PRDM5

Protein identityUniProt · HPA

UniProt accession

Q9NQX1

Gene

PRDM5

Ensembl

ENSG00000138738

Chromosome

4

Canonical length

630 aa

Protein class

Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors

Subcellular location

Nucleoplasm,Nucleoli,Nuclear bodies

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

630 residues, UniProt reviewed canonical sequence.

>Q9NQX1|PRDM5
     1  MLGMYVPDRF SLKSSRVQDG MGLYTARRVR KGEKFGPFAG EKRMPEDLDE NMDYRLMWEV
    61  RGSKGEVLYI LDATNPRHSN WLRFVHEAPS QEQKNLAAIQ EGENIFYLAV EDIETDTELL
   121  IGYLDSDMEA EEEEQQIMTV IKEGEVENSR RQSTAGRKDR LGCKEDYACP QCESSFTSED
   181  ILAEHLQTLH QKPTEEKEFK CKNCGKKFPV KQALQRHVLQ CTAKSSLKES SRSFQCSVCN
   241  SSFSSASSFE QHQETCRGDA RFVCKADSCG KRLKSKDALK RHQENVHTGD PKKKLICSVC
   301  NKKCSSASSL QEHRKIHEIF DCQECMKKFI SANQLKRHMI THSEKRPYNC EICNKSFKRL
   361  DQVGAHKVIH SEDKPYKCKL CGKGFAHRNV YKNHKKTHSE ERPFQCEECK ALFRTPFSLQ
   421  RHLLIHNSER TFKCHHCDAT FKRKDTLNVH VQVVHERHKK YRCELCNKAF VTPSVLRSHK
   481  KTHTGEKEKI CPYCGQKFAS SGTLRVHIRS HTGERPYQCP YCEKGFSKND GLKMHIRTHT
   541  REKPYKCSEC SKAFSQKRGL DEHKRTHTGE KPFQCDVCDL AFSLKKMLIR HKMTHNPNRP
   601  LAECQFCHKK FTRNDYLKVH MDNIHGVADS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PRDM5 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.41

Highest tissue expression

8.1 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PRDM5.

Disease | AllUniProt

Conditions PRDM5 is implicated in, by any mechanism.

• Brittle cornea syndrome 2 (BCS2) MIM:614170

Disease | GeneticClinVar

58 pathogenic / likely-pathogenic of 853 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Brittle cornea syndrome 2
• Cardiovascular phenotype
• Ehlers-Danlos syndrome
• PRDM5-related disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.84

gnomAD pLI

0

gnomAD missense Z

0.7

DepMap mean gene effect

0.01

DepMap dependency class

none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• cellular response to leukemia inhibitory factor
• chromatin organization
• methylation
• mitotic cell cycle
• negative regulation of DNA-templated transcription
• negative regulation of transcription by RNA polymerase II
• positive regulation of transcription by RNA polymerase II
• regulation of extracellular matrix organization

Molecular functions

• DNA-binding transcription factor activity
• DNA-binding transcription factor binding
• DNA-binding transcription repressor activity, RNA polymerase II-specific
• methyltransferase activity
• RNA polymerase II cis-regulatory region sequence-specific DNA binding
• RNA polymerase II transcription regulatory region sequence-specific DNA binding
• sequence-specific DNA binding
• transcription cis-regulatory region binding
• zinc ion binding

Cellular components

• nuclear body
• nucleolus
• nucleoplasm
• nucleus

Protein domainsUniProt · Pfam · InterPro

• SET domain
• Zinc finger C2H2-type
• Zinc finger C2H2 superfamily
• SET domain superfamily
• Zinc finger PRDM4/PRDM1/PRDM14-like
• Zinc finger, C2H2 type
• Zinc-finger of C2H2 type
• C2H2-type zinc finger
• PR domain zinc finger protein 2, PR domain
• PR-domain zinc finger protein PRDM5-like
• PRDM5, PR/SET domain

KeywordsUniProt

• Activator
• Chromatin regulator
• DNA-binding
• Metal-binding
• Methyltransferase
• Nucleus
• Repeat
• Repressor
• S-adenosyl-L-methionine
• Transcription
• Transcription regulation
• Transferase
• Zinc
• Zinc-finger

InteractionsUniProt · HPA

Protein binding partners of PRDM5 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• GFI1
• HDAC1