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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HDLBP Gene

protein-coding   GIFtS: 61
GCID: GC02M242166

High Density Lipoprotein Binding Protein

(Previous name: vigilin)
(Previous symbol: VGL)
  See related diseases
at  

(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
High Density Lipoprotein Binding Protein1 2     HBP2 3
VGL1 2 3 5     HDL-Binding Protein2 3
vigilin1 2     PRO29002
High Density Lipoprotein-Binding Protein2 3     

External Ids:    HGNC: 48571   Entrez Gene: 30692   Ensembl: ENSG000001156777   OMIM: 1426955   UniProtKB: Q003413   

Export aliases for HDLBP gene to outside databases

Previous GC identifers: GC02P239181 GC02P240038 GC02M242188 GC02M242489 GC02M242488 GC02M241888 GC02M233922


(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 HDLBP Gene:
The protein encoded by this gene binds high density lipoprotein (HDL) and may function to regulate excess
cholesterol levels in cells. The encoded protein also binds RNA and can induce heterochromatin formation. Three
transcript variants encoding two different isoforms have been found for this gene. (provided by RefSeq, Aug 2011)

GeneCards Summary for HDLBP Gene: 
HDLBP (high density lipoprotein binding protein) is a protein-coding gene. Diseases associated with HDLBP include familial hdl deficiency, and graves' disease. GO annotations related to this gene include lipid binding and RNA binding. An important paralog of this gene is BICC1.

UniProtKB/Swiss-Prot: VIGLN_HUMAN, Q00341
Function: Appears to play a role in cell sterol metabolism. It may function to protect cells from
over-accumulation of cholesterol

Gene Wiki entry for HDLBP Gene


(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
RefSeq DNA sequence:
NC_000002.11  NT_005416.13  NC_018913.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HDLBP gene promoter:
         Max1   Nkx3-1   Nkx3-1 v4   Nkx3-1 v1   Nkx3-1 v2   Max   Nkx3-1 v3   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HDLBP promoter sequence
   Search SABiosciences Chromatin IP Primers for HDLBP

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HDLBP


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

Entrez Gene cytogenetic band: 2q37.3   Ensembl cytogenetic band:  2q37.3   HGNC cytogenetic band: 2q37.3

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

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M242166:  view genomic region     (about GC identifiers)

Start:
242,166,679 bp from pter      End:
242,256,476 bp from pter
Size:
89,798 bases      Orientation:
minus 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.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: VIGLN_HUMAN, Q00341 (See protein sequence)
Recommended Name: Vigilin  
Size: 1268 amino acids; 141456 Da
Subcellular location: Cytoplasm. Nucleus
6/8 PDB 3D structures from and Proteopedia for HDLBP (see all 8):
1VIG (3D)        1VIH (3D)        2CTE (3D)        2CTF (3D)        2CTJ (3D)        2CTK (3D)    
Secondary accessions: B4DTQ2 E7EM71 Q53QU2 Q9UCY3
Alternative splicing: 2 isoforms:  Q00341-1   Q00341-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for HDLBP: NX_Q00341

Explore proteomics data for HDLBP at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q00341

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

    HDLBP Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001230829.1  NP_005327.1  NP_976221.1  

    ENSEMBL proteins: 
     ENSP00000375836   ENSP00000375837   ENSP00000312042   ENSP00000362389   ENSP00000411211  
     ENSP00000405180   ENSP00000388876   ENSP00000393766   ENSP00000403807   ENSP00000405109  
     ENSP00000413891   ENSP00000387782   ENSP00000416559   ENSP00000403913   ENSP00000396964  
     ENSP00000394205   ENSP00000390290   ENSP00000413805   ENSP00000390942   ENSP00000396202  
     ENSP00000403693   ENSP00000409868   ENSP00000408582   ENSP00000397799   ENSP00000396959  
     ENSP00000391773   ENSP00000399139  

    Human Recombinant Protein Products for HDLBP: 
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    OriGene Purified Protein for HDLBP
    OriGene Protein Over-expression Lysate for HDLBP
    OriGene MassSpec for HDLBP 
    OriGene Custom Protein Services for HDLBP
    GenScript Custom Purified and Recombinant Proteins Services for HDLBP
    Novus Biologicals HDLBP Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for HDLBP 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IDA--
    GO:0005886plasma membrane TAS1318310
    GO:0034364high-density lipoprotein particle IEA--

    HDLBP for ontologies           About GeneDecksing



    HDLBP Antibody Products: 
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    Novus Biologicals HDLBP Antibodies
    Abcam antibodies for HDLBP
    Cloud-Clone Corp. Antibodies for HDLBP 
    ThermoFisher Antibody for HDLBP
    LSBio Antibodies in human, mouse, rat for HDLBP 

    Assay Products for HDLBP: 
    Browse Kits and Assays available from EMD Millipore
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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for HDLBP 
    Cloud-Clone Corp. CLIAs for HDLBP


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR004087 KH_dom
     IPR004088 KH_dom_type_1

    Graphical View of Domain Structure for InterPro Entry Q00341

    ProtoNet protein and cluster: Q00341

    2 Blocks protein domains:
    IPB004087 KH domain
    IPB004088 KH


    UniProtKB/Swiss-Prot: VIGLN_HUMAN, Q00341
    Similarity: Contains 14 KH domains


    HDLBP 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, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, 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: VIGLN_HUMAN, Q00341
    Function: Appears to play a role in cell sterol metabolism. It may function to protect cells from
    over-accumulation of cholesterol

         Genatlas biochemistry entry for HDLBP:
    vigilin,high density lipoprotein binding protein

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding IEA--
    GO:0008289lipid binding TAS1318310
         
    HDLBP for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for HDLBP:
     Synthetic lethal with c-Myc af 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for HDLBP 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for HDLBP

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HDLBP 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HDLBP 

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HDLBP
    8/64 QIAGEN miScript miRNA Assays for microRNAs that regulate HDLBP (see all 64):
    hsa-miR-759 hsa-miR-10b* hsa-miR-642b hsa-miR-92b hsa-miR-761 hsa-miR-4324 hsa-miR-3688-3p hsa-miR-425
    SwitchGear 3'UTR luciferase reporter plasmidHDLBP 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for HDLBP
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HDLBP

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HDLBP
    Sirion Biotech Customized adenovirus for overexpression of HDLBP

    Clone
    Products:
         
    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for HDLBP (see all 11)
    OriGene ORF clones in mouse, rat for HDLBP
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): HDLBP (NM_203346)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HDLBP
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDLBP
    Sirion Biotech Customized lentivirus for stable overexpression of HDLBP 
                         Customized lentivirus expression plasmids for stable overexpression of HDLBP 

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for HDLBP
    Search LifeMap BioReagents cell lines for HDLBP
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HDLBP


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for HDLBP

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    5/969 Interacting proteins for HDLBP (Q003412, 3 ENSP000003120424) via UniProtKB, MINT, STRING, and/or I2D (see all 969)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006869lipid transport IEA--
    GO:0008203cholesterol metabolic process IEA--

    HDLBP for ontologies           About GeneDecksing



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

    HDLBP for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HDLBP (VIGLN)

    4 Novoseek inferred chemical compound relationships for HDLBP gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    trna 58.7 10 12792806 (2), 10657246 (2), 9445390 (2), 14618268 (1)
    cholesterol 30.5 14 12941645 (2), 1318310 (2), 9409201 (2), 10638200 (1) (see all 6)
    estrogen 5.77 4 9632784 (2), 11050168 (1)
    lipid 0 2 12941645 (2)

    Search CenterWatch for drugs/clinical trials and news about HDLBP / VIGLN

    (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,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HDLBP gene (3 alternative transcripts): 
    NM_001243900.1  NM_005336.4  NM_203346.3  

    Unigene Cluster for HDLBP:

    High density lipoprotein binding protein
    Hs.471851  [show with all ESTs]
    Unigene Representative Sequence: NM_005336
    18/47 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 47):
    ENST00000391975(uc021vzg.1 uc002waz.3 uc002wba.3) ENST00000391976(uc010fzn.1)
    ENST00000310931 ENST00000487169 ENST00000373292 ENST00000484412 ENST00000442730
    ENST00000494862 ENST00000488013 ENST00000470482 ENST00000479894 ENST00000483086
    ENST00000479169 ENST00000427487 ENST00000459788 ENST00000471294 ENST00000452931
    ENST00000460826
    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HDLBP
    8/64 QIAGEN miScript miRNA Assays for microRNAs that regulate HDLBP (see all 64):
    hsa-miR-759 hsa-miR-10b* hsa-miR-642b hsa-miR-92b hsa-miR-761 hsa-miR-4324 hsa-miR-3688-3p hsa-miR-425
    SwitchGear 3'UTR luciferase reporter plasmidHDLBP 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for HDLBP
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HDLBP
    Clone
    Products:
         
    OriGene clones in human, mouse for HDLBP (see all 11)
    OriGene ORF clones in mouse, rat for HDLBP
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): HDLBP (NM_203346)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HDLBP
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HDLBP
    Sirion Biotech Customized lentivirus for stable overexpression of HDLBP 
                         Customized lentivirus expression plasmids for stable overexpression of HDLBP 
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for HDLBP
    OriGene qSTAR qPCR primer pairs in human, mouse for HDLBP
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat HDLBP
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HDLBP
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HDLBP

    Additional mRNA sequence: 

    AF116718.1 AK026138.1 AK127833.1 AK296684.1 AK300312.1 AK309075.1 AK312335.1 BC001179.1 
    BC007961.2 BC009422.1 BC014305.2 BC021817.1 BC038965.1 BC058826.1 BC113120.1 BX647759.1 
    M64098.1 

    24/120 DOTS entries (see all 120):

    DT.100060166  DT.100891495  DT.405195  DT.91777154  DT.100891477  DT.97861017  DT.95165709  DT.100891497 
    DT.95293553  DT.100891486  DT.120964777  DT.100891484  DT.120964528  DT.91777150  DT.91773953  DT.420593 
    DT.95165778  DT.100891501  DT.120964358  DT.120964485  DT.454461  DT.120964637  DT.100055634  DT.100891492 

    24/56 AceView cDNA sequences (see all 56):

    BI858125 BQ071302 BM801822 AI336908 AW589798 BP362839 BP335239 H42603 
    AI202956 BM772516 BM554669 BM750590 AW613727 BE278940 AI824841 BQ070368 
    BF437213 CK430628 F01593 AA316561 BM851227 BG254246 BM471172 BU149472 

    GeneLoc Exon Structure

    5/26 Alternative Splicing Database (ASD) splice patterns (SP) for HDLBP (see all 26)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e ^ 11a · 11b ·
    SP1:        -     -     -     -     -     -     -     -     -     -                                                                                             
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:        -     -     -     -     -     -                 -     -                                                                                             
    SP5:              -     -     -     -     -     -     -     -     -                                                                                             

    ExUns: 11c · 11d · 11e ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b · 18c ^ 19 ^ 20 ^ 21a · 21b ^ 22a · 22b · 22c ^ 23 ^ 24a ·
    SP1:                                                                                      -                             -                       -     -         
    SP2:                                -     -     -                                         -                             -                       -     -         
    SP3:                                                                                                                    -                       -     -         
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 24b ^ 25a · 25b · 25c · 25d ^ 26a · 26b ^ 27 ^ 28a · 28b ^ 29 ^ 30 ^ 31 ^ 32a · 32b ^ 33a · 33b ^ 34 ^ 35a · 35b · 35c ^ 36a · 36b ^ 37
    SP1:        -                                               -           -                                                     -                     
    SP2:        -                                               -           -                             -     -     -           -                     
    SP3:        -                                               -           -                                                                           
    SP4:                                                                                                                                                
    SP5:                                                                                                                                                


    ECgene alternative splicing isoforms for HDLBP

    (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

    HDLBP expression in normal human tissues (normalized intensities)      HDLBP embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACCTCAGGAA
    HDLBP Expression
    About this image


    HDLBP expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/23 selected tissues (see all 23) fully expand
     
     Uterus (Reproductive System)    fully expand to see all 3 entries
             uterus, pre-menopause ; glandular cells   
             endometrial endothelial cell   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 3 entries
             colon ; peripheral nerve/ganglion   
     
     Testis (Reproductive System)    fully expand to see all 2 entries
             Testis Somatic Cells Primitive Gonad
             seminal vesicle ; glandular cells   
     
     Intestine (Gastrointestinal Tract)    fully expand to see all 2 entries
             small intestine ; glandular cells   
     
     Tonsil (Hematopoietic System)    fully expand to see all 2 entries
             tonsil ; non-germinal center cells   

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

    SOURCE GeneReport for Unigene cluster: Hs.471851
        SABiosciences Expression via Pathway-Focused PCR Array including HDLBP: 
              Lipoprotein Signaling & Cholesterol Metabolism in human mouse rat

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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 and fungi.

    Orthologs for HDLBP gene from 8/22 species (see all 22)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hdlbp1 , 5 high density lipoprotein (HDL) binding protein1, 5 89.67(n)1
    97.95(a)1
      1 (47.24 cM)5
    1106111  NM_133808.41  NP_598569.11 
     934059405 
    chicken
    (Gallus gallus)
    Aves HDLBP1 high density lipoprotein binding protein 79.77(n)
    87.53(a)
      395984  NM_205096.1  NP_990427.1 
    lizard
    (Anolis carolinensis)
    Reptilia HDLBP6
    --
    --
    89(a)
    76(a)
    1 ↔ 1
    possible ortholog
    3(30209683-30281114)
    GL343466.1(105004-155473)
    African clawed frog
    (Xenopus laevis)
    Amphibia hdlbp-prov2 high density lipoprotein binding protein (vigilin) 77.15(n)    BC044314.1 
    zebrafish
    (Danio rerio)
    Actinopterygii hdlbp2 high density lipoprotein-binding protein (vigilin) 76.84(n)   323312  BC051153.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Dp11 , 3 single-stranded DNA binding3
    Dodeca-satellite-binding protein 11
    39(a)3
    54.34(n)1
    48.75(a)1
      55C83
    371161  NM_079057.21  NP_523781.21 
    worm
    (Caenorhabditis elegans)
    Secernentea C08H9.23
    CELE_C08H9.21
    high-density lipoprotein-binding
    protein3
    Protein C08H9.21
    38(a)3
    49.43(n)1
    40.41(a)1
      II(9886952-9890851)3
    1745431  NM_063735.51  NP_496136.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SCP160(YJL080C)4
    SCP1601
    Essential RNA-binding G protein effector of mating more4
    Scp160p1
    39.74(n)1
    24.95(a)1
      10(289226-285558)4
    8533651, 4  NP_012455.11, 4 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HDLBP gene
    BICC12  
    1 SIMAP similar gene for HDLBP using alignment to 27 protein entries:     VIGLN_HUMAN (see all proteins):
    DKFZp686L08115

    HDLBP for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for HDLBP
    PGOHUM00000244869


    (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

    10/2002 SNPs in HDLBP are shown (see all 2002)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0360534
    A breast cancer sample4--see VAR_0360532 D V mis40--------
    VAR_0360524
    A breast cancer sample4--see VAR_0360522 K N mis40--------
    rs714046881,2
    C--241537716(+) ACCTT-/GGG   
      
    /GGGGG
    GGGGG
    6 -- int1 cds11NA 2
    rs621863601,2
    C--242166212(+) AGGAAC/TACCTA 3 -- ds50016Minor allele frequency- T:0.25NA WA EA 364
    rs1145495161,2
    F--242166283(+) CTCAAC/TGCCCC 3 -- ds50011Minor allele frequency- T:0.02WA 118
    rs16771,2
    C,F,H--242166550(-) CCACAT/CTGAGG 3 -- ds500128Minor allele frequency- C:0.18EA MN NS NA WA CSA 4388
    rs67262261,2
    C,F--242166568(+) GGGGCT/CGTTGA 3 -- ds50013Minor allele frequency- C:0.33WA CSA 6
    rs38321491,2
    C--242166574(-) ACTGT-/GTTCAAC 3 -- ds50010--------
    rs1818632021,2
    --242166577(+) GAACAC/GAGTGT 3 -- ds50010--------
    rs1408959231,2
    C--242166613(+) AAAGAC/TGAACT 3 -- ds50010--------

    HapMap Linkage Disequilibrium report for HDLBP (242166679 - 242256476 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for HDLBP:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2675219CNV Deletion23128226
    nsv508900CNV Insertion20534489
    nsv3242CNV Insertion18451855
    nsv215143CNV Loss16902084
    dgv4492n71CNV Loss21882294
    nsv876116CNV Loss21882294
    nsv470532CNV Loss18288195
    nsv524008CNV Gain19592680


    Human Gene Mutation Database (HGMD): HDLBP
    SABiosciences Cancer Mutation PCR Assays
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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
    OMIM gene information: 142695    OMIM disorders: --

    7 diseases for HDLBP:    About MalaCards
    familial hdl deficiency    graves' disease    atherosclerosis    retinitis
    hepatocellular carcinoma    hepatitis    breast cancer


    HDLBP for disorders           About GeneDecksing

    Genetic Association Database (GAD): HDLBP
    Human Genome Epidemiology (HuGE) Navigator: HDLBP (5 documents)

    Export disorders for HDLBP 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 HDLBP gene, integrated from 9 sources (see all 92):
    (articles sorted by number of sources associating them with HDLBP)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and expression of a cellular high density lipoprotein-binding protein that is up-regulated by cholesterol loading of cells. (PubMed id 1318310)1, 2, 3, 9 McKnight G.L.... Oram J.F. (1992)
    2. Follow-up of potential novel Graves' disease suscepti bility loci, identified in the UK WTCCC genome-wide nonsynonymous SNP study. (PubMed id 20442750)1, 4 Newby P.R....Gough S.C. (2010)
    3. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (2010)
    4. Candidate genetic analysis of plasma high-density lip oprotein-cholesterol and severity of coronary atherosclerosis. (PubMed id 19878569)1, 4 Chen S.N....Marian A.J. (2009)
    5. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PubMed id 15592455)1, 2 Rush J.... Comb M.J. (2005)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    8. Vigilin contains a functional nuclear localisation sequence and is present in both the cytoplasm and the nucleus. (PubMed id 8605996)1, 2 Kugler S....Kruse C. (1996)
    9. Localization of the gene for high-density lipoprotein binding protein (HDLBP) to human chromosome 2q37. (PubMed id 8390966)1, 3 Xia Y.R....Lusis A.J. (1993)
    10. High-density lipoprotein-binding protein (HBP)/vigilin is expressed in human atherosclerotic lesions and colocalizes with apolipoprotein E. (PubMed id 9409201)1, 9 Chiu D.S....O'Brien K.D. (1997)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
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    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: 3069 HGNC: 4857 AceView: HDLBP Ensembl:ENSG00000115677 euGenes: HUgn3069
    ECgene: HDLBP H-InvDB: HDLBP

    (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
    NameDescription
    PharmGKB entry for HDLBP Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HDLBP gene:
    Search GeneIP for patents involving HDLBP

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



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