PCDH9 (protocadherin 9)

Gene

• Entrez ID: 5101
• Gene name: Protocadherin 9
• Gene symbol: PCDH9
• Synonyms (NCBI Gene): -
• Chromosome: 13
• Chromosome location: 13q21.32
• Summary: This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT020565	hsa-miR-155-5p	Reporter assay;Other	20584899
MIRT053695	hsa-miR-188-5p	Microarray	22942087
MIRT449552	hsa-miR-548m	PAR-CLIP	22100165
MIRT449551	hsa-miR-548ag	PAR-CLIP	22100165
MIRT449550	hsa-miR-548ai	PAR-CLIP	22100165
MIRT449549	hsa-miR-548ba	PAR-CLIP	22100165
MIRT449548	hsa-miR-570-5p	PAR-CLIP	22100165
MIRT449547	hsa-miR-18a-5p	PAR-CLIP	22100165
MIRT449546	hsa-miR-18b-5p	PAR-CLIP	22100165
MIRT449544	hsa-miR-4735-3p	PAR-CLIP	22100165
MIRT449545	hsa-miR-1264	PAR-CLIP	22100165
MIRT449542	hsa-miR-4635	PAR-CLIP	22100165
MIRT449543	hsa-miR-7843-3p	PAR-CLIP	22100165
MIRT449541	hsa-miR-127-5p	PAR-CLIP	22100165
MIRT734654	hsa-miR-1260b	Western blotting, Microarray, qRT-PCR	32523124
MIRT449552	hsa-miR-548m	PAR-CLIP	22100165
MIRT449551	hsa-miR-548ag	PAR-CLIP	22100165
MIRT449550	hsa-miR-548ai	PAR-CLIP	22100165
MIRT449549	hsa-miR-548ba	PAR-CLIP	22100165
MIRT449548	hsa-miR-570-5p	PAR-CLIP	22100165
MIRT449547	hsa-miR-18a-5p	PAR-CLIP	22100165
MIRT449546	hsa-miR-18b-5p	PAR-CLIP	22100165
MIRT449544	hsa-miR-4735-3p	PAR-CLIP	22100165
MIRT449545	hsa-miR-1264	PAR-CLIP	22100165
MIRT449542	hsa-miR-4635	PAR-CLIP	22100165
MIRT449543	hsa-miR-7843-3p	PAR-CLIP	22100165
MIRT449541	hsa-miR-127-5p	PAR-CLIP	22100165
MIRT1216917	hsa-miR-1303	CLIP-seq
MIRT1216918	hsa-miR-204	CLIP-seq
MIRT1216919	hsa-miR-211	CLIP-seq
MIRT1216920	hsa-miR-3065-5p	CLIP-seq
MIRT1216921	hsa-miR-583	CLIP-seq
MIRT1216922	hsa-miR-1305	CLIP-seq
MIRT1216923	hsa-miR-141	CLIP-seq
MIRT1216924	hsa-miR-200a	CLIP-seq
MIRT1216920	hsa-miR-3065-5p	CLIP-seq
MIRT1216925	hsa-miR-382	CLIP-seq
MIRT1216926	hsa-miR-421	CLIP-seq
MIRT1216927	hsa-miR-4522	CLIP-seq
MIRT1216928	hsa-miR-4727-5p	CLIP-seq
MIRT1216929	hsa-miR-4769-3p	CLIP-seq
MIRT2062608	hsa-miR-124	CLIP-seq
MIRT1216920	hsa-miR-3065-5p	CLIP-seq
MIRT2062609	hsa-miR-3146	CLIP-seq
MIRT2062610	hsa-miR-330-3p	CLIP-seq
MIRT2062611	hsa-miR-4470	CLIP-seq
MIRT2062612	hsa-miR-4493	CLIP-seq
MIRT2062613	hsa-miR-506	CLIP-seq
MIRT2062614	hsa-miR-802	CLIP-seq
MIRT2291032	hsa-miR-103b	CLIP-seq
MIRT2291033	hsa-miR-1206	CLIP-seq
MIRT2291034	hsa-miR-1256	CLIP-seq
MIRT2291035	hsa-miR-320a	CLIP-seq
MIRT2291036	hsa-miR-320b	CLIP-seq
MIRT2291037	hsa-miR-320c	CLIP-seq
MIRT2291038	hsa-miR-320d	CLIP-seq
MIRT2291039	hsa-miR-376a	CLIP-seq
MIRT2291040	hsa-miR-376b	CLIP-seq
MIRT2291041	hsa-miR-4274	CLIP-seq
MIRT2291042	hsa-miR-4427	CLIP-seq
MIRT2291043	hsa-miR-4429	CLIP-seq
MIRT2291044	hsa-miR-4645-5p	CLIP-seq
MIRT2291045	hsa-miR-4673	CLIP-seq
MIRT2291046	hsa-miR-4722-3p	CLIP-seq
MIRT2291047	hsa-miR-4755-3p	CLIP-seq
MIRT2291034	hsa-miR-1256	CLIP-seq
MIRT2588720	hsa-miR-1263	CLIP-seq
MIRT2588721	hsa-miR-138	CLIP-seq
MIRT2588722	hsa-miR-338-5p	CLIP-seq
MIRT2291044	hsa-miR-4645-5p	CLIP-seq
MIRT2291045	hsa-miR-4673	CLIP-seq
MIRT2291046	hsa-miR-4722-3p	CLIP-seq
MIRT2588723	hsa-miR-4728-3p	CLIP-seq
MIRT2291047	hsa-miR-4755-3p	CLIP-seq
MIRT2588724	hsa-miR-495	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005509	Function	Calcium ion binding	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
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:0016020	Component	Membrane	IEA
GO:0030426	Component	Growth cone	IEA
GO:0030900	Process	Forebrain development	IEA
GO:0044291	Component	Cell-cell contact zone	IEA
GO:0050839	Function	Cell adhesion molecule binding	IBA
GO:0097060	Component	Synaptic membrane	IEA
GO:0098978	Component	Glutamatergic synapse	IBA
GO:0098978	Component	Glutamatergic synapse	IEA

Other IDs

• MIM: 603581
• HGNC: 8661
• e!Ensembl: ENSG00000184226

Protein

• UniProt ID: Q9HC56
• Protein name: Protocadherin-9
• Protein function: Potential calcium-dependent cell-adhesion protein.
• PDB: 2EE0
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08266	Cadherin_2	25 → 118	Cadherin-like	Domain
  PF00028	Cadherin	147 → 243	Cadherin domain	Domain
  PF00028	Cadherin	257 → 349	Cadherin domain	Domain
  PF00028	Cadherin	370 → 460	Cadherin domain	Domain
  PF00028	Cadherin	474 → 563	Cadherin domain	Domain
  PF00028	Cadherin	577 → 666	Cadherin domain	Domain
  PF00028	Cadherin	687 → 772	Cadherin domain	Domain
  PF08374	Protocadherin	777 → 1000	Protocadherin	Family

• Sequence:

  MDLRDFYLLAALIACLRLDSAIAQELIYTIREELPENVPIGNIPKDLNISHINAATGTSA
  SLVYRLVSKAGDAPLVKVSSSTGEIFTTSNRIDREKLCAGASYAEENECFFELEVVILPN
  DFFRLIKIKIIVKDTNDNAPMFPSPVINISIPENTLINSRFPIPSATDPDTGFNGVQHYE
  LLNGQSVFGLDIVETPEGEKWPQLIVQQNLDREQKDTYVMKIKVEDGGTPQKSSTAILQV
  TVSDVNDNRPVFKEGQVEVHIPENAPVGTSVIQLHATDADIGSNAEIRYIFGAQVAPATK
  RLFALNNTTGLITVQRSLDREETAIHKVTVLASDGSSTPARATVTINVTDVNDNPPNIDL
  RYIISPINGTVYLSEKDPVNTKIALITVSDKDTDVNGKVICFIEREVPFHLKAVYDNQYL
  LETSSLLDYEGTKEFSFKIVASDSGKPSLNQTALVRVKLEDENDNPPIFNQPVIELSVSE
  NNRRGLYLTTISATDEDSGKNADIVYQLGPNASFFDLDRKTGVLTASRVFDREEQERFIF
  TVTARDNGTPPLQSQAAVIVTVLDENDNSPKFTHNHFQFFVSENLPKYSTVGVITVTDAD
  AGENKAVTLSILNDNDNFVLDPYSGVIKSNVSFDREQQSSYTFDVKATDGGQPPRSSTAK
  VTINVMDVNDNSPVVISPPSNTSFKLVPLSAIPGSVVAEVFAVDVDTGMNAELKYTIVSG
  NNKGLFRIDPVTGNITLEEKPAPTDVGLHRLVVNISDLGYPKSLHTLVLVFLYVNDTAGN
  ASYIYDLIRRTMETPLDRNIGDSSQPYQNEDYLTIMIAIIAGAMVVIVVIFVTVLVRCRH
  ASRFKAAQRSKQGAEWMSPNQENKQNKKKKRKKRKSPKSSLLNFVTIEESKPDDAVHEPI
  NGTISLPAELEEQSIGRFDWGPAPPTTFKPNSPDLAKHYKSASPQPAFHLKPDTPVSVKK
  HHVIQELPLDNTFVGGCDTLSKRSSTSSDHFSASECSSQGGFKTKGPLHTRQCNSHSKSD
  NIPVTPQKCPSSTGFHIQENEESHYESQRRVTFHLPDGSQESCSDSGLGDHEPVGSGTLI
  SHPLPLVQPQDEFYDQASPDKRTEADGNSDPNSDGPLGPRGLAEATEMCTQECLVLGHSD
  NCWMPPGLGPYQHPKSPLSTFAPQKEWVKKDKLVNGHTLTRAWKEDSNRNQFNDRKQYGS
  NEGHFNNGSHMTDIPLANLKSYKQAGGATESPKEHQL

• Sequence length: 1237

Pathways

KEGG:

Virion - Lassa virus and SFTS virus

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTISM SPECTRUM DISORDER	—	CTD, GWAS catalog CTD, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DENTAL CARIES	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EXOSTOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PCDH9-related disorder	Uncertain significance; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Auditory neuropathy	Auditory Neuropathy	BEFREE	19353688		★☆☆☆☆ Found in Text Mining only
Auditory Neuropathy Autosomal Dominant 1	Auditory neuropathy	Pubtator	19353688	Associate	★☆☆☆☆ Found in Text Mining only
Auditory neuropathy spectrum disorder	Auditory neuropathy	BEFREE	19353688		★☆☆☆☆ Found in Text Mining only
AUDITORY NEUROPATHY, AUTOSOMAL DOMINANT, 1	Auditory Neuropathy	BEFREE	19353688		★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Autism	Pubtator	18252227, 36150388	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	18252227		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autism Spectrum Disorders	Autism Spectrum Disorder	CTD_human_DG	18252227		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	BEFREE	24204716		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	24204716, 36150388, 39766876	Associate	★☆☆☆☆ Found in Text Mining only
Blast Crisis	Blast crisis	Pubtator	33557955	Associate	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	36936167, 37144994	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	25172662, 28791409	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	25032869, 31632082		★☆☆☆☆ Found in Text Mining only
Cerebral Palsy	Cerebral palsy	Pubtator	33557955	Associate	★☆☆☆☆ Found in Text Mining only
Child Development Disorders, Pervasive	Development Disorder	GWASCAT_DG	30804558		★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	GWASCAT_DG	29631575		★☆☆☆☆ Found in Text Mining only
Dermatitis Atopic	Atopic dermatitis	Pubtator	25935106	Associate	★☆☆☆☆ Found in Text Mining only
Dystonia	Dystonia	Pubtator	33557955	Associate	★☆☆☆☆ Found in Text Mining only
Essential Tremor	Essential tremor	Pubtator	36183486	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	18828157	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	24214103, 28055966		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	28055966	Associate	★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	BEFREE	29477871		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	25172662, 28791409, 30045829		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	GWASCAT_DG	30945673, 30945699		★☆☆☆☆ Found in Text Mining only
Major Depressive Disorder	Mental Depression	GWASCAT_DG	27479909, 29728651, 29942085, 30718901		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Major Depressive Disorder	Mental Depression	BEFREE	28990594		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant Glioma	Glioma	BEFREE	28055966		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	25032869, 31632082		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	28927585		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	25869928		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24214103, 25869928		★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor neuron disease	Pubtator	33557955	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25172662, 25869928, 28927585		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	GWASCAT_DG	21552555		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	GWASDB_DG	21552555		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ovarian neoplasm	Ovarian neoplasm	BEFREE	25032869, 31632082		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	28927585		★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	33557955	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	25869928		★☆☆☆☆ Found in Text Mining only
Unipolar Depression	Mental Depression	BEFREE	28990594		★☆☆☆☆ Found in Text Mining only