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PRDM1 Gene

protein-coding   GIFtS: 66
GCID: GC06P106534

PR Domain Containing 1, With ZNF Domain


(Previous symbol: BLIMP1)
Microbiology & Infectious Diseases Congress
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(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
PR Domain Containing 1, With ZNF Domain1 2     PRDI-Binding Factor-12
BLIMP11 2 3 5     EC 2.1.1.-3
BLIMP-12 3     Beta-Interferon Gene Positive Regulatory Domain I-Binding Factor3
PRDI-BF12 3     Positive Regulatory Domain I-Binding Factor 13
B-Lymphocyte-Induced Maturation Protein 12     PR Domain-Containing Protein 13
Beta-Interferon Gene Positive-Regulatory Domain I Binding Factor2     PRDI-Binding Factor 13
PR Domain Zinc Finger Protein 12     

External Ids:    HGNC: 93461   Entrez Gene: 6392   Ensembl: ENSG000000576577   OMIM: 6034235   UniProtKB: O756263   

Export aliases for PRDM1 gene to outside databases

Previous GC identifers: GC06P106371 GC06P106557 GC06P106579 GC06P106640 GC06P103981


(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 PRDM1 Gene:
This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds
specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of
this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different
isoforms have been reported. (provided by RefSeq, Jul 2008)

GeneCards Summary for PRDM1 Gene:
PRDM1 (PR domain containing 1, with ZNF domain) is a protein-coding gene. Diseases associated with PRDM1 include devic disease, and plasmacytoma. GO annotations related to this gene include methyltransferase activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ZNF683.

UniProtKB/Swiss-Prot: PRDM1_HUMAN, O75626
Function: Transcriptional repressor that binds specifically to the PRDI element in the promoter of the
beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells

Gene Wiki entry for PRDM1 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_000006.12  NT_025741.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PRDM1 gene promoter:
         GR   p53   STAT3   IRF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PRDM1 promoter sequence
   Search Chromatin IP Primers for PRDM1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PRDM1


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

Entrez Gene cytogenetic band: 6q21   Ensembl cytogenetic band:  6q21   HGNC cytogenetic band: 6q21

PRDM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P106534:  view genomic region     (about GC identifiers)

Start:
106,534,195 bp from pter      End:
106,557,814 bp from pter
Size:
23,620 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: PRDM1_HUMAN, O75626 (See protein sequence)
Recommended Name: PR domain zinc finger protein 1  
Size: 825 amino acids; 91771 Da
Subunit: Interacts with PRMT5 (By similarity)
Sequence caution: Sequence=AAO45623.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
1 PDB 3D structure from and Proteopedia for PRDM1:
3DAL (3D)    
Secondary accessions: B2REA6 E1P5E0 Q86WM7
Alternative splicing: 3 isoforms:  O75626-1   O75626-2   O75626-3   

Explore the universe of human proteins at neXtProt for PRDM1: NX_O75626

Explore proteomics data for PRDM1 at MOPED

Post-translational modifications: 

  • Sumoylation at Lys-816 by PIAS1 augments transcriptional repressor activity, and is critical for plasma cell
    differentiation1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PRDM1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001189.2  NP_878911.1  

    ENSEMBL proteins: 
     ENSP00000358087   ENSP00000358092   ENSP00000395566   ENSP00000399772   ENSP00000358085  

    PRDM1 Human Recombinant Protein Products:

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    Novus Biologicals PRDM1 Lysates
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for PRDM1

    PRDM1 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of PRDM1
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    LSBio Antibodies in human, mouse, rat for PRDM1

    PRDM1 Assay Products:

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    Cloud-Clone Corp. ELISAs for PRDM1
    Cloud-Clone Corp. CLIAs for PRDM1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

    5 InterPro protein domains:
     IPR001214 SET_dom
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2
     IPR016608 Znf_PRDM1

    Graphical View of Domain Structure for InterPro Entry O75626

    ProtoNet protein and cluster: O75626

    1 Blocks protein domain: IPB007086 C2H2-type zinc finger signature

    UniProtKB/Swiss-Prot: PRDM1_HUMAN, O75626
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 4 C2H2-type zinc fingers
    Similarity: Contains 1 SET domain


    PRDM1 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: PRDM1_HUMAN, O75626
    Function: Transcriptional repressor that binds specifically to the PRDI element in the promoter of the
    beta-interferon gene. Drives the maturation of B-lymphocytes into Ig secreting cells

         Genatlas biochemistry entry for PRDM1:
    PR domain containing 1,B-lymphocyte maturation promoting transcription factor,repressing the expression of IFNB
    promoter,and the transcription by recruiting a complex of Groucho family proteins to DNA,deleted in several
    B-cell non Hodgkin lymphoma and other cancers

         Enzyme Number (IUBMB): EC 2.1.1.-1

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity TAS1851123
    GO:0005515protein binding IPI--
    GO:0008168methyltransferase activity IEA--
    GO:0042826histone deacetylase binding IEA--
    GO:0043565sequence-specific DNA binding IEA--
         
    PRDM1 for ontologies           About GeneDecksing


    Phenotypes:
         Selected MGI mutant phenotypes (inferred from 14 alleles(MGI details for Prdm1) (see all 16):
     cardiovascular system  cellular  craniofacial  embryogenesis  endocrine/exocrine gland 
     growth/size/body  hematopoietic system  homeostasis/metabolism  immune system  limbs/digits/tail 
     mortality/aging  muscle  no phenotypic analysis  normal  renal/urinary system 

    PRDM1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for PRDM1: Prdm1tm1.1Liz Prdm1tm1Rob Prdm1tm1Masu Prdm1tm2Rob Prdm1tm1.1Clme Prdm1tm2.1Liz

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PRDM1
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PRDM1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PRDM1

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  ACTTTCACTTTC 

    miRNA
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    miRTarBase miRNAs that target PRDM1:
    hsa-let-7f-5p (MIRT005514), hsa-mir-9-5p (MIRT001937), hsa-let-7a-5p (MIRT001936), hsa-mir-30a-5p (MIRT007218), hsa-mir-877-3p (MIRT037062), hsa-let-7b-5p (MIRT005513), hsa-mir-127-3p (MIRT004279), hsa-mir-125b-5p (MIRT004533)

    Block miRNA regulation of human, mouse, rat PRDM1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PRDM1 (see all 76):
    hsa-miR-548j hsa-miR-938 hsa-miR-30d hsa-miR-30a hsa-miR-548a-5p hsa-miR-200b hsa-miR-4273 hsa-miR-4324
    SwitchGear 3'UTR luciferase reporter plasmidPRDM1 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for PRDM1
    Predesigned siRNA for gene silencing in human, mouse, rat PRDM1

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    GenScript: all cDNA clones in your preferred vector (see all 2): PRDM1 (NM_182907)
    Sino Biological Human cDNA Clone for PRDM1
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PRDM1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PRDM1

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM1


    (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 UniProtKB/Swiss-Prot
    PRDM1_HUMAN, O75626: Nucleus (By similarity). Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IDA--

    PRDM1 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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    SuperPaths for PRDM1 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
    NOD pathway0.33
    2Lymphocyte Signaling
    Lymphocyte Signaling
    3Direct p53 effectors
    Direct p53 effectors

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for PRDM1
        Lymphocyte Signaling

    2 BioSystems Pathways for PRDM1
        NOD pathway
    Direct p53 effectors




    PRDM1 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PRDM1
    Interactions:

        GeneGlobe Interaction Network for PRDM1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 17)

    Selected Interacting proteins for PRDM1 (O756261, 2, 3 ENSP000003580924) via UniProtKB, MINT, STRING, and/or I2D (see all 26)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PIAS1O759251, 2, ENSP000002496364EBI-948789,EBI-629434 MINT-8397177 MINT-8397208 STRING: ENSP00000249636
    ATXN1P542532, 3, ENSP000002447694MINT-2857170 I2D: score=3 STRING: ENSP00000244769
    ENSG00000227333Q96KQ73, ENSP000003973234I2D: score=1 STRING: ENSP00000397323
    EHMT2Q96KQ73I2D: score=1 
    ENSG00000206376Q96KQ73I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0001701in utero embryonic development ----
    GO:0001892embryonic placenta development ----
    GO:0001893maternal placenta development IEA--
    GO:0006351transcription, DNA-templated IEA--

    PRDM1 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 PRDM1

    3 Novoseek inferred chemical compound relationships for PRDM1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    2-methoxyestradiol 74.2 5 17877160 (3), 18192112 (2)
    cytidine 68.3 4 17339456 (1), 16895557 (1), 16339522 (1)
    zinc 36.1 18 14656887 (1), 11342629 (1), 19433448 (1), 16506071 (1) (see all 9)



    PRDM1 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 PRDM1 gene (2 alternative transcripts): 
    NM_001198.3  NM_182907.2  

    Unigene Cluster for PRDM1:

    PR domain containing 1, with ZNF domain
    Hs.436023  [show with all ESTs]
    Unigene Representative Sequence: AY198414
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000369091 ENST00000369096(uc003prd.2) ENST00000424894 ENST00000489365
    ENST00000450060 ENST00000481163 ENST00000369089(uc003pre.3)
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    Block miRNA regulation of human, mouse, rat PRDM1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PRDM1 (see all 76):
    hsa-miR-548j hsa-miR-938 hsa-miR-30d hsa-miR-30a hsa-miR-548a-5p hsa-miR-200b hsa-miR-4273 hsa-miR-4324
    SwitchGear 3'UTR luciferase reporter plasmidPRDM1 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat PRDM1

    Additional mRNA sequence: 

    AF084199.1 AK129768.1 AK289556.1 AK301341.1 AL832963.1 AY198414.1 AY198415.1 BC103832.1 
    BC103833.1 BC103834.1 BC103835.1 EF151143.1 

    6 DOTS entries:

    DT.100751567  DT.436483  DT.100736390  DT.100751566  DT.91842415  DT.86843045 

    Selected AceView cDNA sequences (see all 76):

    Z38498 NM_001198 AI671598 BM667340 AY198414 BQ018743 Z42260 AI269812 
    BX284091 AY198415 AW594160 AA858171 AA664123 AA743541 AW188348 BF516514 
    AW408568 BE219817 BM710624 AA921725 BU680075 NM_182907 AI346940 AK129768 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PRDM1 (see all 10)    About this scheme

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


    ECgene alternative splicing isoforms for PRDM1

    (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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    PRDM1 expression in normal human tissues (normalized intensities)      PRDM1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTGCATAGC
    PRDM1 Expression
    About this image


    PRDM1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 14) fully expand
     
     Gonad
             Primordial Germ Cells Allantois
             Human oogonial stem cells
     
     Ovary (Reproductive System)    fully expand to see all 3 entries
             Ovarian tissue-dissociated cells (human)
             Ddx4-positive cells
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             Early Photoreceptor Precursor Cells Retinal Neuroblastic Layer
     
     Germ Cells (Reproductive System)    fully expand to see all 2 entries
             Human oogonial stem cells
     
     Neurons
             Early Photoreceptor Precursor Cells Retinal Neuroblastic Layer
    PRDM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PRDM1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.436023
        Custom PCR Arrays for PRDM1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM1

    (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 animals.

    Orthologs for PRDM1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prdm11 , 5 PR domain containing 1, with ZNF domain1, 5 86.94(n)1
    89.17(a)1
      10 (23.24 cM)5
    121421  NM_007548.31  NP_031574.21 
     444371775 
    chicken
    (Gallus gallus)
    Aves PRDM11 PR domain containing 1, with ZNF domain 77.38(n)
    79.68(a)
      445340  XM_004940354.1  XP_004940411.1 
    lizard
    (Anolis carolinensis)
    Reptilia PRDM16
    PR domain containing 1, with ZNF domain
    77(a)
    1 ↔ 1
    1(189137826-189168029)
    African clawed frog
    (Xenopus laevis)
    Amphibia prdm1-prov2 PR domain containing 1, with ZNF domain 78.22(n)    BC044261.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ubo2 u-boot 77.18(n)   394229  AY497217.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG52493   -- 72(a)   64E1   --


    ENSEMBL Gene Tree for PRDM1 (if available)
    TreeFam Gene Tree for PRDM1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PRDM1 gene
    ZNF6832  ZNF8272  
    Selected SIMAP similar genes for PRDM1 using alignment to 6 protein entries:     PRDM1_HUMAN (see all proteins) (see all similar genes):
    DKFZp666P0310    ZNF818P    DKFZp434J0650    ZNF55    ZNF78L1    ZNF
    ZFS-2    ZFS-4    ZKSCAN1    zf30    A-328A3.4    ZNF468
    DKFZp434G1930    DKFZp762K012    DKFZp666C237    ZNF32    ZNF83    kr-znf3

    PRDM1 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 PRDM1 (see all 481)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1448348691,2
    --106529925(+) CTGATA/GTTAAT 1 -- us2k10--------
    rs775125321,2
    C,F--106530099(+) AGTTTG/TATTCT 1 -- us2k11Minor allele frequency- T:0.05EA 120
    rs49467221,2
    C,F,H--106530103(+) TGATTA/CTAAAA 1 -- us2k124Minor allele frequency- N:0.00NS EA NA 2842
    rs175587971,2
    C,F,H--106530203(+) TGTGGT/CGCTGA 1 -- us2k1 tfbs322Minor allele frequency- C:0.05NA NS EA WA 2770
    rs13400641,2
    C,F,O,A,H--106530315(+) TTCCAG/CCCCCA 1 -- us2k119Minor allele frequency- C:0.41EA NA NS WA CSA 888
    rs610015501,2
    C,F--106530319(+) ACCCCC/TAGCAG 1 -- us2k14Minor allele frequency- T:0.08WA CSA EA 242
    rs170665631,2
    C,F,H--106530413(+) AGCAGC/GGAGTG 1 -- us2k1 tfbs311Minor allele frequency- G:0.06NA NS EA WA CSA 804
    rs1891897631,2
    --106530510(+) AAATAA/CTCTTT 1 -- us2k10--------
    rs1818924181,2
    --106530527(+) TCCCCC/TTCTCC 1 -- us2k10--------
    rs1996034461,2
    C--106530596(+) CAGAC-/ATATTTT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for PRDM1 (106534195 - 106557814 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for PRDM1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv5429CNV Insertion18451855
    nsv830755CNV Loss17160897

    Human Gene Mutation Database (HGMD): PRDM1
    3 Site Specific Mutation Identification with PCR Assays for PRDM1:
    Cosmic IdAA Change
    97170p.P48T
    97026p.C203*
    97168p.P48R
    SeqTarget long-range PCR primers for resequencing PRDM1
    DNA2.0 Custom Variant and Variant Library Synthesis for PRDM1

    (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: 603423    OMIM disorders: --

    Selected diseases for PRDM1 (see all 29):    About MalaCards
    devic disease    plasmacytoma    central nervous system lymphoma    neuromyelitis optica
    diffuse large b-cell lymphoma    otitis media    common variable immunodeficiency    myeloma
    adult t-cell leukemia    multiple myeloma    b-cell lymphomas    mantle cell lymphoma
    hodgkin's lymphoma    tonsillitis    germ cell tumors    crohn's disease
    non-hodgkin lymphoma    systemic lupus erythematosus    t-cell leukemia    burkitt's lymphoma

    1 disease from the University of Copenhagen DISEASES database for PRDM1:
    Lymphoma

    PRDM1 for disorders           About GeneDecksing

    9 Novoseek inferred disease relationships for PRDM1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    lymphoma b-cell 55.7 15 17213024 (4), 16585013 (3), 19380033 (2), 18596541 (1) (see all 6)
    plasmacytoma 51.2 3 18089822 (2)
    lymphoma 50.7 12 17682124 (1), 11067898 (1), 16778825 (1), 8168136 (1) (see all 11)
    myeloma 50.3 8 15195108 (2), 16982896 (1), 18192112 (1), 17877160 (1) (see all 6)
    lymphoma large cell diffuse 41.6 1 16492805 (1)
    virus infection 3.17 6 19664943 (3), 16708403 (1), 14985713 (1)
    hodgkin disease 0.852 1 16585013 (1)
    leukemia 0 3 11841448 (1), 8921366 (1)
    tumors 0 10 16585013 (2), 20047096 (2), 16492805 (2), 18596541 (1) (see all 5)

    Genetic Association Database (GAD): PRDM1
    Human Genome Epidemiology (HuGE) Navigator: PRDM1 (13 documents)

    Export disorders for PRDM1 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 PRDM1 gene, integrated from 10 sources (see all 182):
    (articles sorted by number of sources associating them with PRDM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a novel repressor of beta- interferon gene expression. (PubMed id 1851123)1, 2, 3, 9 Keller A.D. and Maniatis T. (Genes Dev. 1991)
    2. Identification of a functionally impaired positive regulatory domain I binding factor 1 transcription repressor in myeloma cell lines. (PubMed id 12626569)1, 2, 9 Gyory I.... Wright K.L. (J. Immunol. 2003)
    3. Lack of evidence of a role of XBP1 and PRDM1 polymorphisms in Spanish patients with immunoglobulin A deficiency. (PubMed id 19735688)1, 4, 9 del Pozo N....NA_A+ez C. (Hum. Immunol. 2009)
    4. SUMOylation of Blimp-1 is critical for plasma cell differentiation. (PubMed id 22555612)1, 2 Ying H.Y.... Lin K.I. (EMBO Rep. 2012)
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    6. Analysis of 39 Crohn's disease risk loci in Swedish inflammatory bowel disease patients. (PubMed id 19760754)1, 4 TAPrkvist L....Pettersson S. (Inflamm. Bowel Dis. 2010)
    7. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. (PubMed id 19838193)1, 4 Han J.W....Zhang X.J. (Nat. Genet. 2009)
    8. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. (PubMed id 19898481)1, 4 Raychaudhuri S....Plenge R.M. (Nat. Genet. 2009)
    9. A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus. (PubMed id 19838195)1, 4 Gateva V....Graham R.R. (Nat. Genet. 2009)
    10. Regulation and functions of Blimp-1 in T and B lymphocytes. (PubMed id 18370921)1, 9 Martins G. and Calame K. (Annu. Rev. Immunol. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    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)
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    Entrez Gene: 639 HGNC: 9346 AceView: PRDM1 Ensembl:ENSG00000057657 euGenes: HUgn639
    ECgene: PRDM1 H-InvDB: PRDM1

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for PRDM1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PRDM1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PRDM1 gene:
    Search GeneIP for patents involving PRDM1

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



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