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PRDM5 PR/SET domain 5 [ Homo sapiens (human) ]

Gene ID: 11107, updated on 5-Mar-2024

Summary

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Official Symbol
PRDM5provided by HGNC
Official Full Name
PR/SET domain 5provided by HGNC
Primary source
HGNC:HGNC:9349
See related
Ensembl:ENSG00000138738 MIM:614161; AllianceGenome:HGNC:9349
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BCS2; PFM2
Summary
The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 2.4), endometrium (RPKM 1.5) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
4q27
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (120684291..120922726, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (123965980..124226930, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (121613070..121843881, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene secretion associated Ras related GTPase 1A pseudogene 3 Neighboring gene uncharacterized LOC124900771 Neighboring gene Sharpr-MPRA regulatory region 8715 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72414 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72419 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21861 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:121655223-121655429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:121662174-121662740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:121662741-121663307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21862 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72556 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72587 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72607 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72637 Neighboring gene RNA, U6 small nuclear 550, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr4:121806618-121806798 Neighboring gene uncharacterized LOC105377399 Neighboring gene SET pseudogene 12 Neighboring gene NANOG hESC enhancer GRCh37_chr4:121885637-121886160 Neighboring gene RN7SK pseudogene 137 Neighboring gene neuron derived neurotrophic factor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Deregulation of PRDM5 promotes cell proliferation by regulating JAK/STAT signaling pathway through SOCS1 in human lung adenocarcinoma. Ren Y, et al. Cancer Med, 2023 Feb. PMID 36127737, Free PMC Article
  2. Low expression of PRDM5 predicts poor prognosis of esophageal squamous cell carcinoma. Guo J, et al. BMC Cancer, 2022 Jul 7. PMID 35799142, Free PMC Article
  3. Silencing of PRDM5 increases cell proliferation and inhibits cell apoptosis in glioma. Wang X, et al. Int J Neurosci, 2021 Feb. PMID 32083978
  4. PRDM5 promotes the apoptosis of epithelial cells induced by IFN-γ during Crohn's disease. Wu H, et al. Pathol Res Pract, 2017 Jun. PMID 28476379
  5. Identification of Mutations in the PRDM5 Gene in Brittle Cornea Syndrome. Micheal S, et al. Cornea, 2016 Jun. PMID 27032025

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Deregulation of PRDM5 promotes cell proliferation by regulating JAK/STAT signaling pathway through SOCS1 in human lung adenocarcinoma.
    Title: Deregulation of PRDM5 promotes cell proliferation by regulating JAK/STAT signaling pathway through SOCS1 in human lung adenocarcinoma.
  2. Low expression of PRDM5 predicts poor prognosis of esophageal squamous cell carcinoma.
    Title: Low expression of PRDM5 predicts poor prognosis of esophageal squamous cell carcinoma.
  3. PRDM5 suppresses oesophageal squamous carcinoma cells and modulates 14-3-3zeta/Akt signalling pathway.
    Title: PRDM5 suppresses oesophageal squamous carcinoma cells and modulates 14-3-3zeta/Akt signalling pathway.
  4. More than meets the eye: Expanding and reviewing the clinical and mutational spectrum of brittle cornea syndrome.
    Title: More than meets the eye: Expanding and reviewing the clinical and mutational spectrum of brittle cornea syndrome.
  5. Silencing of PRDM5 increases cell proliferation and inhibits cell apoptosis in glioma.
    Title: Silencing of PRDM5 increases cell proliferation and inhibits cell apoptosis in glioma.
  6. Truncations may be the primary mutation type in PITX2. Glaucoma onset may be earlier in patients with mutations in PITX2 than in those without mutations in PITX2 and FOXC1. A block of the anterior chamber angle by the end of the iris might represent the main factor influencing the development of glaucoma in ARS patients with an asymmetric aniridia phenotype.
    Title: Mutation Survey of Candidate Genes and Genotype-Phenotype Analysis in 20 Southeastern Chinese Patients with Axenfeld-Rieger Syndrome.
  7. Inhibiting PRDM5 expression by siRNA attenuated the IFN-gamma-triggered accumulation of active caspase-3 and cleaved PARP in intestinal epithelial cells. Moreover, flow cytometry assay and CCK-8 analysis revealed that PRDM5 knockdown significantly alleviated the IFN-gamma-induced cellular apoptosis in HT29 cells.
    Title: PRDM5 promotes the apoptosis of epithelial cells induced by IFN-γ during Crohn's disease.
  8. Both Prdm 4 and Prdm 5 are expressed in human corneal endothelium, primary hCECs and in HCECs-12 cells, characterised by expression of the Na(+)/K(+)-ATPase.
    Title: Identification of Prdm genes in human corneal endothelium.
  9. The miR-182 promoter is rarely methylated in epithelial ovarian cancers (EOCs), and its methylation status is associated with lower miR-182 expression. Deletion of the PRDM5 locus may play a supportive role in miR-182 overexpression in EOC. miR-182 is an unfavorable prognostic factor in EOC.
    Title: Molecular bases of aberrant miR-182 expression in ovarian cancer.
  10. The current study revealed a novel mutation in the PRDM5 gene in a Brittle cornea syndrome (BCS) family and recurrent mutation in a sporadic BCS patient.
    Title: Identification of Mutations in the PRDM5 Gene in Brittle Cornea Syndrome.
Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Brittle cornea syndrome 2
MedGen: C3280011 OMIM: 614170 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
EBI GWAS Catalog
Genome-wide association with diabetes-related traits in the Framingham Heart Study.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of PR domain containing 5 (PRDM5) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of extracellular matrix organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
PR domain zinc finger protein 5
Names
PR domain 5
PR domain containing 5
NP_001287752.1
NP_001287753.1
NP_001366033.1
NP_001366035.1
NP_061169.2
XP_005262765.1
XP_011529865.1
XP_011529866.1
XP_011529867.1
XP_011529868.1
XP_011529870.1
XP_016863157.1
XP_016863159.1
XP_016863160.1
XP_047305510.1
XP_047305511.1
XP_047305512.1
XP_047305513.1
XP_047305514.1
XP_047305515.1
XP_054204795.1
XP_054204796.1
XP_054204797.1
XP_054204798.1
XP_054204799.1
XP_054204800.1
XP_054204801.1
XP_054204802.1
XP_054204803.1
XP_054204804.1
XP_054204805.1
XP_054204806.1
XP_054204807.1
XP_054204808.1
XP_054204809.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031862.3 RefSeqGene

    Range
    5000..235811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300823.2 → NP_001287752.1  PR domain zinc finger protein 5 isoform 2

    See identical proteins and their annotated locations for NP_001287752.1

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Consensus CDS
    CCDS75188.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000404832.2, ENST00000428209.6
    Conserved Domains (3) summary
    COG5048
    Location:174 → 589
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:460 → 480
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2 → 128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins

  2. NM_001300824.2 → NP_001287753.1  PR domain zinc finger protein 5 isoform 3

    See identical proteins and their annotated locations for NP_001287753.1

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Consensus CDS
    CCDS75187.1
    UniProtKB/Swiss-Prot
    Q9NQX1
    Related
    ENSP00000422309.1, ENST00000515109.5
    Conserved Domains (3) summary
    COG5048
    Location:145 → 337
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:319 → 339
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2 → 128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins

  3. NM_001379104.1 → NP_001366033.1  PR domain zinc finger protein 5 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Conserved Domains (3) summary
    COG5048
    Location:262 → 631
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502 → 522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2 → 128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins

  4. NM_001379106.1 → NP_001366035.1  PR domain zinc finger protein 5 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Conserved Domains (5) summary
    COG5048
    Location:145 → 337
    COG5048; FOG: Zn-finger [General function prediction only]
    COG5189
    Location:482 → 559
    SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
    sd00017
    Location:432 → 452
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:511 → 529
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2 → 128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins

  5. NM_018699.4 → NP_061169.2  PR domain zinc finger protein 5 isoform 1

    See identical proteins and their annotated locations for NP_061169.2

    Status: REVIEWED

    Source sequence(s)
    AC025741, AC104068, AC104795
    Consensus CDS
    CCDS3716.1
    UniProtKB/Swiss-Prot
    Q0VAI9, Q0VAJ0, Q6NXQ7, Q9NQX1
    Related
    ENSP00000264808.3, ENST00000264808.8
    Conserved Domains (4) summary
    COG5048
    Location:262 → 620
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:491 → 511
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2 → 128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
    cd20908
    Location:172 → 220
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    120684291..120922726 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449558.1 → XP_047305514.1  PR domain zinc finger protein 5 isoform X12

  2. XM_047449557.1 → XP_047305513.1  PR domain zinc finger protein 5 isoform X10

  3. XM_011531566.4 → XP_011529868.1  PR domain zinc finger protein 5 isoform X5

    Conserved Domains (4) summary
    COG5048
    Location:225 → 463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502 → 522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20 → 123
    SET; SET domain
    pfam13465
    Location:543 → 567
    zf-H2C2_2; Zinc-finger double domain

  4. XM_011531563.3 → XP_011529865.1  PR domain zinc finger protein 5 isoform X2

    Conserved Domains (4) summary
    COG5048
    Location:174 → 600
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:471 → 491
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20 → 123
    SET; SET domain
    pfam13465
    Location:512 → 536
    zf-H2C2_2; Zinc-finger double domain

  5. XM_047449554.1 → XP_047305510.1  PR domain zinc finger protein 5 isoform X4

  6. XM_011531564.3 → XP_011529866.1  PR domain zinc finger protein 5 isoform X3

    Conserved Domains (5) summary
    COG5048
    Location:225 → 463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:474 → 494
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:553 → 571
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20 → 123
    SET; SET domain
    pfam13465
    Location:515 → 538
    zf-H2C2_2; Zinc-finger double domain

  7. XM_017007668.3 → XP_016863157.1  PR domain zinc finger protein 5 isoform X1

  8. XM_017007671.2 → XP_016863160.1  PR domain zinc finger protein 5 isoform X15

  9. XM_047449555.1 → XP_047305511.1  PR domain zinc finger protein 5 isoform X7

  10. XM_011531565.3 → XP_011529867.1  PR domain zinc finger protein 5 isoform X6

    Conserved Domains (4) summary
    COG5048
    Location:225 → 463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:502 → 522
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20 → 123
    SET; SET domain
    pfam13465
    Location:543 → 567
    zf-H2C2_2; Zinc-finger double domain

  11. XM_011531568.3 → XP_011529870.1  PR domain zinc finger protein 5 isoform X9

    See identical proteins and their annotated locations for XP_011529870.1

    Conserved Domains (3) summary
    COG5048
    Location:225 → 463
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:361 → 381
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20 → 123
    SET; SET domain

  12. XM_017007670.2 → XP_016863159.1  PR domain zinc finger protein 5 isoform X11

    Conserved Domains (4) summary
    COG5048
    Location:264 → 423
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:350 → 370
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19190
    Location:2 → 128
    PR-SET_PRDM5; PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins
    cd20908
    Location:172 → 220
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins

  13. XM_047449559.1 → XP_047305515.1  PR domain zinc finger protein 5 isoform X13

  14. XM_047449556.1 → XP_047305512.1  PR domain zinc finger protein 5 isoform X8

  15. XM_005262708.4 → XP_005262765.1  PR domain zinc finger protein 5 isoform X14

    Conserved Domains (3) summary
    COG5048
    Location:145 → 338
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:269 → 287
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00856
    Location:20 → 123
    SET; SET domain

RNA

  1. XR_938678.2 RNA Sequence

  2. XR_938680.3 RNA Sequence

  3. XR_938679.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    123965980..124226930 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348829.1 → XP_054204804.1  PR domain zinc finger protein 5 isoform X10

  2. XM_054348830.1 → XP_054204805.1  PR domain zinc finger protein 5 isoform X12

  3. XM_054348825.1 → XP_054204800.1  PR domain zinc finger protein 5 isoform X5

  4. XM_054348821.1 → XP_054204796.1  PR domain zinc finger protein 5 isoform X2

  5. XM_054348823.1 → XP_054204798.1  PR domain zinc finger protein 5 isoform X4

  6. XM_054348822.1 → XP_054204797.1  PR domain zinc finger protein 5 isoform X3

  7. XM_054348820.1 → XP_054204795.1  PR domain zinc finger protein 5 isoform X1

  8. XM_054348834.1 → XP_054204809.1  PR domain zinc finger protein 5 isoform X15

  9. XM_054348826.1 → XP_054204801.1  PR domain zinc finger protein 5 isoform X7

  10. XM_054348824.1 → XP_054204799.1  PR domain zinc finger protein 5 isoform X6

  11. XM_054348828.1 → XP_054204803.1  PR domain zinc finger protein 5 isoform X9

  12. XM_054348831.1 → XP_054204806.1  PR domain zinc finger protein 5 isoform X11

  13. XM_054348832.1 → XP_054204807.1  PR domain zinc finger protein 5 isoform X13

  14. XM_054348827.1 → XP_054204802.1  PR domain zinc finger protein 5 isoform X8

  15. XM_054348833.1 → XP_054204808.1  PR domain zinc finger protein 5 isoform X14

RNA

  1. XR_008486889.1 RNA Sequence

  2. XR_008486891.1 RNA Sequence

  3. XR_008486890.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQX1.2 GenPept UniProtKB/Swiss-Prot:Q9NQX1

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