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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PCDH12 Gene

protein-coding GIFtS: 49
GCID: GC05M141305

protocadherin 12

Explore 4 diseases affiliated with
PCDH12 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Protocadherin 12¹ ²		VECAD2² ⁵
VE-Cadherin-2¹		Protocadherin-12¹
Vascular Cadherin-2² ³		Vascular Endothelial Cadherin 2²
Vascular Endothelial Cadherin-2² ³		VE-Cadherin 2²
VE-Cad-2¹

External Ids:	HGNC: 8657¹	Entrez Gene: 51294²	Ensembl: ENSG00000113555⁷	OMIM: 605622⁵	UniProtKB: Q9NPG4³

Export aliases for PCDH12 gene to outside databases

Previous GC identifers: GC05M141146 GC05M141907 GC05M141307 GC05M141353 GC05M136467

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PCDH12:

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 the classical cadherins. The gene localizes to the region on chromosome 5 where the

protocadherin gene clusters reside. The exon organization of this transcript is similar to that of the gene cluster

transcripts, notably the first large exon, but no significant sequence homology exists. The function of this cellular

adhesion protein is undetermined but mouse protocadherin 12 does not bind catenins and appears to have no affect on

cell migration or growth. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PCD12_HUMAN, Q9NPG4

Function: Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial

junctions. Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions.

Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity)

Gene Wiki entry for PCDH12

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000005.9 NC_018916.1 NT_029289.11

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PCDH12 gene promoter:
RelA Tal-1beta NF-kappaB Evi-1 FOXL1 AREB6 HFH-1 Zic1 NF-kappaB1 ITF-2
Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PCDH12 promoter sequence

Search SABiosciences Chromatin IP Primers for PCDH12

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDH12

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31.3

PCDH12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDH12 gene location

GeneLoc information about chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05M141305: view genomic region (about GC identifiers)

Start:	141,323,150 bp from pter	End:	141,349,304 bp from pter
Size:	26,155 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PCD12_HUMAN, Q9NPG4 (See protein sequence)

Recommended Name: Protocadherin-12 precursor

Size: 1184 amino acids; 128995 Da

Subcellular location: Cell membrane; Single-pass type I membrane protein. Cell junction

Secondary accessions: Q6UXB6 Q96KB8 Q9H7Y6 Q9H8E0

Explore the universe of human proteins at neXtProt for PCDH12: NX_Q9NPG4

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9NPG4

PCDH12 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_057664.1

ENSEMBL proteins:

ENSP00000231484 ENSP00000429094

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	Uscn Proteins for PCDH12

Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	TAS	10380929
GO:0005887	integral to plasma membrane	TAS	10716726
GO:0005911	cell-cell junction	IEA	--

PCDH12 for ontologies About GeneDecksing

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	Uscn ELISAs and CLIAs for PCDH12

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

PCDH12 for domains About GeneDecksing

4 InterPro domains/families:

IPR015919 Cadherin-like

IPR013164 Cadherin_N

IPR020894 Cadherin_CS

IPR002126 Cadherin

Graphical View of Domain Structure for InterPro Entry Q9NPG4

ProtoNet protein and cluster: Q9NPG4

1 Blocks protein family: IPB002126 Cadherin

UniProtKB/Swiss-Prot: PCD12_HUMAN, Q9NPG4

Similarity: Contains 6 cadherin domains

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: PCD12_HUMAN, Q9NPG4

Function: Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial

junctions. Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions.

Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity)

miRNA Products:		OriGene 3'-UTR Clone: PCDH12 Browse MicroRNA Expression Plasmids
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In Situ Assay
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Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005509	calcium ion binding	IEA	--

PCDH12 for ontologies           About GeneDecksing

Animal Models:
     Mouse knock-out Pcdh12^tm1Hub for PCDH12
     1 MGI mutant phenotype (inferred from 1 allele) (MGI details for Pcdh12):

normal

PCDH12 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PCDH12

1 Interacting protein for PCDH12 (Q9NPG4³) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
PRKCE	Q02156³	I2D: score=1

About this table

Gene Ontology (GO): 5 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005977	glycogen metabolic process	IEA	--
GO:0007156	homophilic cell adhesion	IEA	--
GO:0008038	neuron recognition	TAS	10380929
GO:0016339	calcium-dependent cell-cell adhesion	IEA	--
GO:0060711	labyrinthine layer development	IEA	--

PCDH12 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for PCDH12

1 HMDB Compound for PCDH12 About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

Search CenterWatch for drugs/clinical trials and news about PCDH12 / PCD12

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for PCDH12 gene:

NM_016580.2

Unigene Cluster for PCDH12:

Protocadherin 12

Hs.439474 [show with all ESTs]

Unigene Representative Sequence: NM_016580

3 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000231484(uc003llx.3) ENST00000510041 ENST00000512221

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Additional cDNA sequence:

AB026893.1 AF231025.1 AF240635.1 AK023785.1 AK024140.1 AK027282.1 AK226049.1 AK315029.1

AY358428.1 BC042634.1 BC052973.1

3 DOTS entries:

DT.95365720 DT.86849860 DT.95146654

24/48 AceView cDNA sequences (see all 48):

AF231025 AB026893 AF240635 AY358428 AI682162 CA444262 NM_016580 BX479492

BC042634 AK024140 BM973938 BP344766 BC052973 F35830 BX100182 AU140154

AK023785 BU626399 BE328204 AI652388 AU121079 BI769534 BU687515 AU140396

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for PCDH12 About this scheme

ExUns:	1a	·	1b	^	2a	·	2b	^	3	^	4	^	5
SP1:
SP2:

ECgene alternative splicing isoforms for PCDH12

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

PCDH12 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image

PCDH12 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 5 LifeMap Cells

Name

Category

Endothelial progenitor cells (Adult Stem / Progenitor Cell)

Endothelium

PureStem™ endothelial progenitor 30-MV2-12 (Embryonic Progenitor Cell)

Blood, Endothelium

PureStem™ endothelial Progenitor 30-SM2-3 (Embryonic Progenitor Cell)

Blood, Endothelium

PureStem™ endothelial progenitor 30-SM2-1 (Embryonic Progenitor Cell)

Endothelium

PureStem™ endothelial progenitor RP1-MV2-18 (Embryonic Progenitor Cell)

Endothelium

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See PCDH12 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDH12

SOURCE GeneReport for Unigene cluster: Hs.439474

UniProtKB/Swiss-Prot: PCD12_HUMAN, Q9NPG4

Tissue specificity: Expressed in highly vascularized tissues including the heart and placenta, but most tissues contain

a low level of expression. Prominent expression in the spleen

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for PCDH12 gene from 4/12 species (see all 12) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Pcdh12^{1 , 5}	protocadherin 12^{1, 5}	82.69(n)¹ 81.57(a)¹		18 (20.17 cM)⁵ 53601¹ NM_017378.2¹ NP_059074.2¹ 38267092⁵
chicken (Gallus gallus)	Aves	PCDH12¹	protocadherin 12	61.79(n) 56.72(a)		416191 XM_414518.3 XP_414518.3
zebrafish (Danio rerio)	Actinopterygii	pcdh12¹	protocadherin 12	53.42(n) 46.58(a)		555419 XM_677918.4 XP_683010.4
worm (Caenorhabditis elegans)	Secernentea	cdh-10⁶	CaDHerin family member (cdh-10)	7(a)	1 → many	IV(2436514-2463368)

ENSEMBL Gene Tree for PCDH12 (if available)
TreeFam Gene Tree for PCDH12 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for PCDH12 gene

PCDH17² PCDH7² PCDH11X² PCDH20² PCDH1² PCDH10² PCDH11Y² PCDH18²

PCDH9² PCDH8² PCDH19²

18/60 SIMAP similar genes for PCDH12 using alignment to 4 protein entries: PCD12_HUMAN (see all proteins) (see all similar genes):

PCDH19 PCDHB17 PCDHB8 PCDH17 PCDHB10 PCDHB11

PCDHB13 PCDHB15 PCDHB9 PCDHGA1 PCDHGA11 PCDHGA12

PCDHGA2 PCDHGA8 PCDHGB2 PCDHGB4 PCDHGB7 PCDH10

PCDH12 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 5 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs183147327^1,2		--	141324186(+)	`TATCCA/GTGTCT`	1	--	ds500¹		0	--	--	--	--
rs111833932^1,2	F,	--	141324211(+)	`ATAATA/GCCTCC`	1	--	ds500¹		3		CSA WA	122
rs187828186^1,2		--	141324289(+)	`CTTTAC/TAAATA`	1	--	ds500¹		0	--	--	--	--
rs138521835^1,2		--	141324296(+)	`AATAGC/TTGTGC`	1	--	ds500¹		0	--	--	--	--
rs191135580^1,2		--	141324372(+)	`GGTAAA/GAGCAC`	1	--	ds500¹		0	--	--	--	--
rs141496818^1,2		--	141324447(+)	`TGTGAC/TGGTCT`	1	--	ds500¹		0	--	--	--	--
rs114438566^1,2	F,	--	141324516(+)	`ACAGGT/AGCAAA`	1	--	ds500¹		1		WA	118
rs153148^1,2	C,F,O,A,H,	--	141324623(+)	`GGCCAT/CCCTTT`	1	--	ut3¹		28		MN NA NS EA WA CSA	2646
rs150724917^1,2		--	141324646(+)	`ACTCCA/GTGGCA`	1	--	ut3¹		0	--	--	--	--
rs139068319^1,2		--	141324650(+)	`CGTGGC/TATCTG`	1	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for PCDH12 (141323150 - 141349304 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for PCDH12: --

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDH12

DNA2.0 Custom Variant and Variant Library Synthesis for PCDH12

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

PCDH12 for disorders           About GeneDecksing

OMIM gene information: 605622    OMIM disorders: --

4 diseases for PCDH12:    About MalaCards

pre-eclampsia eclampsia schizophrenia neuronitis

Human Genome Epidemiology (HuGE) Navigator: PCDH12 (2 documents)

Export disorders for PCDH12 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for PCDH12 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with PCDH12)

Utopia: connect your pdf to the dynamic
world of online information

Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)^{1, 2, 3, 9} Wu Q. and Maniatis T. (2000)
cDNA cloning, chromosomal mapping, and expression analysis of human VE-cadherin-2. (PubMed id 11063261)^{1, 2, 9} Ludwig D....Pytowski B. (2000)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{1, 2} Ota T.... Sugano S. (2004)
The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)^{1, 2} Clark H.F.... Gray A.M. (2003)
A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)^{1, 3} Wu Q. and Maniatis T. (1999)
Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PubMed id 19054571)^{1, 9} GregA^rio S.P....Dias-Neto E. (2009)
Protocadherin-12 cleavage is a regulated process medi ated by ADAM10 protein: evidence of shedding up-regulation in pre-eclampsia. (PubMed id 21402705)¹ Bouillot S....Huber P. (2011)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)¹ Nollet F....van Roy F. (2000)
Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)¹ Yagi T. and Takeichi M. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

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Query String		PubMed OMIM NCBI Bookshelf
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 51294	HGNC: 8657	AceView: PCDH12	Ensembl:ENSG00000113555	euGenes: HUgn51294
ECgene: PCDH12	H-InvDB: PCDH12

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for PCDH12	Pharmacogenomics, SNPs, Pathways

Intellectual Property for PCDH12 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for PCDH12 gene:
Search GeneIP for patents involving PCDH12

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
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protocadherin 12

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