Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	51294
Gene name	Protocadherin 12
Gene symbol	PCDH12
Synonyms (NCBI Gene)	DMJDS1VE-cadherin-2VECAD2
Chromosome	5
Chromosome location	5q31.3
Summary	This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 6 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of th

Show/Hide all (8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs370283860	G>A	Pathogenic	Coding sequence variant, stop gained
rs375346212	G>A,T	Pathogenic	Coding sequence variant, synonymous variant, stop gained
rs531630376	C>A	Likely-pathogenic	Coding sequence variant, stop gained
rs776111123	G>-,GG	Pathogenic	Coding sequence variant, frameshift variant
rs1199523766	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1596646165	AG>-	Pathogenic	Coding sequence variant, frameshift variant
rs1596646372	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1596646556	G>A	Pathogenic	Coding sequence variant, stop gained

Show/Hide all (3)

miRTarBase ID	miRNA	Experiments
MIRT1216729	hsa-miR-4432	CLIP-seq
MIRT1216730	hsa-miR-548u	CLIP-seq
MIRT1216731	hsa-miR-558	CLIP-seq

Show/Hide all (18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005509	Function	Calcium ion binding	IEA
GO:0005576	Component	Extracellular region	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	10380929, 10716726
GO:0005911	Component	Cell-cell junction	IEA
GO:0005977	Process	Glycogen metabolic process	IEA
GO:0007155	Process	Cell adhesion	IEA
GO:0007156	Process	Homophilic cell adhesion via plasma membrane adhesion molecules	IEA
GO:0007156	Process	Homophilic cell adhesion via plasma membrane adhesion molecules	IEA
GO:0008038	Process	Neuron recognition	TAS	10380929
GO:0016020	Component	Membrane	IEA
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IBA
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IEA
GO:0050839	Function	Cell adhesion molecule binding	IBA
GO:0060711	Process	Labyrinthine layer development	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0070161	Component	Anchoring junction	IEA

MIM	HGNC	e!Ensembl
605622	8657	ENSG00000113555

Q9NPG4

Protein name

Protocadherin-12 (Vascular cadherin-2) (Vascular endothelial cadherin-2) (VE-cad-2) (VE-cadherin-2) [Cleaved into: Protocadherin-12, secreted form]

Protein function

Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial junctions (By similarity). Acts as a regulator of cell migration, probably via increasing cell-cell adhesion (PubMed:21402705). Promotes hom

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08266	Cadherin_2	31 → 114	Cadherin-like	Domain
PF00028	Cadherin	140 → 235	Cadherin domain	Domain
PF00028	Cadherin	249 → 343	Cadherin domain	Domain
PF00028	Cadherin	360 → 451	Cadherin domain	Domain
PF00028	Cadherin	465 → 556	Cadherin domain	Domain
PF00028	Cadherin	612 → 694	Cadherin domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in highly vascularized tissues including the heart and placenta, but most tissues contain a low level of expression (PubMed:11063261). Prominent expression in the spleen (PubMed:11063261). Present in villous and extravillous

Sequence

MMQLLQLLLGLLGPGGYLFLLGDCQEVTTLTVKYQVSEEVPSGTVIGKLSQELGREERRR
QAGAAFQVLQLPQALPIQVDSEEGLLSTGRRLDREQLCRQWDPCLVSFDVLATGDLALIH
VEIQVLDINDHQPRFPKGEQELEISESASLRTRIPLDRALDPDTGPNTLHTYTLSPSEHF
ALDVIVGPDETKHAELIVVKELDREIHSFFDLVLTAYDNGNPPKSGTSLVKVNVLDSNDN
SPAFAESSLALEIQEDAAPGTLLIKLTATDPDQGPNGEVEFFLSKHMPPEVLDTFSIDAK
TGQVILRRPLDYEKNPAYEVDVQARDLGPNPIPAHCKVLIKVLDVNDNIPSIHVTWASQP
SLVSEALPKDSFIALVMADDLDSGHNGLVHCWLSQELGHFRLKRTNGNTYMLLTNATLDR
EQWPKYTLTLLAQDQGLQPLSAKKQLSIQISDINDNAPVFEKSRYEVSTRENNLPSLHLI
TIKAHDADLGINGKVSYRIQDSPVAHLVAIDSNTGEVTAQRSLNYEEMAGFEFQVIAEDS
GQPMLASSVSVWVSLLDANDNAPEVVQPVLSDGKASLSVLVNASTGHLLVPIETPNGLGP
AGTDTPPLATHSSRPFLLTTIVARDADSGANGEPLYSIRSGNEAHLFILNPHTGQLFVNV
TNASSLIGSEWELEIVVEDQGSPPLQTRALLRVMFVTSVDHLRDSARKPGALSMSMLTVI
CLAVLLGIFGLILALFMSICRTEKKDNRAYNCREAESTYRQQPKRPQKHIQKADIHLVPV
LRGQAGEPCEVGQSHKDVDKEAMMEAGWDPCLQAPFHLTPTLYRTLRNQGNQGAPAESRE
VLQDTVNLLFNHPRQRNASRENLNLPEPQPATGQPRSRPLKVAGSPTGRLAGDQGSEEAP
QRPPASSATLRRQRHLNGKVSPEKESGPRQILRSLVRLSVAAFAERNPVEELTVDSPPVQ
QISQLLSLLHQGQFQPKPNHRGNKYLAKPGGSRSAIPDTDGPSARAGGQTDPEQEEGPLD
PEEDLSVKQLLEEELSSLLDPSTGLALDRLSAPDPAWMARLSLPLTTNYRDNVISPDAAA
TEEPRTFQTFGKAEAPELSPTGTRLASTFVSEMSSLLEMLLEQRSSMPVEAASEALRRLS
VCGRTLSLDLATSAASGMKVQGDPGGKTGTEGKSRGSSSSSRCL

Sequence length

1184

Interactions

View interactions

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal facial shape	Likely pathogenic	rs531630376	RCV000758009
Cerebellar ataxia	Likely pathogenic	rs531630376	RCV000758009
Coats disease	Likely pathogenic	rs531630376	RCV000758009
Diencephalic-mesencephalic junction dysplasia	Pathogenic; Likely pathogenic	rs1175979418, rs148884293, rs1596646372, rs1199523766	RCV001842235 RCV004018303 RCV003312998 RCV003312999
Diencephalic-mesencephalic junction dysplasia syndrome 1	Likely pathogenic; Pathogenic	rs1753211537, rs2126927387, rs1048025807, rs1175979418, rs1389877870, rs764897668, rs2126931148, rs765136839, rs2532556080, rs375346212, rs370283860, rs1596646372, rs776111123	RCV001332140 RCV001376160 RCV001784803 RCV002468643 RCV001843792 RCV005397204 RCV002226903 RCV002468758 RCV003493239 RCV000509062 RCV002470971 RCV000855436 RCV003141929
Disorder of development or morphogenesis	Likely pathogenic	rs148884293	RCV005626877
Dystonic disorder	Likely pathogenic	rs531630376	RCV000758009

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Adrenocortical carcinoma, hereditary	Benign; Likely benign	rs78397925	RCV005903846
Cervical cancer	Benign; Likely benign	rs78397925	RCV005903847
Clear cell carcinoma of kidney	Benign	rs140883612	RCV005911984
Gastric cancer	Benign; Likely benign	rs78397925	RCV005903849
Hepatocellular carcinoma	Benign; Likely benign	rs78397925	RCV005903845
Marshall syndrome	Conflicting classifications of pathogenicity	rs763363704	RCV002471253
Neurodevelopmental disorder	Uncertain significance	rs374457419	RCV002472057
Ovarian cancer	Benign; Likely benign	rs78397925	RCV005903848
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs78397925	RCV005903850
PCDH12-related disorder	Benign; Likely benign	rs138035071, rs2434322, rs114795118, rs138689340, rs5871792, rs149882545, rs542402907, rs150674592, rs114449118, rs78397925, rs375775264, rs142624712, rs61737138, rs10040926	RCV003980641 RCV003980559 RCV003980599 RCV003980575 RCV003916283 RCV003933508 RCV003936497 RCV003901868 RCV003983289 RCV003960656 RCV003935885 RCV003968041 RCV003968157 RCV003912867 RCV003932869
Uterine corpus endometrial carcinoma	Benign	rs140883612	RCV005911985

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Aicardi Goutieres syndrome	Associate	27164683
Blood Coagulation Disorders	Associate	35005846
Blood Platelet Disorders	Associate	35005846
Brain Stem Neoplasms	Associate	30178464
Carcinoma Renal Cell	Associate	31948514
Developmental Disabilities	Associate	27164683
Fahr's disease	Associate	30178464
Heart Diseases	Associate	35005846
Infections	Associate	27164683
Leukoencephalopathies	Associate	30178464
Microcephaly	Associate	27164683, 30178464
Pre Eclampsia	Associate	21402705
Pregnancy in Diabetics	Associate	21402705

PCDH12 (protocadherin 12)