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Protein

Protocadherin-12

Gene

PCDH12

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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 homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions (By similarity). Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity).By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

Keywordsi

Biological processCell adhesion
LigandCalcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin-12Curated
Alternative name(s):
Vascular cadherin-21 Publication
Vascular endothelial cadherin-21 Publication
Short name:
VE-cad-21 Publication
Short name:
VE-cadherin-21 Publication
Cleaved into the following chain:
Gene namesi
Name:PCDH12Imported
ORF Names:UNQ395/PRO7311 Publication
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

EuPathDBiHostDB:ENSG00000113555.5
HGNCiHGNC:8657 PCDH12
MIMi605622 gene
neXtProtiNX_Q9NPG4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini25 – 718ExtracellularSequence analysisAdd BLAST694
Transmembranei719 – 739HelicalSequence analysisAdd BLAST21
Topological domaini740 – 1184CytoplasmicSequence analysisAdd BLAST445

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane, Secreted

Pathology & Biotechi

Involvement in diseasei

Microcephaly, seizures, spasticity, and brain calcifications (MISSBC)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive syndrome characterized by congenital microcephaly, hypothalamic midbrain dysplasia, epilepsy, and severe global developmental delay with profound intellectual disability, spasticity or dystonia. Brain imaging shows intracerebral calcifications.
See also OMIM:251280
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_080386147S → I in MISSBC; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs759794990Ensembl.1
Natural variantiVAR_080387332I → N in MISSBC; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs146725009Ensembl.1
Natural variantiVAR_080388839 – 1184Missing in MISSBC. 1 PublicationAdd BLAST346
Natural variantiVAR_0803891091G → S in MISSBC; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs779814208Ensembl.1

Keywords - Diseasei

Disease mutation, Epilepsy, Mental retardation, Primary microcephaly

Organism-specific databases

DisGeNETi51294
MalaCardsiPCDH12
MIMi251280 phenotype
OpenTargetsiENSG00000113555
PharmGKBiPA32998

Polymorphism and mutation databases

BioMutaiPCDH12
DMDMi22095989

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 24Sequence analysisAdd BLAST24
ChainiPRO_000000399625 – 1184Protocadherin-12Add BLAST1160
ChainiPRO_000044404125 – ?Protocadherin-12, secreted form1 Publication

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi415N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi582N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi659N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi662N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei859PhosphoserineBy similarity1
Modified residuei1062PhosphoserineCombined sources1

Post-translational modificationi

Protocadherin-12: Cleaved by ADAM10 close to the transmembrane domain to release the Protocadherin-12, secreted form in the serum. Cleavage results in reduced cellular adhesion in a cell migration assay.1 Publication

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

EPDiQ9NPG4
PaxDbiQ9NPG4
PeptideAtlasiQ9NPG4
PRIDEiQ9NPG4
ProteomicsDBi81993

PTM databases

iPTMnetiQ9NPG4
PhosphoSitePlusiQ9NPG4

Expressioni

Tissue specificityi

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 trophoblast (at protein level) (PubMed:21402705).2 Publications

Gene expression databases

BgeeiENSG00000113555 Expressed in 194 organ(s), highest expression level in tendon of biceps brachii
CleanExiHS_PCDH12
ExpressionAtlasiQ9NPG4 baseline and differential
GenevisibleiQ9NPG4 HS

Organism-specific databases

HPAiHPA051242

Interactioni

Protein-protein interaction databases

BioGridi119445, 19 interactors
DIPiDIP-47292N
IntActiQ9NPG4, 2 interactors
MINTiQ9NPG4

Structurei

3D structure databases

ProteinModelPortaliQ9NPG4
SMRiQ9NPG4
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini28 – 135Cadherin 1PROSITE-ProRule annotationAdd BLAST108
Domaini136 – 244Cadherin 2PROSITE-ProRule annotationAdd BLAST109
Domaini245 – 352Cadherin 3PROSITE-ProRule annotationAdd BLAST108
Domaini355 – 460Cadherin 4PROSITE-ProRule annotationAdd BLAST106
Domaini461 – 565Cadherin 5PROSITE-ProRule annotationAdd BLAST105
Domaini600 – 711Cadherin 6PROSITE-ProRule annotationAdd BLAST112

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1177 – 1181Poly-Ser5

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594 Eukaryota
ENOG410XQHI LUCA
GeneTreeiENSGT00900000140770
HOVERGENiHBG101142
InParanoidiQ9NPG4
KOiK16499
OMAiWELEIVV
OrthoDBiEOG091G00QD
PhylomeDBiQ9NPG4
TreeFamiTF352008

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin-like_dom
IPR015919 Cadherin-like_sf
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
IPR030720 Protocadherin-12
PANTHERiPTHR24028:SF42 PTHR24028:SF42, 1 hit
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 5 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits

Sequence (1+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q9NPG4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MMQLLQLLLG LLGPGGYLFL LGDCQEVTTL TVKYQVSEEV PSGTVIGKLS
60 70 80 90 100
QELGREERRR QAGAAFQVLQ LPQALPIQVD SEEGLLSTGR RLDREQLCRQ
110 120 130 140 150
WDPCLVSFDV LATGDLALIH VEIQVLDIND HQPRFPKGEQ ELEISESASL
160 170 180 190 200
RTRIPLDRAL DPDTGPNTLH TYTLSPSEHF ALDVIVGPDE TKHAELIVVK
210 220 230 240 250
ELDREIHSFF DLVLTAYDNG NPPKSGTSLV KVNVLDSNDN SPAFAESSLA
260 270 280 290 300
LEIQEDAAPG TLLIKLTATD PDQGPNGEVE FFLSKHMPPE VLDTFSIDAK
310 320 330 340 350
TGQVILRRPL DYEKNPAYEV DVQARDLGPN PIPAHCKVLI KVLDVNDNIP
360 370 380 390 400
SIHVTWASQP SLVSEALPKD SFIALVMADD LDSGHNGLVH CWLSQELGHF
410 420 430 440 450
RLKRTNGNTY MLLTNATLDR EQWPKYTLTL LAQDQGLQPL SAKKQLSIQI
460 470 480 490 500
SDINDNAPVF EKSRYEVSTR ENNLPSLHLI TIKAHDADLG INGKVSYRIQ
510 520 530 540 550
DSPVAHLVAI DSNTGEVTAQ RSLNYEEMAG FEFQVIAEDS GQPMLASSVS
560 570 580 590 600
VWVSLLDAND NAPEVVQPVL SDGKASLSVL VNASTGHLLV PIETPNGLGP
610 620 630 640 650
AGTDTPPLAT HSSRPFLLTT IVARDADSGA NGEPLYSIRS GNEAHLFILN
660 670 680 690 700
PHTGQLFVNV TNASSLIGSE WELEIVVEDQ GSPPLQTRAL LRVMFVTSVD
710 720 730 740 750
HLRDSARKPG ALSMSMLTVI CLAVLLGIFG LILALFMSIC RTEKKDNRAY
760 770 780 790 800
NCREAESTYR QQPKRPQKHI QKADIHLVPV LRGQAGEPCE VGQSHKDVDK
810 820 830 840 850
EAMMEAGWDP CLQAPFHLTP TLYRTLRNQG NQGAPAESRE VLQDTVNLLF
860 870 880 890 900
NHPRQRNASR ENLNLPEPQP ATGQPRSRPL KVAGSPTGRL AGDQGSEEAP
910 920 930 940 950
QRPPASSATL RRQRHLNGKV SPEKESGPRQ ILRSLVRLSV AAFAERNPVE
960 970 980 990 1000
ELTVDSPPVQ QISQLLSLLH QGQFQPKPNH RGNKYLAKPG GSRSAIPDTD
1010 1020 1030 1040 1050
GPSARAGGQT DPEQEEGPLD PEEDLSVKQL LEEELSSLLD PSTGLALDRL
1060 1070 1080 1090 1100
SAPDPAWMAR LSLPLTTNYR DNVISPDAAA TEEPRTFQTF GKAEAPELSP
1110 1120 1130 1140 1150
TGTRLASTFV SEMSSLLEML LEQRSSMPVE AASEALRRLS VCGRTLSLDL
1160 1170 1180
ATSAASGMKV QGDPGGKTGT EGKSRGSSSS SRCL
Length:1,184
Mass (Da):128,995
Last modified:October 1, 2000 - v1
Checksum:i45314473DC503E8D
GO

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E5RJD4E5RJD4_HUMAN
Protocadherin-12
PCDH12
23Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti385 – 386HN → KD in BAB55016 (PubMed:14702039).Curated2
Sequence conflicti389 – 390VH → LG in BAB55016 (PubMed:14702039).Curated2
Sequence conflicti442A → V in BAB14677 (PubMed:14702039).Curated1
Sequence conflicti753R → W in BAB14677 (PubMed:14702039).Curated1
Sequence conflicti814A → T in BAB14837 (PubMed:14702039).Curated1
Sequence conflicti970H → Y in BAB14837 (PubMed:14702039).Curated1
Sequence conflicti1051S → C in BAB14677 (PubMed:14702039).Curated1
Sequence conflicti1181S → SSSS in BAB14837 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_08038555R → G Polymorphism. 1 PublicationCorresponds to variant dbSNP:rs200451693Ensembl.1
Natural variantiVAR_080386147S → I in MISSBC; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs759794990Ensembl.1
Natural variantiVAR_080387332I → N in MISSBC; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs146725009Ensembl.1
Natural variantiVAR_020368385H → N1 PublicationCorresponds to variant dbSNP:rs164075EnsemblClinVar.1
Natural variantiVAR_020369640S → N2 PublicationsCorresponds to variant dbSNP:rs164515Ensembl.1
Natural variantiVAR_080388839 – 1184Missing in MISSBC. 1 PublicationAdd BLAST346
Natural variantiVAR_0803891091G → S in MISSBC; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs779814208Ensembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF231025 mRNA Translation: AAF61931.1
AF240635 mRNA Translation: AAF73962.1
AB026893 mRNA Translation: BAA95162.1
AK023785 mRNA Translation: BAB14677.1
AK024140 mRNA Translation: BAB14837.1
AK027282 mRNA Translation: BAB55016.1
AY358428 mRNA Translation: AAQ88794.1
CCDSiCCDS4269.1
RefSeqiNP_057664.1, NM_016580.3
UniGeneiHs.439474
Hs.600230

Genome annotation databases

EnsembliENST00000231484; ENSP00000231484; ENSG00000113555
GeneIDi51294
KEGGihsa:51294
UCSCiuc003llx.4 human

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF231025 mRNA Translation: AAF61931.1
AF240635 mRNA Translation: AAF73962.1
AB026893 mRNA Translation: BAA95162.1
AK023785 mRNA Translation: BAB14677.1
AK024140 mRNA Translation: BAB14837.1
AK027282 mRNA Translation: BAB55016.1
AY358428 mRNA Translation: AAQ88794.1
CCDSiCCDS4269.1
RefSeqiNP_057664.1, NM_016580.3
UniGeneiHs.439474
Hs.600230

3D structure databases

ProteinModelPortaliQ9NPG4
SMRiQ9NPG4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119445, 19 interactors
DIPiDIP-47292N
IntActiQ9NPG4, 2 interactors
MINTiQ9NPG4

PTM databases

iPTMnetiQ9NPG4
PhosphoSitePlusiQ9NPG4

Polymorphism and mutation databases

BioMutaiPCDH12
DMDMi22095989

Proteomic databases

EPDiQ9NPG4
PaxDbiQ9NPG4
PeptideAtlasiQ9NPG4
PRIDEiQ9NPG4
ProteomicsDBi81993

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000231484; ENSP00000231484; ENSG00000113555
GeneIDi51294
KEGGihsa:51294
UCSCiuc003llx.4 human

Organism-specific databases

CTDi51294
DisGeNETi51294
EuPathDBiHostDB:ENSG00000113555.5
GeneCardsiPCDH12
HGNCiHGNC:8657 PCDH12
HPAiHPA051242
MalaCardsiPCDH12
MIMi251280 phenotype
605622 gene
neXtProtiNX_Q9NPG4
OpenTargetsiENSG00000113555
PharmGKBiPA32998
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594 Eukaryota
ENOG410XQHI LUCA
GeneTreeiENSGT00900000140770
HOVERGENiHBG101142
InParanoidiQ9NPG4
KOiK16499
OMAiWELEIVV
OrthoDBiEOG091G00QD
PhylomeDBiQ9NPG4
TreeFamiTF352008

Miscellaneous databases

ChiTaRSiPCDH12 human
GeneWikiiPCDH12
GenomeRNAii51294
PROiPR:Q9NPG4
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000113555 Expressed in 194 organ(s), highest expression level in tendon of biceps brachii
CleanExiHS_PCDH12
ExpressionAtlasiQ9NPG4 baseline and differential
GenevisibleiQ9NPG4 HS

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin-like_dom
IPR015919 Cadherin-like_sf
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
IPR030720 Protocadherin-12
PANTHERiPTHR24028:SF42 PTHR24028:SF42, 1 hit
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 5 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits
ProtoNetiSearch...

Entry informationi

Entry nameiPCD12_HUMAN
AccessioniPrimary (citable) accession number: Q9NPG4
Secondary accession number(s): Q6UXB6
, Q96KB8, Q9H7Y6, Q9H8E0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: October 1, 2000
Last modified: November 7, 2018
This is version 153 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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