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

RAG2 Gene

protein-coding   GIFtS: 59
GCID: GC11M036613

Recombination Activating Gene 2

Pneumococci & Pneumococcal Diseases Congress
  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
Recombination Activating Gene 21 2
RAG-22 3
V(D)J Recombination-Activating Protein 22

External Ids:    HGNC: 98321   Entrez Gene: 58972   Ensembl: ENSG000001750977   OMIM: 1796165   UniProtKB: P558953   

Export aliases for RAG2 gene to outside databases

Previous GC identifers: GC11M038170 GC11M037290 GC11M036652 GC11M036577 GC11M036570 GC11M036316


(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 RAG2 Gene:
This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell
development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and
this complex can form double-strand breaks by cleaving DNA at conserved recombination signal sequences. The
recombination activating gene 1 component is thought to contain most of the catalytic activity, while the
N-terminal of the recombination activating gene 2 component is thought to form a six-bladed propeller in the
active core that serves as a binding scaffold for the tight association of the complex with DNA. A C-terminal
plant homeodomain finger-like motif in this protein is necessary for interactions with chromatin components,
specifically with histone H3 that is trimethylated at lysine 4. Mutations in this gene cause Omenn syndrome, a
form of severe combined immunodeficiency associated with autoimmune-like symptoms. (provided by RefSeq, Jul 2008)

GeneCards Summary for RAG2 Gene: 
RAG2 (recombination activating gene 2) is a protein-coding gene. Diseases associated with RAG2 include omenn syndrome, and t lymphocyte deficiency. GO annotations related to this gene include chromatin binding and methylated histone residue binding.

UniProtKB/Swiss-Prot: RAG2_HUMAN, P55895
Function: Core component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during
V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor
genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D
(diversity), and J (joining) gene segments. DNA cleavage by the RAG complex occurs in 2 steps: a first nick is
introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack
the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA
ends: 2 hairpin coding ends and 2 blunt, 5'-phosphorylated ends. The chromatin structure plays an essential role
in the V(D)J recombination reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates
both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a
process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific
recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA
breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to
pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second
allele. In the RAG complex, RAG2 is not the catalytic component but is required for all known catalytic
activities mediated by RAG1. It probably acts as a sensor of chromatin state that recruits the RAG complex to
H3K4me3 (By similarity)




(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_000011.9  NC_018922.2  NT_009237.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RAG2 gene promoter:
         AP-1   SREBP-1c   ATF-2   Nkx2-5   NF-kappaB   SREBP-1b   SREBP-1a   STAT3   c-Jun   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRAG2 promoter sequence
   Search SABiosciences Chromatin IP Primers for RAG2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAG2


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

Entrez Gene cytogenetic band: 11p13   Ensembl cytogenetic band:  11p12   HGNC cytogenetic band: 11p13

RAG2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RAG2 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M036613:  view genomic region     (about GC identifiers)

Start:
36,597,124 bp from pter      End:
36,619,829 bp from pter
Size:
22,706 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: RAG2_HUMAN, P55895 (See protein sequence)
Recommended Name: V(D)J recombination-activating protein 2  
Size: 527 amino acids; 59241 Da
Subunit: Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or
HMGB2 (By similarity)
Subcellular location: Nucleus (By similarity)
Secondary accessions: A8K9E9 Q8TBL4

Explore the universe of human proteins at neXtProt for RAG2: NX_P55895

Explore proteomics data for RAG2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P55895

  • RAG2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RAG2 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_000527.2  NP_001230714.1  NP_001230715.1  

    ENSEMBL proteins: 
     ENSP00000308620   ENSP00000436327   ENSP00000436895   ENSP00000432174  

    Human Recombinant Protein Products for RAG2: 
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    OriGene Protein Over-expression Lysate for RAG2
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    Novus Biologicals RAG2 Proteins
    Novus Biologicals RAG2 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for RAG2 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS--

    RAG2 for ontologies           About GeneDecksing



    RAG2 Antibody Products: 
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    ThermoFisher Antibody for RAG2
    LSBio Antibodies in human, mouse, rat for RAG2 

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    Cloud-Clone Corp. ELISAs for RAG2 
    Cloud-Clone Corp. CLIAs for RAG2


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    4 InterPro protein domains:
     IPR011043 Gal_Oxase/kelch_b-propeller
     IPR004321 RAG2
     IPR025162 RAG2_PHD
     IPR015915 Kelch-typ_b-propeller

    Graphical View of Domain Structure for InterPro Entry P55895

    ProtoNet protein and cluster: P55895

    1 Blocks protein domain: IPB004321 V-D-J recombination activating protein 2 (RAG2)

    UniProtKB/Swiss-Prot: RAG2_HUMAN, P55895
    Domain: The atypical PHD-type zinc finger recognizes and binds histone H3 trimethylated on 'Lys-4' (H3K4me3). The
    presence Tyr-445 instead of a carboxylate in classical PHD-type zinc fingers results in an enhanced binding to
    H3K4me3 in presence of dimethylated on 'Arg-2' (H3R2me2) rather than inhibited. The atypical PHD-type zinc finger
    also binds various phosphoinositides, such as phosphatidylinositol 3,4-bisphosphate binding (PtdIns(3,4)P2),
    phosphatidylinositol 3,5-bisphosphate binding (PtdIns(3,5)P2), phosphatidylinositol 4,5-bisphosphate
    (PtdIns(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate binding (PtdIns(3,4,5)P3) (By similarity)
    Similarity: Belongs to the RAG2 family
    Similarity: Contains 1 PHD-type zinc finger


    RAG2 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: RAG2_HUMAN, P55895
    Function: Core component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during
    V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor
    genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D
    (diversity), and J (joining) gene segments. DNA cleavage by the RAG complex occurs in 2 steps: a first nick is
    introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack
    the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA
    ends: 2 hairpin coding ends and 2 blunt, 5'-phosphorylated ends. The chromatin structure plays an essential role
    in the V(D)J recombination reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates
    both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a
    process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific
    recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA
    breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to
    pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second
    allele. In the RAG complex, RAG2 is not the catalytic component but is required for all known catalytic
    activities mediated by RAG1. It probably acts as a sensor of chromatin state that recruits the RAG complex to
    H3K4me3 (By similarity)

         Genatlas biochemistry entry for RAG2:
    recombination V(D)J activating gene 2,acting,in conjunction with RAG1,at a pair of recombination signal sequences
    and making double strand breaks,next to these signals,located 8kb apart from RAG1,convergently oriented

         Gene Ontology (GO): 5/11 molecular function terms (GO ID links to tree view) (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS--
    GO:0003682chromatin binding ISS--
    GO:0004519endonuclease activity NAS--
    GO:0005515protein binding ----
    GO:0005546phosphatidylinositol-4,5-bisphosphate binding ISS--
         
    RAG2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for RAG2:
     Synthetic lethal with Ras 

         15/19 MGI mutant phenotypes (inferred from 13 alleles(MGI details for Rag2) (see all 19):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     endocrine/exocrine gland  growth/size  hematopoietic system  homeostasis/metabolism  immune system 
     integument  liver/biliary system  mortality/aging  nervous system  normal 

    RAG2 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for RAG2: Rag2tm1Libo Rag2tm1.1Cgn Rag2tm1Fwa Rag2tm1.1Flv

       inGenious Targeting Laboratory - Custom generated mouse model solutions for RAG2 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for RAG2

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RAG2 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RAG2 

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat RAG2
    3 QIAGEN miScript miRNA Assays for microRNAs that regulate RAG2:
    hsa-miR-1206 hsa-miR-507 hsa-miR-450b-5p
    SwitchGear 3'UTR luciferase reporter plasmidRAG2 3' UTR sequence
    Inhib. RNA
    Products:
        
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    Gene Editing
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    Clone
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                         Customized lentivirus expression plasmids for stable overexpression of RAG2 

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAG2


    (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

    SuperPaths for RAG2 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1C-MYB transcription factor network
    C-MYB transcription factor network
    2Primary immunodeficiency
    Primary immunodeficiency

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for RAG2
        C-MYB transcription factor network


    1         Kegg Pathway  (Kegg details for RAG2):
        Primary immunodeficiency


    RAG2 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for RAG2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    5/13 Interacting proteins for RAG2 (P558953 ENSP000003086204) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RAG1P159183, ENSP000002994404I2D: score=3 STRING: ENSP00000299440
    SKP2Q133093, ENSP000002742554I2D: score=2 STRING: ENSP00000274255
    IPO5O004103, ENSP000002615744I2D: score=1 STRING: ENSP00000261574
    KPNA1P522943, ENSP000003437014I2D: score=1 STRING: ENSP00000343701
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 5/12 biological process terms (GO ID links to tree view) (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002326B cell lineage commitment IEA--
    GO:0002331pre-B cell allelic exclusion ISS--
    GO:0002358B cell homeostatic proliferation IEA--
    GO:0002360T cell lineage commitment IEA--
    GO:0006310DNA recombination ----

    RAG2 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

    RAG2 for compounds           About GeneDecksing

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

    Browse Tocris compounds for RAG2

    6 Novoseek inferred chemical compound relationships for RAG2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cytidine 41.5 4 16504994 (1), 15135294 (1), 17174398 (1), 17475920 (1)
    probenecid 14.8 2 8833898 (1), 9232432 (1)
    zinc 0 2 10820261 (1), 15094381 (1)
    serine 0 2 8493533 (1)
    caffeine 0 1 10681585 (1)
    dmso 0 1 11215815 (1)

    Search CenterWatch for drugs/clinical trials and news about RAG2

    (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 RAG2 gene (3 alternative transcripts): 
    NM_000536.3  NM_001243785.1  NM_001243786.1  

    Unigene Cluster for RAG2:

    Recombination activating gene 2
    Hs.714519  [show with all ESTs]
    Unigene Representative Sequence: NM_001243786
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000524423 ENST00000311485(uc021qgc.1 uc021qgd.1 uc001mwv.4)
    ENST00000529083 ENST00000527033 ENST00000532616 ENST00000534379 ENST00000528428
    ENST00000530276

    miRNA
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    3 QIAGEN miScript miRNA Assays for microRNAs that regulate RAG2:
    hsa-miR-1206 hsa-miR-507 hsa-miR-450b-5p
    SwitchGear 3'UTR luciferase reporter plasmidRAG2 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RAG2

    Additional mRNA sequence: 

    AF080577.1 AK292664.1 BC022397.1 S78372.1 

    6 DOTS entries:

    DT.75178642  DT.91970703  DT.91660697  DT.120734403  DT.100783792  DT.120734378 

    17 AceView cDNA sequences:

    BM463455 BG389099 S78372 BG503568 BQ421024 AW629088 BE247400 BM457214 
    BC022397 AF080577 BE247239 BG612991 NM_000536 T25429 AW058148 T25437 
    BG387433 

    GeneLoc Exon Structure


    (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

    RAG2 expression in normal human tissues (normalized intensities)      RAG2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGATGGGCA
    RAG2 Expression
    About this image


    RAG2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Blood (Hematopoietic System)    fully expand to see all 4 entries
             Pro B-Cells Hematopoietic Bone Marrow
     
     Thymus (Hematopoietic System)    fully expand to see all 2 entries
             Double Negative 3 Thymocytes Thymus
     
     Testis (Reproductive System)

    See RAG2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RAG2

    SOURCE GeneReport for Unigene cluster: Hs.714519

    UniProtKB/Swiss-Prot: RAG2_HUMAN, P55895
    Tissue specificity: Cells of the B- and T-lymphocyte lineages

        SABiosciences Custom PCR Arrays for RAG2
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RAG2
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAG2

    (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 chordates.

    Orthologs for RAG2 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rag21 , 5 recombination activating gene 21, 5 87.54(n)1
    88.43(a)1
      2 (53.87 cM)5
    193741  NM_009020.31  NP_033046.11 
     1016247185 
    chicken
    (Gallus gallus)
    Aves RAG21 recombination activating gene 2 72.62(n)
    72.81(a)
      423165  XM_421091.2  XP_421091.2 
    lizard
    (Anolis carolinensis)
    Reptilia RAG26
    Uncharacterized protein
    68(a)
    1 ↔ 1
    1(53505713-53507305)
    zebrafish
    (Danio rerio)
    Actinopterygii rag21 recombination activating gene 2 57.7(n)
    51.91(a)
      30658  NM_131385.2  NP_571460.2 


    ENSEMBL Gene Tree for RAG2 (if available)
    TreeFam Gene Tree for RAG2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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

    10/37 SNPs in RAG2 are shown (see all 37)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0459604
    Combined cellular and humoral immune defects with granulomas (CHIDG)4--see VAR_0459602 T N mis40--------
    VAR_0088954
    Omenn syndrome (OS)4--see VAR_0088952 C W mis40--------
    VAR_0459624
    Combined cellular and humoral immune defects with granulomas (CHIDG)4--see VAR_0459622 G A mis40--------
    VAR_0088964
    Omenn syndrome (OS)4--see VAR_0088962 M R mis40--------
    rs1219185751,2
    Cpathogenic136543313(-) GGATGC/GGCACT 6 A G mis10--------
    rs356912921,2
    C,F,Hpathogenic136544021(-) TGACAA/C/TCATCT 6 T I mis15NA NS 4806
    rs1939225731,2
    Cprobable-pathogenic136543356(-) CAACTA/GAGCTC 6 K E mis10--------
    rs1485087541,2
    Cprobable-pathogenic136544561(+) GCCAGC/GCTTTT 6 A G mis11Minor allele frequency- G:0.00NA 4546
    VAR_0459614
    ----see VAR_0459612 E G mis40--------
    VAR_0055704
    ----see VAR_0055702 R Q mis40--------

    HapMap Linkage Disequilibrium report for RAG2 (36597124 - 36619829 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RAG2:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2422305CNV Duplication17116639
    nsv832123CNV Gain17160897
    nsv467791CNV Gain19166990


    Human Gene Mutation Database (HGMD): RAG2

    Locus Specific Mutation Databases (LSDB): RAG2
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing RAG2
    DNA2.0 Custom Variant and Variant Library Synthesis for RAG2

    (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.)
    About This Section
    OMIM gene information: 179616   
    OMIM disorders: 601457  603554  233650  
    UniProtKB/Swiss-Prot: RAG2_HUMAN, P55895
  • Combined cellular and humoral immune defects with granulomas (CHIDG) [MIM:233650]: Immunodeficiency
    disease with granulomas in the skin, mucous membranes, and internal organs. Other characteristics include
    hypogammaglobulinemia, a diminished number of T and B cells, and sparse thymic tissue on ultrasonography.
    Note=The disease is caused by mutations affecting the gene represented in this entry
  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive
    (T(-)B(-)NK(+) SCID) [MIM:601457]: A form of severe combined immunodeficiency (SCID), a genetically and
    clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and
    cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent,
    persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of
    T-cell-mediated cellular immunity due to a defect in T-cell development. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Omenn syndrome (OS) [MIM:603554]: Severe immunodeficiency characterized by the presence of activated,
    anergic, oligoclonal T-cells, hypereosinophilia, and high IgE levels. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • 20/30 diseases for RAG2 (see all 30):    About MalaCards
    omenn syndrome    t lymphocyte deficiency    combined cellular and humoral immune defects with granulomas    artemis deficiency
    severe combined immune deficiency, autosomal recessive, t cell-negative, b cell-negative, nk cell-positive, rag1/rag2-related    severe combined immunodeficiency    leukopenia    was-related disorders
    lymphopenia    anaplastic large cell lymphoma    cutaneous t cell lymphoma    tonsillitis
    conjunctivitis    autoimmune thyroiditis    ataxia telangiectasia    atherosclerosis
    herpes simplex    multiple myeloma    systemic lupus erythematosus    myeloma

    3 diseases from the University of Copenhagen DISEASES database for RAG2:
    Omenn syndrome     Severe combined immunodeficiency     Inflammatory bowel disease

    RAG2 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:  
    The International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD) 9 - 13 March 2014

    10/12 Novoseek inferred disease relationships for RAG2 gene (see all 12)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    omenn syndrome 92.6 16 10226883 (2), 11313270 (1), 11908269 (1), 15025726 (1) (see all 15)
    severe combined immunodeficiency 75.6 9 15025726 (1), 15845893 (1), 20128425 (1), 14726805 (1) (see all 9)
    immunodeficiency 35.5 10 10891502 (2), 1428003 (1), 11908269 (1), 15640693 (1) (see all 9)
    leukemia 20.9 2 12393742 (1), 15611260 (1)
    leukemia t-cell 15.7 1 17059760 (1)
    lymphoma 14.6 3 7873997 (1), 11279609 (1), 16982894 (1)
    autoimmune thyroid disease 11.5 1 8077352 (1)
    hodgkin disease 10.5 1 1450411 (1)
    tumors 4.3 9 11372175 (3), 18987320 (1), 8892673 (1), 19779066 (1) (see all 6)
    cancer 1.33 5 14521728 (1), 17174398 (1), 18682256 (1), 17475920 (1) (see all 5)

    Genetic Association Database (GAD): RAG2
    Human Genome Epidemiology (HuGE) Navigator: RAG2 (7 documents)

    Export disorders for RAG2 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 RAG2 gene, integrated from 9 sources (see all 235):
    (articles sorted by number of sources associating them with RAG2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Expression of human recombination activating genes (RAG1 and RAG2) in neoplastic lymphoid cells: correlation with cell differentiation and antigen receptor expression. (PubMed id 1832998)1, 2, 9 Bories J.C.... Sigaux F. (1991)
    2. Sequence and chromosome assignment to 11p13-p12 of human RAG genes. (PubMed id 1428003)1, 2, 9 Ichihara Y.... Kurosawa Y. (1992)
    3. Mutations in genes required for T-cell development: IL7R, CD45, IL2RG, JAK3, RAG1, RAG2, ARTEMIS, and ADA and severe combined immunodeficiency: HuGE review. (PubMed id 14726805)1, 4, 9 Kalman L....Buckley R. (2004)
    4. Human RAG2, like RAG1, is on chromosome 11 band p13 a nd therefore not linked to ataxia telangiectasia complementation groups. (PubMed id 1283330)1, 3, 9 Sherrington P.D....Rabbitts T.H. (1992)
    5. Partial V(D)J recombination activity leads to Omenn syndrome. (PubMed id 9630231)1, 2, 9 Villa A....Spanopoulou E. (1998)
    6. Polymorphisms in DNA repair genes and risk of non-Hod gkin lymphoma in a pooled analysis of three studies. (PubMed id 20813000)1, 4 Shen M....Zheng T. (2010)
    7. Common single nucleotide polymorphisms in immunoregul atory genes and multiple myeloma risk among women in Connecticut. (PubMed id 20568250)1, 4 Lee K.M....Lan Q. (2010)
    8. Association between genetic variants in VEGF, ERCC3 a nd occupational benzene haematotoxicity. (PubMed id 19773279)1, 4 Hosgood H.D....Lan Q. (2009)
    9. Customised molecular diagnosis of primary immune defi ciency disorders in New Zealand: an efficient strategy for a small developed co untry. (PubMed id 19859091)1, 4 Ameratunga R. and Woon S.T. (2009)
    10. Common genetic variants in candidate genes and risk o f familial lymphoid malignancies. (PubMed id 19573080)1, 4 Liang X.S....Goldin L.R. (2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 5897 HGNC: 9832 AceView: RAG2 Ensembl:ENSG00000175097 euGenes: HUgn5897
    ECgene: RAG2 Kegg: 5897 H-InvDB: RAG2

    (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 RAG2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RAG2 Genetics and Cytogenetics in Oncology and Haematology
    RAG2basehttp://bioinf.uta.fi/RAG2base/
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/RAG2

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RAG2 gene:
    Search GeneIP for patents involving RAG2

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



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