• Gene id: 639

Gene Summary

• Gene Symbol: PRDM1   Gene   UCSC   Ensembl
• Aliases: BLIMP1, PRDI-BF1
• Gene name: PR/SET domain 1
• Alternate names: PR domain zinc finger protein 1, B-lymphocyte-induced maturation protein 1, BLIMP-1, PR domain 1, PR domain containing 1, with ZNF domain, PRDI-binding factor-1, beta-interferon gene positive-regulatory domain I binding factor,
• Gene location: 6q21 (106046728: 106109937)     Exons: 11     NC_000006.12
• Gene summary(Entrez): 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 induc
• OMIM: 603423

SNPs

rs397515461

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000008.11   g.132632831G>A
NC_000008.10   g.133645077G>A
NG_033068.1   g.47787C>T
NM_012472.5   c.562C>T
NM_012472.6   c.562C>T
NM_012472.4   c.562C>T
NR_073525.2   n.686C>T
NR_073525.1   n.686C>T
NM_001321965.1   c.202C>T
NM_001321965.2   c.202C>T
NM_001321964.1   c.2

rs397515425

Strand:    Allele origin:   Allele change:   Mutation type: delins

NC_000008.11   g.132632818dup
NC_000008.10   g.133645064dup
NG_033068.1   g.47801dup
NM_012472.5   c.576dup
NM_012472.6   c.576dup
NM_012472.4   c.576dup
NR_073525.2   n.700dup
NR_073525.1   n.700dup
NM_001321965.1   c.216dup
NM_001321965.2   c.216dup
NM_001321964.1   c.2

rs397515424

Strand:    Allele origin:   Allele change:   Mutation type: del

NC_000008.11   g.132632794_132632795del
NC_000008.10   g.133645040_133645041del
NG_033068.1   g.47823_47824del
NM_012472.5   c.598_599del
NM_012472.6   c.598_599del
NM_012472.4   c.598_599del
NR_073525.2   n.722_723del
NR_073525.1   n.722_723del
NM_001321965.1   c.238

rs397514596

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000008.11   g.132656866C>G
NC_000008.10   g.133669112C>G
NG_033068.1   g.23752G>C
NM_012472.5   c.220G>C
NM_012472.6   c.220G>C
NM_012472.4   c.220G>C
NR_073525.2   n.344G>C
NR_073525.1   n.344G>C
NM_001321965.1   c.-454G>C
NM_001321965.2   c.-454G>C
NR_135912.1   n.10

rs200321595

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000008.11   g.132632957C>G
NC_000008.10   g.133645203C>G
NG_033068.1   g.47661G>C
NM_012472.5   c.436G>C
NM_012472.6   c.436G>C
NM_012472.4   c.436G>C
NR_073525.2   n.560G>C
NR_073525.1   n.560G>C
NM_001321965.1   c.76G>C
NM_001321965.2   c.76G>C
NM_001321964.1   c.76G

rs141945265

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000008.11   g.132632819G>A
NC_000008.11   g.132632819G>C
NC_000008.10   g.133645065G>A
NC_000008.10   g.133645065G>C
NG_033068.1   g.47799C>T
NG_033068.1   g.47799C>G
NM_012472.5   c.574C>T
NM_012472.5   c.574C>G
NM_012472.6   c.574C>T
NM_012472.6   c.574C>G
NM_01247  

rs200847762

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000006.12   g.32129371G>A
NC_000006.11   g.32097148G>A
NG_033940.1   g.3870C>T
NT_113891.3   g.3567702G>A
NT_113891.2   g.3567808G>A
NT_167247.2   g.3471391G>A
NT_167247.1   g.3476976G>A
NT_167245.2   g.3370735G>A
NT_167245.1   g.3376320G>A
NM_022110.4   c.410C>T
NM_  

rs35033974

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000019.10   g.43416460G>T
NC_000019.9   g.43920612G>T
NM_031451.4   c.350G>T
XM_005259303.3   c.464G>T
XM_005259303.1   c.392G>T
NM_001130011.1   c.296G>T
NM_001130011.3   c.296G>T
NM_001130011.2   c.296G>T
NP_113639.4   p.Gly117Val
XP_005259360.2   p.Gly155Val
NP_00  

Protein Summary

• Protein general information: O75626  
  • Name: PR domain zinc finger protein 1 (EC 2.1.1. ) (BLIMP 1) (Beta interferon gene positive regulatory domain I binding factor) (PR domain containing protein 1) (Positive regulatory domain I binding factor 1) (PRDI BF1) (PRDI binding factor 1)
  • Length: 825  
  • Mass: 91771
• Sequence:

  MLDICLEKRVGTTLAAPKCNSSTVRFQGLAEGTKGTMKMDMEDADMTLWTEAEFEEKCTYIVNDHPWDSGADGGT
  SVQAEASLPRNLLFKYATNSEEVIGVMSKEYIPKGTRFGPLIGEIYTNDTVPKNANRKYFWRIYSRGELHHFIDG
  FNEEKSNWMRYVNPAHSPREQNLAACQNGMNIYFYTIKPIPANQELLVWYCRDFAERLHYPYPGELTMMNLTQTQ
  SSLKQPSTEKNELCPKNVPKREYSVKEILKLDSNPSKGKDLYRSNISPLTSEKDLDDFRRRGSPEMPFYPRVVYP
  IRAPLPEDFLKASLAYGIERPTYITRSPIPSSTTPSPSARSSPDQSLKSSSPHSSPGNTVSPVGPGSQEHRDSYA
  YLNASYGTEGLGSYPGYAPLPHLPPAFIPSYNAHYPKFLLPPYGMNCNGLSAVSSMNGINNFGLFPRLCPVYSNL
  LGGGSLPHPMLNPTSLPSSLPSDGARRLLQPEHPREVLVPAPHSAFSFTGAAASMKDKACSPTSGSPTAGTAATA
  EHVVQPKATSAAMAAPSSDEAMNLIKNKRNMTGYKTLPYPLKKQNGKIKYECNVCAKTFGQLSNLKVHLRVHSGE
  RPFKCQTCNKGFTQLAHLQKHYLVHTGEKPHECQVCHKRFSSTSNLKTHLRLHSGEKPYQCKVCPAKFTQFVHLK
  LHKRLHTRERPHKCSQCHKNYIHLCSLKVHLKGNCAAAPAPGLPLEDLTRINEEIEKFDISDNADRLEDVEDDIS
  VISVVEKEILAVVRKEKEETGLKVSLQRNMGNGLLSSGCSLYESSDLPLMKLPPSNPLPLVPVKVKQETVEPMDP

• Structural information:
  • Protein Domains: (84..20-)
    (/note="SET-)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00190"-)
  • Interpro: IPR001214  IPR036236  IPR013087  
  • Prosite: PS50280 PS00028 PS50157
  • PDB: 3DAL
  • PDBsum: 3DAL
  • STRING: ENSP00000358092
• Other Databases: GeneCards:  PRDM1  Malacards:  PRDM1

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0000122	negative regulation of transcription by RNA polymerase II	IDA	biological process
GO:0001227	DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA	molecular function
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	molecular function
GO:0042826	histone deacetylase binding	IBA	molecular function
GO:0010468	regulation of gene expression	IBA	biological process
GO:0005737	cytoplasm	IBA	cellular component
GO:0005634	nucleus	IBA	cellular component
GO:0045165	cell fate commitment	IBA	biological process
GO:0006357	regulation of transcription by RNA polymerase II	IBA	biological process
GO:0003700	DNA-binding transcription factor activity	IBA	molecular function
GO:0000978	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA	molecular function
GO:0005634	nucleus	IDA	cellular component
GO:0005737	cytoplasm	IDA	cellular component
GO:1990841	promoter-specific chromatin binding	ISS	molecular function
GO:0051136	regulation of NK T cell differentiation	ISS	biological process
GO:0033082	regulation of extrathymic T cell differentiation	ISS	biological process
GO:0032823	regulation of natural killer cell differentiation	ISS	biological process
GO:0005515	protein binding	IPI	molecular function
GO:0003700	DNA-binding transcription factor activity	IEA	molecular function
GO:0048869	cellular developmental process	IEA	biological process
GO:0000122	negative regulation of transcription by RNA polymerase II	IEA	biological process
GO:0005634	nucleus	IEA	cellular component
GO:0005737	cytoplasm	IEA	cellular component
GO:0045087	innate immune response	IEA	biological process
GO:0016740	transferase activity	IEA	molecular function
GO:0002376	immune system process	IEA	biological process
GO:0032259	methylation	IEA	biological process
GO:0046872	metal ion binding	IEA	molecular function
GO:0005634	nucleus	IEA	cellular component
GO:0002250	adaptive immune response	IEA	biological process
GO:0008168	methyltransferase activity	IEA	molecular function
GO:0003677	DNA binding	IEA	molecular function
GO:0005737	cytoplasm	IEA	cellular component
GO:0003700	DNA-binding transcription factor activity	TAS	molecular function
GO:0000122	negative regulation of transcription by RNA polymerase II	TAS	biological process
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005654	nucleoplasm	TAS	cellular component
GO:0005515	protein binding	IPI	molecular function
GO:1990841	promoter-specific chromatin binding	IEA	molecular function
GO:0060976	coronary vasculature development	IEA	biological process
GO:0051136	regulation of NK T cell differentiation	IEA	biological process
GO:0045165	cell fate commitment	IEA	biological process
GO:0042127	regulation of cell population proliferation	IEA	biological process
GO:0033082	regulation of extrathymic T cell differentiation	IEA	biological process
GO:0010628	positive regulation of gene expression	IEA	biological process
GO:0009791	post-embryonic development	IEA	biological process
GO:0001763	morphogenesis of a branching structure	IEA	biological process
GO:1990654	sebum secreting cell proliferation	IEA	biological process
GO:0060707	trophoblast giant cell differentiation	IEA	biological process
GO:0060576	intestinal epithelial cell development	IEA	biological process
GO:0048844	artery morphogenesis	IEA	biological process
GO:0042462	eye photoreceptor cell development	IEA	biological process
GO:0035904	aorta development	IEA	biological process
GO:0032823	regulation of natural killer cell differentiation	IEA	biological process
GO:0010629	negative regulation of gene expression	IEA	biological process
GO:0007281	germ cell development	IEA	biological process
GO:0005634	nucleus	IEA	cellular component
GO:0003281	ventricular septum development	IEA	biological process
GO:0003279	cardiac septum development	IEA	biological process
GO:0003170	heart valve development	IEA	biological process
GO:0001893	maternal placenta development	IEA	biological process
GO:0001892	embryonic placenta development	IEA	biological process
GO:0001701	in utero embryonic development	IEA	biological process
GO:0000122	negative regulation of transcription by RNA polymerase II	IEA	biological process
GO:0005737	cytoplasm	IEA	cellular component
GO:0005634	nucleus	IEA	cellular component

Diseases

Associated diseases	References
Aberrant CpGs in Low Motility Sperm	MIK: 21674046
Spermatogenic defects	MIK: 31037746
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			13 (5 controls, 8 cases)	Male infertility	GSE6967 analyzed by GEO2R (cutoff 1.5 fold)
21674046	Aberrant CpGs in Low Motility Sperm			18	Male infertility	GSE26881
31037746	Spermatogenic defects			16 (1 control, 15 cases)	Male infertility	GSE6023 analyzed using GEO2R