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

Summary

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: mouse all
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Genomic context

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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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	Compare labs

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

SHGC-12163 (e-PCR)
- UniSTS:16923

SHGC-50733 (e-PCR)
- UniSTS:72488

SHGC-85678 (e-PCR)
- UniSTS:103722

D4S247 (e-PCR)
- UniSTS:91239

D4S247 (e-PCR)
- UniSTS:147050

D4S1125 (e-PCR)
- UniSTS:30616

SHGC-146118 (e-PCR)
- UniSTS:175017

D4S2881 (e-PCR)
- UniSTS:8148

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

EC 2.1.1.-

NP_001287753.1

EC 2.1.1.-

NP_001366033.1

EC 2.1.1.-

NP_001366035.1

EC 2.1.1.-

NP_061169.2

EC 2.1.1.-

XP_005262765.1

EC 2.1.1.-

XP_011529865.1

EC 2.1.1.-

XP_011529866.1

EC 2.1.1.-

XP_011529867.1

EC 2.1.1.-

XP_011529868.1

EC 2.1.1.-

XP_011529870.1

EC 2.1.1.-

XP_016863157.1

EC 2.1.1.-

XP_016863159.1

EC 2.1.1.-

XP_016863160.1

EC 2.1.1.-

XP_047305510.1

EC 2.1.1.-

XP_047305511.1

EC 2.1.1.-

XP_047305512.1

EC 2.1.1.-

XP_047305513.1

EC 2.1.1.-

XP_047305514.1

EC 2.1.1.-

XP_047305515.1

EC 2.1.1.-

XP_054204795.1

EC 2.1.1.-

XP_054204796.1

EC 2.1.1.-

XP_054204797.1

EC 2.1.1.-

XP_054204798.1

EC 2.1.1.-

XP_054204799.1

EC 2.1.1.-

XP_054204800.1

EC 2.1.1.-

XP_054204801.1

EC 2.1.1.-

XP_054204802.1

EC 2.1.1.-

XP_054204803.1

EC 2.1.1.-

XP_054204804.1

EC 2.1.1.-

XP_054204805.1

EC 2.1.1.-

XP_054204806.1

EC 2.1.1.-

XP_054204807.1

EC 2.1.1.-

XP_054204808.1

EC 2.1.1.-

XP_054204809.1

EC 2.1.1.-

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

NG_031862.3 RefSeqGene

Range

5000..235811

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

120684291..120922726 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047449558.1 → XP_047305514.1 PR domain zinc finger protein 5 isoform X12
XM_047449557.1 → XP_047305513.1 PR domain zinc finger protein 5 isoform X10
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
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
XM_047449554.1 → XP_047305510.1 PR domain zinc finger protein 5 isoform X4
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
XM_017007668.3 → XP_016863157.1 PR domain zinc finger protein 5 isoform X1
XM_017007671.2 → XP_016863160.1 PR domain zinc finger protein 5 isoform X15
XM_047449555.1 → XP_047305511.1 PR domain zinc finger protein 5 isoform X7
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
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
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
XM_047449559.1 → XP_047305515.1 PR domain zinc finger protein 5 isoform X13
XM_047449556.1 → XP_047305512.1 PR domain zinc finger protein 5 isoform X8
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