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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PCDHGB5 Gene

protein-coding GIFtS: 35
GCID: GC05P141327

Protocadherin Gamma Subfamily B, 5

1 related disease
at

MalaCards

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
About This Section

Aliases
Protocadherin Gamma Subfamily B, 5¹ ²
PCDH-GAMMA-B5²
Protocadherin Gamma-B5²
PCDH-gamma-B5³

External Ids:	HGNC: 8712¹	Entrez Gene: 56101²	OMIM: 606302⁵	UniProtKB: Q9Y5G0³

Export aliases for PCDHGB5 gene to outside databases

Previous GC identifers: GC05P140594 GC05P141311 GC05P140713 GC05P140771 GC05P140792 GC05P140731 GC05P140808 GC05P140828 GC05P140845 GC05P140870 GC05P140877 GC05P140897 GC05P140930 GC05P140952 GC05P140973 GC05P140995 GC05P141025 GC05P141043 GC05P141070 GC05P141090 GC05P141109 GC05P141151 GC05P141168 GC05P141204 GC05P141244

(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 PCDHGB5 Gene:

This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on

chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may

be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies.

Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related

subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region,

containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region,

which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common

cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the

establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for

the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGB5 Gene:

PCDHGB5 (protocadherin gamma subfamily B, 5) is a protein-coding gene. Diseases associated with PCDHGB5 include neuronitis. GO annotations related to this gene include calcium ion binding.

UniProtKB/Swiss-Prot: PCDGH_HUMAN, Q9Y5G0

Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of

specific neuronal connections in the brain

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PCDHGB5 gene promoter:
p300 Pax-2 FOXD3 Pax-2a FOXL1 Max Egr-2 COMP1 c-Myc
Other transcription factors

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Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHGB5

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

Entrez Gene cytogenetic band: 5q31 HGNC cytogenetic band: 5q31

PCDHGB5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGB5 gene location

GeneLoc information about chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05P141327: view genomic region (about GC identifiers)

Start:	140,777,695 bp from pter	End:	140,892,546 bp from pter
Size:	114,852 bases	Orientation:	plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MAXQB 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 Cloud-Clone Corp.,
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About This Section

UniProtKB/Swiss-Prot: PCDGH_HUMAN, Q9Y5G0 (See protein sequence)

Recommended Name: Protocadherin gamma-B5 precursor

Size: 923 amino acids; 99875 Da

Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)

Secondary accessions: Q52LK8 Q9Y5C6

Alternative splicing: 2 isoforms: Q9Y5G0-1 Q9Y5G0-2

Explore the universe of human proteins at neXtProt for PCDHGB5: NX_Q9Y5G0

Explore proteomics data for PCDHGB5 at MOPED

Post-translational modifications:

View modification sites using PhosphoSitePlus

View neXtProt modification sites for NX_Q9Y5G0

PCDHGB5 Protein expression data from MOPED¹, PaxDb² and MAXQB³ : About this image

REFSEQ proteins (2 alternative transcripts):

NP_061748.1 NP_115270.1

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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	IEA	--
GO:0016021	integral to membrane	IEA	--

PCDHGB5 for ontologies About GeneDecksing

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

HGNC Gene Families:

PCDHC: Cadherins / Protocadherins : Clustered

4 InterPro protein domains:

IPR015919 Cadherin-like

IPR013164 Cadherin_N

IPR020894 Cadherin_CS

IPR002126 Cadherin

Graphical View of Domain Structure for InterPro Entry Q9Y5G0

ProtoNet protein and cluster: Q9Y5G0

1 Blocks protein domain: IPB002126 Cadherin

UniProtKB/Swiss-Prot: PCDGH_HUMAN, Q9Y5G0

Similarity: Contains 6 cadherin domains

PCDHGB5 for domains About GeneDecksing

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

Molecular Function:

UniProtKB/Swiss-Prot Summary: PCDGH_HUMAN, Q9Y5G0

Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of

specific neuronal connections in the brain

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	--

PCDHGB5 for ontologies About GeneDecksing

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About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PCDHGB5

Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007156	homophilic cell adhesion	IEA	--

PCDHGB5 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, IUPHAR, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

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1 HMDB Compound for PCDHGB5 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 PCDHGB5 / PCDGH

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
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About This Section

REFSEQ mRNAs for PCDHGB5 gene (2 alternative transcripts):

NM_018925.2 NM_032099.1

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24/737 AceView cDNA sequences (see all 737):

NM_032403 BM664891 NM_032091 CB305621 BU145848 AF152332 BQ318895 CA443353

NM_018912 CA390638 BM694643 BF513666 AB000896 BQ877616 BM738372 AF152318

NM_018913 BF511055 BQ677045 BM673359 NM_018925 AF152521 AW407884 BQ183224

GeneLoc Exon Structure

(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

PCDHGB5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

See PCDHGB5 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDHGB5

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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 human and mouse.

Orthologs for PCDHGB5 gene from 1/4 species (see all 4) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Pcdhgb5^{1 , 5}	protocadherin gamma subfamily B, 5^{1, 5}	83.35(n)¹ 85.05(a)¹		18 (19.59 cM)⁵ 93702¹ NM_033577.1¹ NP_291055.1¹ 37731154⁵

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

Paralogs for PCDHGB5 gene

18/61 SIMAP similar genes for PCDHGB5 using alignment to 1 protein entry: PCDGH_HUMAN(see all similar genes):

PCDHGB4 PCDHGB6 PCDHGB7 PCDHGB1 PCDHGB2 PCDHGC3

PCDHGB3 PCDHGA1 PCDHGA11 PCDHGA8 PCDHGA9 PCDHGA12

PCDHGA2 PCDHGA4 PCDHGA5 PCDHGA3 PCDHGA10 PCDHGA6

PCDHGB5 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, ⁴UniProtKB, 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	Clinical significance	Chr 5 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data				Transcription Related Data				Allele Frequencies
			--	--	--		--	--
VAR_048571⁴	--	--	see VAR_048571	2	G S	mis⁴		0	--	--	--	--

HapMap Linkage Disequilibrium report for PCDHGB5 (140777695 - 140892546 bp)

Structural Variations
Database of Genomic Variants (DGV) 10/13 variations for PCDHGB5 (see all 13): About this table

Variant ID	Type	Subtype	PubMed ID
esv2730847	CNV	Deletion	23290073
esv267823	CNV	Insertion	20981092
nsv462470	CNV	Loss	19166990
nsv327707	CNV	Loss	16902084
dgv6351n71	CNV	Loss	21882294
nsv882990	CNV	Loss	21882294
dgv6352n71	CNV	Loss	21882294
nsv518799	CNV	Loss	19592680
dgv6353n71	CNV	Loss	21882294
nsv519627	CNV	Loss	19592680

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

PCDHGB5 for disorders           About GeneDecksing

OMIM gene information: 606302    OMIM disorders: --

2 diseases for PCDHGB5:    About MalaCards

neuronitis

Genetic Association Database (GAD): PCDHGB5

Export disorders for PCDHGB5 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 PCDHGB5 gene integrated from 9 sources:
(articles sorted by number of sources associating them with PCDHGB5)

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

A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)^{1, 2, 3} Wu Q. and Maniatis T. (1999)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)
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)
Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)¹ Wu Q.... Maniatis T. (2001)
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)
Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)¹ Wu Q. and Maniatis T. (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

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 56101	HGNC: 8712	AceView: PCDHGC3	euGenes: HUgn56101	ECgene: PCDHGB5
H-InvDB: PCDHGB5

(According to HUGE)
About This Section

(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 PCDHGB5	Pharmacogenomics, SNPs, Pathways

Intellectual Property for PCDHGB5 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for PCDHGB5 gene:
Search GeneIP for patents involving PCDHGB5

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

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About This Section


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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013

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Category			TGFB1 (GIFtS: 73) transforming growth factor, beta 1
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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PCDHGB5 Gene

Protocadherin Gamma Subfamily B, 5

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PCDHGB5 Gene

Protocadherin Gamma Subfamily B, 5

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