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VPREB1 Gene

protein-coding   GIFtS: 60
GCID: GC22P022600

Pre-B Lymphocyte 1

  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)
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Aliases
Pre-B Lymphocyte 11 2     IGVPB2
VPREB2 3 5     Immunoglobulin Iota Chain2
V(Pre)B Protein2 3     CD179a Antigen3
CD179 Antigen-Like Family Member A2 3     Protein VPreB13
IGI2 5     VpreB Protein3
CD179a2     

External Ids:    HGNC: 127091   Entrez Gene: 74412   Ensembl: ENSG000001695757   OMIM: 6051415   UniProtKB: P120183   

Export aliases for VPREB1 gene to outside databases

Previous GC identifers: GC22P019297 GC22P020923 GC22P005557


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for VPREB1 Gene:
The protein encoded by this gene belongs to the immunoglobulin superfamily and is expressed selectively at the
early stages of B cell development, namely, in proB and early preB cells. This gene encodes the iota polypeptide
chain that is associated with the Ig-mu chain to form a molecular complex which is expressed on the surface of
pre-B cells. The complex is thought to regulate Ig gene rearrangements in the early steps of B-cell
differentiation. (provided by RefSeq, Oct 2008)

GeneCards Summary for VPREB1 Gene:
VPREB1 (pre-B lymphocyte 1) is a protein-coding gene. Diseases associated with VPREB1 include conidiobolomycosis, and common variable immunodeficiency. GO annotations related to this gene include antigen binding. An important paralog of this gene is IGLV5-37.

UniProtKB/Swiss-Prot: VPREB_HUMAN, P12018
Function: Associates with the Ig-mu chain to form a molecular complex that is expressed on the surface of
pre-B-cells. This complex presumably regulates Ig gene rearrangements in the early steps of B-cell
differentiation

Gene Wiki entry for VPREB1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000022.11  NC_018933.2  NT_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the VPREB1 gene promoter:
         HOXA9   HOXA9B   STAT1   MIF-1   Meis-1b   RORalpha1   HEN1   FAC1   Zic3   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVPREB1 promoter sequence
   Search Chromatin IP Primers for VPREB1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat VPREB1


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

Entrez Gene cytogenetic band: 22q11.22   Ensembl cytogenetic band:  22q11.22   HGNC cytogenetic band: 22q11.2

VPREB1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VPREB1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P022600:  view genomic region     (about GC identifiers)

Start:
22,599,087 bp from pter      End:
22,599,927 bp from pter
Size:
841 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: VPREB_HUMAN, P12018 (See protein sequence)
Recommended Name: Immunoglobulin iota chain precursor  
Size: 145 amino acids; 16605 Da
Subunit: Associates non-covalently with IGLL1
3 PDB 3D structures from and Proteopedia for VPREB1:
2H32 (3D)        2H3N (3D)        3BJ9 (3D)    
Secondary accessions: B5MCG2

Explore the universe of human proteins at neXtProt for VPREB1: NX_P12018

Explore proteomics data for VPREB1 at MOPED


See VPREB1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_009059.1  
ENSEMBL proteins: 
 ENSP00000385361   ENSP00000304590  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
CD: CD molecules
VSET: Immunoglobulin superfamily / V-set domain containing

4 InterPro protein domains:
 IPR003596 Ig_V-set_subgr
 IPR013783 Ig-like_fold
 IPR013106 Ig_V-set
 IPR007110 Ig-like_dom

Graphical View of Domain Structure for InterPro Entry P12018

ProtoNet protein and cluster: P12018

2 Blocks protein domains:
IPB003596 Immunoglobulin V-type
IPB013106 Immunoglobulin V-set


UniProtKB/Swiss-Prot: VPREB_HUMAN, P12018
Similarity: Belongs to the immunoglobulin superfamily
Similarity: Contains 1 Ig-like V-type (immunoglobulin-like) domain


VPREB1 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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: VPREB_HUMAN, P12018
Function: Associates with the Ig-mu chain to form a molecular complex that is expressed on the surface of
pre-B-cells. This complex presumably regulates Ig gene rearrangements in the early steps of B-cell
differentiation

     Genatlas biochemistry entry for VPREB1:
immunoglobulin-like V gene,expressed in pre-B cells

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003823antigen binding ----
GO:0005515protein binding ----
     
VPREB1 for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for VPREB1:
 Decreased Salmonella enterica  

     2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Vpreb1):
 hematopoietic system  immune system 

VPREB1 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for VPREB1: Vpreb1tm1Shim Vpreb1tm1Ilm

   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for VPREB1
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   genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for VPREB1

miRNA
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miRTarBase miRNAs that target VPREB1:
hsa-mir-26b-5p (MIRT030217)

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
plasma membrane2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region ----

VPREB1 for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VPREB1
Interactions:

    GeneGlobe Interaction Network for VPREB1

STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

Selected Interacting proteins for VPREB1 (P120182, 3 ENSP000003853614) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
InteractantInteraction Details
GeneCardExternal ID(s)
ABL1P005192, 3, ENSP000003614234MINT-8110863 I2D: score=3 STRING: ENSP00000361423
LGALS1P093823, ENSP000002159094I2D: score=1 STRING: ENSP00000215909
VPREB3Q9UKI33, ENSP000002489484I2D: score=1 STRING: ENSP00000248948
IGHMP018713I2D: score=1 
IGLL1ENSP000003293124STRING: ENSP00000329312
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006955immune response ----

VPREB1 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for VPREB1 (VPREB)

1 Novoseek inferred chemical compound relationship for VPREB1 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
probenecid 69.1 3 8833898 (1), 11187899 (1), 9232432 (1)



VPREB1 for compounds           About GeneDecksing



(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for VPREB1 gene: 
NM_007128.2  

Unigene Cluster for VPREB1:

Pre-B lymphocyte 1
Hs.247979  [show with all ESTs]
Unigene Representative Sequence: BU180896
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000403807(uc002zvx.1) ENST00000302273
miRNA
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Primer
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  QuantiTect SYBR Green Assays in human, mouse, rat VPREB1
  QuantiFast Probe-based Assays in human, mouse, rat VPREB1

Additional mRNA sequence: 

BC017922.1 CR456609.1 

3 DOTS entries:

DT.91716305  DT.120678050  DT.91716303 

3 AceView cDNA sequences:

NM_007128 CR456609 BC017922 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for VPREB1    About this scheme

ExUns: 1a · 1b ^ 2a · 2b
SP1:              -         
SP2:                        


ECgene alternative splicing isoforms for VPREB1

(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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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VPREB1 expression in normal human tissues (normalized intensities)      VPREB1 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAAGAGGGTG
VPREB1 Expression
About this image


VPREB1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Limb (Muscoskeletal System)
         Mesenchymal Condensate Cells Zeugopod
 
 Bone (Muscoskeletal System)
         Mesenchymal Condensate Cells Zeugopod
 
 Cartilage (Muscoskeletal System)
         Mesenchymal Condensate Cells Zeugopod
VPREB1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

VPREB1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.247979

UniProtKB/Swiss-Prot: VPREB_HUMAN, P12018
Tissue specificity: Only expressed by pre-B-cells

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In Situ
Assay Products:
 

 
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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)
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This gene was present in the common ancestor of chordates.

Orthologs for VPREB1 gene from Selected species (see all 5)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Vpreb15
Vpreb21
pre-B lymphocyte gene 15
pre-B lymphocyte gene 21
83.75(n)1
77.69(a)1
  16 (10.46 cM)5
223631  NM_016983.11  NP_058679.11 
 168684025 
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
28(a)
1 → many
GL343282.1(564790-565724)


ENSEMBL Gene Tree for VPREB1 (if available)
TreeFam Gene Tree for VPREB1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for VPREB1 gene
IGLV5-372  VPREB32  IGLV11-552  IGLV5-482  IGLV9-492  IGLV4-32  IGLV5-522  IGLV5-452  
IGLV4-602  IGLV4-692  
Selected SIMAP similar genes for VPREB1 using alignment to 2 protein entries:     VPREB_HUMAN (see all proteins) (see all similar genes):
IGLV4-3    IGLV5-37    IGLV5-45    IGLV11-55    V4-4    IGLV4-60
V4-3    BV05S1J2.2    IGLV4-69    VLC8    BV05S1J2.1    IGLV1-40
V5-2    V1-18    VKA17    V1    VL3L    IGKV1-5

VPREB1 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for VPREB1 (see all 129)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs115744541,2
C,F--5555696(+) TGAAAC/GAAAGT 1 -- us2k16Minor allele frequency- G:0.09NA EA 418
rs57507981,2
C--5555731(+) GAGGGC/GTGGGC 1 -- us2k17Minor allele frequency- G:0.39NA WA EA 404
rs791068621,2
C,F--5555758(+) TATAAT/CTGTAA 1 -- us2k11Minor allele frequency- C:0.04EA 120
rs60015511,2
C,F,A--5555770(+) AGCAAA/GTAGAA 1 -- us2k111Minor allele frequency- G:0.29NA WA CSA EA 409
rs1502658211,2
--5555791(+) TCTCTC/GAGCTT 1 -- us2k10--------
rs57507991,2
C,F,A--5555846(+) CAGGGA/GCTGCA 1 -- us2k113Minor allele frequency- G:0.33NA WA CSA EA 414
rs1922176191,2
--5555964(+) ACACAC/TGAATG 1 -- us2k10--------
rs115744551,2
C,F,H--5555971(+) AATGAG/ACTACT 1 -- us2k15Minor allele frequency- A:0.00NA NS EA 454
rs792264941,2
F--5555996(+) ATGAAT/CGAATG 1 -- us2k11Minor allele frequency- C:0.02WA 118
rs115744561,2
C,F--5556036(+) GGAGTT/CAGCAA 1 -- us2k12Minor allele frequency- C:0.10NA 160

HapMap Linkage Disequilibrium report for VPREB1 (22599087 - 22599927 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for VPREB1 (see all 19):    About this table    
Variant IDTypeSubtypePubMed ID
dgv22e196CNV Deletion17116639
esv2422480CNV Deletion17116639
esv2670821CNV Deletion23128226
esv2544553CNV Deletion19546169
nsv433331CNV Loss18776910
dgv37n64CNV Loss17921354
nsv834147CNV Loss17160897
nsv817937CNV Loss17921354
nsv469749CNV Loss16826518
dgv548n27CNV Loss19166990

Human Gene Mutation Database (HGMD): VPREB1
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing VPREB1
DNA2.0 Custom Variant and Variant Library Synthesis for VPREB1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 605141    OMIM disorders: --

10 diseases for VPREB1:    About MalaCards
conidiobolomycosis    common variable immunodeficiency    crouzon syndrome    agammaglobulinemia
lymphoblastic leukemia    hepatitis b    rheumatoid arthritis    arthritis
leukemia    hepatitis

1 disease from the University of Copenhagen DISEASES database for VPREB1:
Conidiobolomycosis

VPREB1 for disorders           About GeneDecksing

3 Novoseek inferred disease relationships for VPREB1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
common variable immunodeficiency 57.2 3 8031574 (2), 7710759 (1)
lymphoblastic leukemia acute 27 1 1884024 (1)
leukemia 24.3 2 1884024 (2)

Genetic Association Database (GAD): VPREB1
Human Genome Epidemiology (HuGE) Navigator: VPREB1 (2 documents)

Export disorders for VPREB1 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)
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PubMed articles for VPREB1 gene, integrated from 10 sources (see all 45):
(articles sorted by number of sources associating them with VPREB1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The human pre-B cell receptor: structural constraints for a tentative model of the pseudo-light (psi L) chain. (PubMed id 7935499)1, 2, 9 Guelpa-Fonlupt V....Schiff C. (Mol. Immunol. 1994)
  2. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
  3. One-megabase sequence analysis of the human immunoglobulin lambda gene locus. (PubMed id 9074928)1, 2 Kawasaki K.... Shimizu N. (Genome Res. 1997)
  4. The human Vpre B gene is located on chromosome 22 near a cluster of V lambda gene segments. (PubMed id 3139558)1, 3 Bauer S.R....Melchers F. (Immunogenetics 1988)
  5. Structure and pre-B lymphocyte restricted expression of the VpreB in humans and conservation of its structure in other mammalian species. (PubMed id 3258819)1, 2 Bauer S.R.... Melchers F. (EMBO J. 1988)
  6. The products of pre-B cell-specific genes (lambda 5 and VpreB) and the immunoglobulin mu chain form a complex that is transported onto the cell surface. (PubMed id 2117639)1, 9 Tsubata T. and Reth M. (J. Exp. Med. 1990)
  7. Engineering and characterization of a single chain surrogate light chain variable domain. (PubMed id 18287279)2, 9 Morstadt L.... Baleja J.D. (Protein Sci. 2008)
  8. Secretion of soluble pre-B cell receptors by pre-B cells. (PubMed id 9058786)1, 9 Bornemann K.D....Corley R.B. (J. Immunol. 1997)
  9. VPREB1 deletions occur independent of lambda light chain rearrangement in childhood acute lymphoblastic leukemia. (PubMed id 23881307)1 Mangum D.S....Schiffman J.D. (Leukemia 2014)
  10. Genome-wide association study of chronic periodontitis in a general German population. (PubMed id 24024966)1 Teumer A....Kocher T. (J. Clin. Periodontol. 2013)

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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 7441 HGNC: 12709 AceView: VPREB1 Ensembl:ENSG00000169575 euGenes: HUgn7441
ECgene: VPREB1 H-InvDB: VPREB1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for VPREB1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for VPREB1 Genetics and Cytogenetics in Oncology and Haematology
IMGT entry for VPREB The international ImMunoGeneTics information system® specializing in Immunoglobulins (IG), T cell receptors (TR), Major Histocompatibility Complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrate species.
Wikipedia http://en.wikipedia.org/wiki/VPREB1

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