR-4283	CLIP-seq
MIRT2588631	hsa-miR-4690-3p	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0005509	Function	Calcium ion binding	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IDA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	8508762
GO:0005911	Component	Cell-cell junction	TAS	8508762
GO:0007155	Process	Cell adhesion	IBA
GO:0007155	Process	Cell adhesion	IEA
GO:0007156	Process	Homophilic cell adhesion via plasma membrane adhesion molecules	IEA
GO:0007267	Process	Cell-cell signaling	TAS	8508762
GO:0007399	Process	Nervous system development	TAS	8508762
GO:0016020	Component	Membrane	IEA
GO:0030054	Component	Cell junction	IDA
GO:0050839	Function	Cell adhesion molecule binding	IBA
GO:0070161	Component	Anchoring junction	IEA

MIM	HGNC	e!Ensembl
603626	8655	ENSG00000156453

Q08174

Protein name

Protocadherin-1 (Cadherin-like protein 1) (Protocadherin-42) (PC42)

Protein function

May be involved in cell-cell interaction processes and in cell adhesion.

PDB

6BX7 , 6MGA , 6PIM , 6VFP

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00028	Cadherin	511 → 603	Cadherin domain	Domain
PF00028	Cadherin	285 → 378	Cadherin domain	Domain
PF00028	Cadherin	617 → 706	Cadherin domain	Domain
PF00028	Cadherin	727 → 813	Cadherin domain	Domain
PF00028	Cadherin	173 → 271	Cadherin domain	Domain
PF00028	Cadherin	401 → 497	Cadherin domain	Domain
PF08266	Cadherin_2	59 → 142	Cadherin-like	Domain
PF08374	Protocadherin	815 → 1029	Protocadherin	Family

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in the brain and neuro-glial cells.

Sequence

MDSGAGGRRCPEAALLILGPPRMEHLRHSPGPGGQRLLLPSMLLALLLLLAPSPGHATRV
VYKVPEEQPPNTLIGSLAADYGFPDVGHLYKLEVGAPYLRVDGKTGDIFTTETSIDREGL
RECQNQLPGDPCILEFEVSITDLVQNGSPRLLEGQIEVQDINDNTPNFASPVITLAIPEN
TNIGSLFPIPLASDRDAGPNGVASYELQAGPEAQELFGLQVAEDQEEKQPQLIVMGNLDR
ERWDSYDLTIKVQDGGSPPRASSALLRVTVLDTNDNAPKFERPSYEAELSENSPIGHSVI
QVKANDSDQGANAEIEYTFHQAPEVVRRLLRLDRNTGLITVQGPVDREDLSTLRFSVLAK
DRGTNPKSARAQVVVTVKDMNDNAPTIEIRGIGLVTHQDGMANISEDVAEETAVALVQVS
DRDEGENAAVTCVVAGDVPFQLRQASETGSDSKKKYFLQTTTPLDYEKVKDYTIEIVAVD
SGNPPLSSTNSLKVQVVDVNDNAPVFTQSVTEVAFPENNKPGEVIAEITASDADSGSNAE
LVYSLEPEPAAKGLFTISPETGEIQVKTSLDREQRESYELKVVAADRGSPSLQGTATVLV
NVLDCNDNDPKFMLSGYNFSVMENMPALSPVGMVTVIDGDKGENAQVQLSVEQDNGDFVI
QNGTGTILSSLSFDREQQSTYTFQLKAVDGGVPPRSAYVGVTINVLDENDNAPYITAPSN
TSHKLLTPQTRLGETVSQVAAEDFDSGVNAELIYSIAGGNPYGLFQIGSHSGAITLEKEI
ERRHHGLHRLVVKVSDRGKPPRYGTALVHLYVNETLANRTLLETLLGHSLDTPLDIDIAG
DPEYERSKQRGNILFGVVAGVVAVALLIALAVLVRYCRQREAKSGYQAGKKETKDLYAPK
PSGKASKGNKSKGKKSKSPKPVKPVEDEDEAGLQKSLKFNLMSDAPGDSPRIHLPLNYPP
GSPDLGRHYRSNSPLPSIQLQPQSPSASKKHQVVQDLPPANTFVGTGDTTSTGSEQYSDY
SYRTNPPKYPSKQVGQPFQLSTPQPLPHPYHGAIWTEVWE

Sequence length

1060

Interactions

View interactions

KEGG Pathway
Virion - Lassa virus and SFTS virus

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Esophageal atresia/tracheoesophageal fistula	Likely pathogenic	rs1753000062	RCV001172297	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal. Show/Hide Unknown Diseases (13)
COLOR VISION DISORDER	—	GWAS catalog	37359372	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Conflicting classifications of pathogenicity	ClinVar	—	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	40465716	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	30804565, 34343768, 35835914	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	28604730	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity	ClinVar GWAS catalog	28604730	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
LUNG CARCINOMA	—	GWAS catalog	28604730	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	23377640	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	39349817	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR HYPOTENSION	—	GWAS catalog	39024449	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSYCHIATRIC DISORDER	—	GWAS catalog	38469033	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL CARCINOMA	—	GWAS catalog	28604730	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	39349817	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (16)
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	27846146		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	BEFREE	21929597, 23050600, 23988763, 26209277, 26227965, 27701444, 30464266, 30510870		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	23988763, 26209277, 27701444	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Bronchial Hyperreactivity	Bronchial Hyperreactivity	BEFREE	19729670, 23988763, 26227965, 30510870		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	35864095	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Childhood asthma	Asthma	BEFREE	23050600, 30510870		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic sinusitis	Sinusitis	BEFREE	26227965		★★★★★ ★☆☆☆☆ Found in Text Mining only
Craniosynostosis	Craniosynostosis	BEFREE	26227965		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dermatitis Atopic	Atopic dermatitis	Pubtator	23988763	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dermatitis, Atopic	Dermatitis	BEFREE	23988763		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyslexia	Dyslexia	Pubtator	29409727	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Eczema	Eczema	BEFREE	21929597, 23988763, 30510870		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic metastasis	Pubtator	35864095	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	9182820	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	37957639	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	34326372	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

PCDH1 (protocadherin 1)

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