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Aliases for HDLBP Gene

Aliases for HDLBP Gene

  • High Density Lipoprotein Binding Protein 2 3 5
  • HDL-Binding Protein 3 4
  • Vigilin 2 3
  • HBP 3 4
  • VGL 3 4
  • High Density Lipoprotein-Binding Protein 4
  • PRO2900 3

External Ids for HDLBP Gene

Previous HGNC Symbols for HDLBP Gene

  • VGL

Previous GeneCards Identifiers for HDLBP Gene

  • GC02P239181
  • GC02P240038
  • GC02M242188
  • GC02M242489
  • GC02M242488
  • GC02M241888
  • GC02M233922
  • GC02M242166

Summaries for HDLBP Gene

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. [provided by RefSeq, Mar 2016]

GeneCards Summary for HDLBP Gene

HDLBP (High Density Lipoprotein Binding Protein) is a Protein Coding gene. Among its related pathways are Lipoprotein metabolism and Metabolism. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is BICC1.

UniProtKB/Swiss-Prot for HDLBP Gene

  • 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HDLBP Gene

Genomics for HDLBP Gene

Regulatory Elements for HDLBP Gene

Enhancers for HDLBP Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G241372 1.1 ENCODE dbSUPER 32.3 -57.0 -56996 3.9 PKNOX1 TBL1XR1 KLF17 BMI1 NFXL1 RAD21 SCRT2 FOS RCOR1 ETV6 HDLBP ANO7 SEPT2 STK25 PASK PPP1R7 ENSG00000234793 D2HGDH LOC105373973 GC02P241444
GH02G241223 1.2 Ensembl ENCODE 27.5 +92.7 92689 2.0 FOXA2 DMAP1 DNMT3B THRB ZNF48 RAD21 PCBP1 FOS MIXL1 EGR2 HDLBP ANO7 FARP2 SEPT2 GC02M241212 GC02M241259
GH02G241313 1.4 ENCODE dbSUPER 22.2 +1.0 1008 4.9 CREB3L1 ZFP64 FEZF1 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC SSRP1 SEPT2 HDLBP FARP2 ANO7 LINC01238 LINC01237 ENSG00000235351
GH02G241308 1.3 Ensembl ENCODE dbSUPER 21.9 +7.2 7216 2.3 HDGF TBP CTCF PKNOX1 MXI1 TBL1XR1 FEZF1 EBF1 ZNF366 POLR2A HDLBP SEPT2 FARP2 ANO7 LOC101927509
GH02G241354 1.3 ENCODE dbSUPER 21.5 -40.3 -40309 6.0 HDGF PKNOX1 WRNIP1 ARID4B SIN3A DMAP1 ZNF143 PAF1 ZNF263 SP3 SEPT2 HDLBP FARP2 ANO7 LOC105373973
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HDLBP on UCSC Golden Path with GeneCards custom track

Promoters for HDLBP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000133263 1161 3401 CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC SSRP1 ZNF610

Genomic Location for HDLBP Gene

Chromosome:
2
Start:
241,227,264 bp from pter
End:
241,317,061 bp from pter
Size:
89,798 bases
Orientation:
Minus strand

Genomic View for HDLBP Gene

Genes around HDLBP on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HDLBP Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HDLBP Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HDLBP Gene

Proteins for HDLBP Gene

  • Protein details for HDLBP Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q00341-VIGLN_HUMAN
    Recommended name:
    Vigilin
    Protein Accession:
    Q00341
    Secondary Accessions:
    • B4DTQ2
    • E7EM71
    • Q53QU2
    • Q9UCY3

    Protein attributes for HDLBP Gene

    Size:
    1268 amino acids
    Molecular mass:
    141456 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for HDLBP Gene

    Alternative splice isoforms for HDLBP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HDLBP Gene

Post-translational modifications for HDLBP Gene

  • Ubiquitination at posLast=231231
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HDLBP Gene

Domains & Families for HDLBP Gene

Protein Domains for HDLBP Gene

Suggested Antigen Peptide Sequences for HDLBP Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HDLBP: view

No data available for Gene Families and UniProtKB/Swiss-Prot for HDLBP Gene

Function for HDLBP Gene

Molecular function for HDLBP Gene

GENATLAS Biochemistry:
vigilin,high density lipoprotein binding protein
UniProtKB/Swiss-Prot Function:
Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

Gene Ontology (GO) - Molecular Function for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 24725430
GO:0008289 lipid binding TAS 1318310
GO:0045296 cadherin binding IDA 25468996
genes like me logo Genes that share ontologies with HDLBP: view
genes like me logo Genes that share phenotypes with HDLBP: view

Animal Model Products

miRNA for HDLBP Gene

miRTarBase miRNAs that target HDLBP

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for HDLBP Gene

Localization for HDLBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for HDLBP Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HDLBP gene
Compartment Confidence
plasma membrane 5
cytosol 5
extracellular 4
nucleus 4
cytoskeleton 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane TAS --
GO:0034364 high-density lipoprotein particle IEA --
genes like me logo Genes that share ontologies with HDLBP: view

Pathways & Interactions for HDLBP Gene

genes like me logo Genes that share pathways with HDLBP: view

Gene Ontology (GO) - Biological Process for HDLBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0006810 transport IEA --
GO:0006869 lipid transport IEA --
GO:0008202 steroid metabolic process IEA --
GO:0008203 cholesterol metabolic process IEA,TAS --
genes like me logo Genes that share ontologies with HDLBP: view

No data available for SIGNOR curated interactions for HDLBP Gene

Drugs & Compounds for HDLBP Gene

(2) Drugs for HDLBP Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for HDLBP Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HDLBP: view

Transcripts for HDLBP Gene

Unigene Clusters for HDLBP Gene

High density lipoprotein binding protein:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HDLBP Gene

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: - - - - - - - - -
SP6:
SP7: - - - - - - -
SP8:
SP9:
SP10: - - - - - - - - - - - - - - - - - - - - -
SP11: - - - - - - -
SP12: - - - -
SP13: - - - - -
SP14: - - - - - - - - - - - - -
SP15:
SP16: - - - - - - - - - - - - -
SP17:
SP18:
SP19:
SP20: - - -
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:

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:
SP6:
SP7:
SP8: - -
SP9: - - -
SP10: -
SP11:
SP12:
SP13:
SP14:
SP15: - - -
SP16:
SP17:
SP18: - -
SP19:
SP20:
SP21:
SP22: - -
SP23:
SP24:
SP25:
SP26:

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:
SP6: - -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18: - - - -
SP19: -
SP20:
SP21:
SP22:
SP23: -
SP24:
SP25:
SP26:

Relevant External Links for HDLBP Gene

GeneLoc Exon Structure for
HDLBP
ECgene alternative splicing isoforms for
HDLBP

Expression for HDLBP Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HDLBP Gene

Protein differential expression in normal tissues from HIPED for HDLBP Gene

This gene is overexpressed in Bone marrow stromal cell (15.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HDLBP Gene



Protein tissue co-expression partners for HDLBP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HDLBP Gene:

HDLBP

SOURCE GeneReport for Unigene cluster for HDLBP Gene:

Hs.471851

Evidence on tissue expression from TISSUES for HDLBP Gene

  • Liver(4.9)
  • Nervous system(4.9)
  • Muscle(4.8)
  • Lung(4.7)
  • Skin(4.6)
  • Intestine(4.5)
  • Pancreas(4.5)
  • Eye(4.3)
  • Kidney(4.3)
  • Stomach(4)
  • Heart(3.1)
  • Adrenal gland(2.4)
  • Spleen(2.3)
  • Blood(2.2)
  • Bone(2.2)
  • Thyroid gland(2.1)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with HDLBP: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HDLBP Gene

Orthologs for HDLBP Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for HDLBP Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HDLBP 34 35
  • 99.58 (n)
oppossum
(Monodelphis domestica)
Mammalia HDLBP 35
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HDLBP 34 35
  • 90.06 (n)
mouse
(Mus musculus)
Mammalia Hdlbp 34 16 35
  • 89.67 (n)
rat
(Rattus norvegicus)
Mammalia Hdlbp 34
  • 89.46 (n)
cow
(Bos Taurus)
Mammalia HDLBP 34 35
  • 88.41 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HDLBP 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves HDLBP 34 35
  • 79.77 (n)
lizard
(Anolis carolinensis)
Reptilia HDLBP 35
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hdlbp 34
  • 74.93 (n)
African clawed frog
(Xenopus laevis)
Amphibia hdlbp-prov 34
zebrafish
(Danio rerio)
Actinopterygii hdlbpa 34 35
  • 74.17 (n)
hdlbp 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10616 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005467 34
  • 56.62 (n)
fruit fly
(Drosophila melanogaster)
Insecta Dp1 36 34 35
  • 54.86 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_C08H9.2 34
  • 49.22 (n)
C08H9.2 36 35
  • 38 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SCP160 35 37
  • 4 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4516 35
  • 48 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4245 34
Species where no ortholog for HDLBP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for HDLBP Gene

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

Paralogs for HDLBP Gene

Variants for HDLBP Gene

Sequence variations from dbSNP and Humsavar for HDLBP Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
VAR_036052 A breast cancer sample
VAR_036053 A breast cancer sample
rs1000012733 -- 241,260,276(+) GCTAG(A/G)ATTAT intron-variant
rs1000089054 -- 241,293,598(+) CAGAG(C/T)GAGAC intron-variant
rs1000099145 -- 241,293,999(+) AAGCA(A/G)TTGAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HDLBP Gene

Variant ID Type Subtype PubMed ID
esv2675219 CNV deletion 23128226
esv3594822 CNV loss 21293372
esv3594823 CNV gain 21293372
esv3594825 CNV gain 21293372
nsv1118901 CNV deletion 24896259
nsv215143 CNV deletion 16902084
nsv3242 CNV insertion 18451855
nsv470532 CNV loss 18288195
nsv508900 CNV insertion 20534489
nsv524008 CNV gain 19592680
nsv584955 CNV loss 21841781
nsv584956 CNV loss 21841781
nsv584957 CNV loss 21841781

Variation tolerance for HDLBP Gene

Residual Variation Intolerance Score: 3.57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.43; 42.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HDLBP Gene

Human Gene Mutation Database (HGMD)
HDLBP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HDLBP

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HDLBP Gene

Disorders for HDLBP Gene

Relevant External Links for HDLBP

Genetic Association Database (GAD)
HDLBP
Human Genome Epidemiology (HuGE) Navigator
HDLBP
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HDLBP

No disorders were found for HDLBP Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HDLBP Gene

Publications for HDLBP Gene

  1. Cloning and expression of a cellular high density lipoprotein-binding protein that is up-regulated by cholesterol loading of cells. (PMID: 1318310) McKnight G.L. … Oram J.F. (J. Biol. Chem. 1992) 2 3 4 22 64
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64
  3. Follow-up of potential novel Graves' disease susceptibility loci, identified in the UK WTCCC genome-wide nonsynonymous SNP study. (PMID: 20442750) Newby P.R. … Gough S.C. (Eur. J. Hum. Genet. 2010) 3 46 64
  4. [VIGILIN involves in regulation of imprinting gene IGF2 and H19 in human hepatocellular carcinoma cell]. (PMID: 19950580) Ge Y.J. … Qin Y. (Sichuan Da Xue Xue Bao Yi Xue Ban 2009) 3 22 64
  5. Candidate genetic analysis of plasma high-density lipoprotein-cholesterol and severity of coronary atherosclerosis. (PMID: 19878569) Chen S.N. … Marian A.J. (BMC Med. Genet. 2009) 3 46 64

Products for HDLBP Gene

Sources for HDLBP Gene

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