Atlas of Genetics and Cytogenetics in Oncology and Haematology

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PCDHGB1 (protocadherin gamma subfamily B, 1)

Identity

Alias_symbol (synonym)PCDH-GAMMA-B1
Other alias
HGNC (Hugo) PCDHGB1
LocusID (NCBI) 56104
Atlas_Id 71747
Location 5q31.3  [Link to chromosome band 5q31]
Location_base_pair Starts at 141350261 and ends at 141512979 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

External links

Nomenclature
HGNC (Hugo)PCDHGB1   8708
Cards
Entrez_Gene (NCBI)PCDHGB1  56104  protocadherin gamma subfamily B, 1
AliasesPCDH-GAMMA-B1
GeneCards (Weizmann)PCDHGB1
Ensembl hg19 (Hinxton)ENSG00000254221 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000254221 [Gene_View]  chr5:141350261-141512979 [Contig_View]  PCDHGB1 [Vega]
ICGC DataPortalENSG00000254221
TCGA cBioPortalPCDHGB1
AceView (NCBI)PCDHGB1
Genatlas (Paris)PCDHGB1
WikiGenes56104
SOURCE (Princeton)PCDHGB1
Genetics Home Reference (NIH)PCDHGB1
Genomic and cartography
GoldenPath hg38 (UCSC)PCDHGB1  -     chr5:141350261-141512979 +  5q31.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PCDHGB1  -     5q31.3   [Description]    (hg19-Feb_2009)
EnsemblPCDHGB1 - 5q31.3 [CytoView hg19]  PCDHGB1 - 5q31.3 [CytoView hg38]
Mapping of homologs : NCBIPCDHGB1 [Mapview hg19]  PCDHGB1 [Mapview hg38]
OMIM606299   
Gene and transcription
Genbank (Entrez)AF152330 AF152517 BC103926 BC103927 BC103928
RefSeq transcript (Entrez)NM_018922 NM_032095
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PCDHGB1
Cluster EST : UnigeneHs.368160 [ NCBI ]
CGAP (NCI)Hs.368160
Alternative Splicing GalleryENSG00000254221
Gene ExpressionPCDHGB1 [ NCBI-GEO ]   PCDHGB1 [ EBI - ARRAY_EXPRESS ]   PCDHGB1 [ SEEK ]   PCDHGB1 [ MEM ]
Gene Expression Viewer (FireBrowse)PCDHGB1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56104
GTEX Portal (Tissue expression)PCDHGB1
Human Protein AtlasENSG00000254221-PCDHGB1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y5G3   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y5G3  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y5G3
Splice isoforms : SwissVarQ9Y5G3
PhosPhoSitePlusQ9Y5G3
Domaine pattern : Prosite (Expaxy)CADHERIN_1 (PS00232)    CADHERIN_2 (PS50268)   
Domains : Interpro (EBI)Cadherin    Cadherin-like    Cadherin_C    Cadherin_CBD    Cadherin_CS    Cadherin_N   
Domain families : Pfam (Sanger)Cadherin (PF00028)    Cadherin_2 (PF08266)    Cadherin_C_2 (PF16492)    Cadherin_tail (PF15974)   
Domain families : Pfam (NCBI)pfam00028    pfam08266    pfam16492    pfam15974   
Domain families : Smart (EMBL)CA (SM00112)  
Conserved Domain (NCBI)PCDHGB1
DMDM Disease mutations56104
Blocks (Seattle)PCDHGB1
SuperfamilyQ9Y5G3
Human Protein Atlas [tissue]ENSG00000254221-PCDHGB1 [tissue]
Peptide AtlasQ9Y5G3
HPRD09389
IPIIPI00215841   IPI00028615   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y5G3
IntAct (EBI)Q9Y5G3
FunCoupENSG00000254221
BioGRIDPCDHGB1
STRING (EMBL)PCDHGB1
ZODIACPCDHGB1
Ontologies - Pathways
QuickGOQ9Y5G3
Ontology : AmiGOcalcium ion binding  integral component of plasma membrane  cell adhesion  homophilic cell adhesion via plasma membrane adhesion molecules  cell-cell signaling  nervous system development  growth cone  
Ontology : EGO-EBIcalcium ion binding  integral component of plasma membrane  cell adhesion  homophilic cell adhesion via plasma membrane adhesion molecules  cell-cell signaling  nervous system development  growth cone  
NDEx NetworkPCDHGB1
Atlas of Cancer Signalling NetworkPCDHGB1
Wikipedia pathwaysPCDHGB1
Orthology - Evolution
OrthoDB56104
GeneTree (enSembl)ENSG00000254221
Phylogenetic Trees/Animal Genes : TreeFamPCDHGB1
HOVERGENQ9Y5G3
HOGENOMQ9Y5G3
Homologs : HomoloGenePCDHGB1
Homology/Alignments : Family Browser (UCSC)PCDHGB1
Gene fusions - Rearrangements
Fusion : QuiverPCDHGB1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPCDHGB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PCDHGB1
dbVarPCDHGB1
ClinVarPCDHGB1
1000_GenomesPCDHGB1 
Exome Variant ServerPCDHGB1
ExAC (Exome Aggregation Consortium)ENSG00000254221
GNOMAD BrowserENSG00000254221
Genetic variants : HAPMAP56104
Genomic Variants (DGV)PCDHGB1 [DGVbeta]
DECIPHERPCDHGB1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPCDHGB1 
Mutations
ICGC Data PortalPCDHGB1 
TCGA Data PortalPCDHGB1 
Broad Tumor PortalPCDHGB1
OASIS PortalPCDHGB1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPCDHGB1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPCDHGB1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PCDHGB1
DgiDB (Drug Gene Interaction Database)PCDHGB1
DoCM (Curated mutations)PCDHGB1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PCDHGB1 (select a term)
intoGenPCDHGB1
Cancer3DPCDHGB1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606299   
Orphanet
DisGeNETPCDHGB1
MedgenPCDHGB1
Genetic Testing Registry PCDHGB1
NextProtQ9Y5G3 [Medical]
TSGene56104
GENETestsPCDHGB1
Target ValidationPCDHGB1
Huge Navigator PCDHGB1 [HugePedia]
snp3D : Map Gene to Disease56104
BioCentury BCIQPCDHGB1
ClinGenPCDHGB1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD56104
Chemical/Pharm GKB GenePA33056
Clinical trialPCDHGB1
Miscellaneous
canSAR (ICR)PCDHGB1 (select the gene name)
Probes
Litterature
PubMed6 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePCDHGB1
EVEXPCDHGB1
GoPubMedPCDHGB1
iHOPPCDHGB1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Feb 23 18:47:03 CET 2018
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