Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

HDLBP (high density lipoprotein binding protein)

Identity

Alias_namesVGL
vigilin
Alias_symbol (synonym)HBP
Other aliasPRO2900
HGNC (Hugo) HDLBP
LocusID (NCBI) 3069
Atlas_Id 47432
Location 2q37.3  [Link to chromosome band 2q37]
Location_base_pair Starts at 241227264 and ends at 241272886 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
BTBD11 (12q23.3) / HDLBP (2q37.3)DNAH14 (1q42.12) / HDLBP (2q37.3)HDLBP (2q37.3) / ARID5B (10q21.2)
HDLBP (2q37.3) / BIRC6 (2p22.3)HDLBP (2q37.3) / CADM2 (3p12.1)HDLBP (2q37.3) / DDX27 (20q13.13)
HDLBP (2q37.3) / FAM174A (5q21.1)HDLBP (2q37.3) / HDLBP (2q37.3)HDLBP (2q37.3) / MACROD2 (20p12.1)
HDLBP (2q37.3) / MAVS (20p13)HDLBP (2q37.3) / NXPH4 (12q13.3)HDLBP (2q37.3) / RPS14 (5q33.1)
HDLBP (2q37.3) / SMARCE1 (17q21.2)HDLBP (2q37.3) / SNX33 (15q24.2)HDLBP (2q37.3) / UNC13A (19p13.11)
MGLL (3q21.3) / HDLBP (2q37.3)MTERF4 (2q37.3) / HDLBP (2q37.3)NTN1 (17p13.1) / HDLBP (2q37.3)
OS9 (12q13.3) / HDLBP (2q37.3)PLK1 (16p12.2) / HDLBP (2q37.3)PRAME (22q11.22) / HDLBP (2q37.3)
PSMD8 (19q13.2) / HDLBP (2q37.3)RABGGTB (1p31.1) / HDLBP (2q37.3)SARNP (12q13.2) / HDLBP (2q37.3)
HDLBP 2q37.3 / BIRC6 2p22.3HDLBP 2q37.3 / CADM2 3p12.1HDLBP 2q37.3 / DDX27 20q13.13
HDLBP 2q37.3 / SMARCE1 17q21.2OS9 12q13.3 / HDLBP 2q37.3PRAME 22q11.22 / HDLBP 2q37.3

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)HDLBP   4857
Cards
Entrez_Gene (NCBI)HDLBP  3069  high density lipoprotein binding protein
AliasesHBP; PRO2900; VGL
GeneCards (Weizmann)HDLBP
Ensembl hg19 (Hinxton)ENSG00000115677 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000115677 [Gene_View]  chr2:241227264-241272886 [Contig_View]  HDLBP [Vega]
ICGC DataPortalENSG00000115677
TCGA cBioPortalHDLBP
AceView (NCBI)HDLBP
Genatlas (Paris)HDLBP
WikiGenes3069
SOURCE (Princeton)HDLBP
Genetics Home Reference (NIH)HDLBP
Genomic and cartography
GoldenPath hg38 (UCSC)HDLBP  -     chr2:241227264-241272886 -  2q37.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HDLBP  -     2q37.3   [Description]    (hg19-Feb_2009)
EnsemblHDLBP - 2q37.3 [CytoView hg19]  HDLBP - 2q37.3 [CytoView hg38]
Mapping of homologs : NCBIHDLBP [Mapview hg19]  HDLBP [Mapview hg38]
OMIM142695   
Gene and transcription
Genbank (Entrez)###############################################################################################################################################################################################################################################################
RefSeq transcript (Entrez)NM_001243900 NM_001320965 NM_001320966 NM_001320967 NM_005336 NM_203346
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)HDLBP
Cluster EST : UnigeneHs.732361 [ NCBI ]
CGAP (NCI)Hs.732361
Alternative Splicing GalleryENSG00000115677
Gene ExpressionHDLBP [ NCBI-GEO ]   HDLBP [ EBI - ARRAY_EXPRESS ]   HDLBP [ SEEK ]   HDLBP [ MEM ]
Gene Expression Viewer (FireBrowse)HDLBP [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3069
GTEX Portal (Tissue expression)HDLBP
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ00341   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ00341  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ00341
Splice isoforms : SwissVarQ00341
PhosPhoSitePlusQ00341
Domaine pattern : Prosite (Expaxy)KH_TYPE_1 (PS50084)   
Domains : Interpro (EBI)KH_dom    KH_dom_type_1   
Domain families : Pfam (Sanger)KH_1 (PF00013)   
Domain families : Pfam (NCBI)pfam00013   
Domain families : Smart (EMBL)KH (SM00322)  
Conserved Domain (NCBI)HDLBP
DMDM Disease mutations3069
Blocks (Seattle)HDLBP
PDB (SRS)1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
PDB (PDBSum)1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
PDB (IMB)1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
PDB (RSDB)1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
Structural Biology KnowledgeBase1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
SCOP (Structural Classification of Proteins)1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
CATH (Classification of proteins structures)1VIG    1VIH    2CTE    2CTF    2CTJ    2CTK    2CTL    2CTM   
SuperfamilyQ00341
Human Protein AtlasENSG00000115677
Peptide AtlasQ00341
HPRD00813
IPI###############################################################################################################################################################################################################################################################   
Protein Interaction databases
DIP (DOE-UCLA)Q00341
IntAct (EBI)Q00341
FunCoupENSG00000115677
BioGRIDHDLBP
STRING (EMBL)HDLBP
ZODIACHDLBP
Ontologies - Pathways
QuickGOQ00341
Ontology : AmiGORNA binding  protein binding  nucleus  cytosol  plasma membrane  lipid transport  cholesterol metabolic process  lipid binding  high-density lipoprotein particle  lipoprotein metabolic process  cadherin binding  
Ontology : EGO-EBIRNA binding  protein binding  nucleus  cytosol  plasma membrane  lipid transport  cholesterol metabolic process  lipid binding  high-density lipoprotein particle  lipoprotein metabolic process  cadherin binding  
NDEx NetworkHDLBP
Atlas of Cancer Signalling NetworkHDLBP
Wikipedia pathwaysHDLBP
Orthology - Evolution
OrthoDB3069
GeneTree (enSembl)ENSG00000115677
Phylogenetic Trees/Animal Genes : TreeFamHDLBP
HOVERGENQ00341
HOGENOMQ00341
Homologs : HomoloGeneHDLBP
Homology/Alignments : Family Browser (UCSC)HDLBP
Gene fusions - Rearrangements
Fusion : MitelmanHDLBP/BIRC6 [2q37.3/2p22.3]  
Fusion : MitelmanHDLBP/CADM2 [2q37.3/3p12.1]  [t(2;3)(q37;p12)]  
Fusion : MitelmanHDLBP/DDX27 [2q37.3/20q13.13]  [t(2;20)(q37;q13)]  
Fusion : MitelmanHDLBP/SMARCE1 [2q37.3/17q21.2]  [t(2;17)(q37;q21)]  
Fusion : MitelmanNTN1/HDLBP [17p13.1/2q37.3]  [t(2;17)(q37;p13)]  
Fusion : MitelmanPRAME/HDLBP [22q11.22/2q37.3]  [t(2;22)(q37;q11)]  
Fusion: TCGAHDLBP 2q37.3 BIRC6 2p22.3 HNSC
Fusion: TCGAHDLBP 2q37.3 CADM2 3p12.1 LUAD
Fusion: TCGAHDLBP 2q37.3 DDX27 20q13.13 PRAD
Fusion: TCGAHDLBP 2q37.3 SMARCE1 17q21.2 PRAD
Fusion: TCGAOS9 12q13.3 HDLBP 2q37.3 PRAD
Fusion: TCGAPRAME 22q11.22 HDLBP 2q37.3 SKCM
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHDLBP [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HDLBP
dbVarHDLBP
ClinVarHDLBP
1000_GenomesHDLBP 
Exome Variant ServerHDLBP
ExAC (Exome Aggregation Consortium)HDLBP (select the gene name)
Genetic variants : HAPMAP3069
Genomic Variants (DGV)HDLBP [DGVbeta]
DECIPHERHDLBP [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHDLBP 
Mutations
ICGC Data PortalHDLBP 
TCGA Data PortalHDLBP 
Broad Tumor PortalHDLBP
OASIS PortalHDLBP [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHDLBP  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHDLBP
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 HDLBP
DgiDB (Drug Gene Interaction Database)HDLBP
DoCM (Curated mutations)HDLBP (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HDLBP (select a term)
intoGenHDLBP
Cancer3DHDLBP(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM142695   
Orphanet
MedgenHDLBP
Genetic Testing Registry HDLBP
NextProtQ00341 [Medical]
TSGene3069
GENETestsHDLBP
Target ValidationHDLBP
Huge Navigator HDLBP [HugePedia]
snp3D : Map Gene to Disease3069
BioCentury BCIQHDLBP
ClinGenHDLBP
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3069
Chemical/Pharm GKB GenePA29235
Clinical trialHDLBP
Miscellaneous
canSAR (ICR)HDLBP (select the gene name)
Probes
Litterature
PubMed67 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHDLBP
EVEXHDLBP
GoPubMedHDLBP
iHOPHDLBP
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Sep 25 19:11:15 CEST 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.