PRDM2

Protein identityUniProt · HPA

UniProt accession

Q13029

Gene

PRDM2

Ensembl

ENSG00000116731

Chromosome

1

Canonical length

1718 aa

Protein class

Enzymes, Predicted intracellular proteins, Transcription factors

Subcellular location

Nucleoplasm,Golgi apparatus

OverviewNCBI Gene

This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]

Canonical amino-acid sequenceUniProt

1718 residues, UniProt reviewed canonical sequence.

>Q13029|PRDM2
     1  MNQNTTEPVA ATETLAEVPE HVLRGLPEEV RLFPSAVDKT RIGVWATKPI LKGKKFGPFV
    61  GDKKKRSQVK NNVYMWEVYY PNLGWMCIDA TDPEKGNWLR YVNWACSGEE QNLFPLEINR
   121  AIYYKTLKPI APGEELLVWY NGEDNPEIAA AIEEERASAR SKRSSPKSRK GKKKSQENKN
   181  KGNKIQDIQL KTSEPDFTSA NMRDSAEGPK EDEEKPSASA LEQPATLQEV ASQEVPPELA
   241  TPAPAWEPQP EPDERLEAAA CEVNDLGEEE EEEEEEDEEE EEDDDDDELE DEGEEEASMP
   301  NENSVKEPEI RCDEKPEDLL EEPKTTSEET LEDCSEVTPA MQIPRTKEEA NGDVFETFMF
   361  PCQHCERKFT TKQGLERHMH IHISTVNHAF KCKYCGKAFG TQINRRRHER RHEAGLKRKP
   421  SQTLQPSEDL ADGKASGENV ASKDDSSPPS LGPDCLIMNS EKASQDTINS SVVEENGEVK
   481  ELHPCKYCKK VFGTHTNMRR HQRRVHERHL IPKGVRRKGG LEEPQPPAEQ AQATQNVYVP
   541  STEPEEEGEA DDVYIMDISS NISENLNYYI DGKIQTNNNT SNCDVIEMES ASADLYGINC
   601  LLTPVTVEIT QNIKTTQVPV TEDLPKEPLG STNSEAKKRR TASPPALPKI KAETDSDPMV
   661  PSCSLSLPLS ISTTEAVSFH KEKSVYLSSK LKQLLQTQDK LTPAGISATE IAKLGPVCVS
   721  APASMLPVTS SRFKRRTSSP PSSPQHSPAL RDFGKPSDGK AAWTDAGLTS KKSKLESHSD
   781  SPAWSLSGRD ERETVSPPCF DEYKMSKEWT ASSAFSSVCN QQPLDLSSGV KQKAEGTGKT
   841  PVQWESVLDL SVHKKHCSDS EGKEFKESHS VQPTCSAVKK RKPTTCMLQK VLLNEYNGID
   901  LPVENPADGT RSPSPCKSLE AQPDPDLGPG SGFPAPTVES TPDVCPSSPA LQTPSLSSGQ
   961  LPPLLIPTDP SSPPPCPPVL TVATPPPPLL PTVPLPAPSS SASPHPCPSP LSNATAQSPL
  1021  PILSPTVSPS PSPIPPVEPL MSAASPGPPT LSSSSSSSSS SSSFSSSSSS SSPSPPPLSA
  1081  ISSVVSSGDN LEASLPMISF KQEELENEGL KPREEPQSAA EQDVVVQETF NKNFVCNVCE
  1141  SPFLSIKDLT KHLSIHAEEW PFKCEFCVQL FKDKTDLSEH RFLLHGVGNI FVCSVCKKEF
  1201  AFLCNLQQHQ RDLHPDKVCT HHEFESGTLR PQNFTDPSKA HVEHMQSLPE DPLETSKEEE
  1261  ELNDSSEELY TTIKIMASGI KTKDPDVRLG LNQHYPSFKP PPFQYHHRNP MGIGVTATNF
  1321  TTHNIPQTFT TAIRCTKCGK GVDNMPELHK HILACASASD KKRYTPKKNP VPLKQTVQPK
  1381  NGVVVLDNSG KNAFRRMGQP KRLNFSVELS KMSSNKLKLN ALKKKNQLVQ KAILQKNKSA
  1441  KQKADLKNAC ESSSHICPYC NREFTYIGSL NKHAAFSCPK KPLSPPKKKV SHSSKKGGHS
  1501  SPASSDKNSN SNHRRRTADA EIKMQSMQTP LGKTRARSSG PTQVPLPSSS FRSKQNVKFA
  1561  ASVKSKKPSS SSLRNSSPIR MAKITHVEGK KPKAVAKNHS AQLSSKTSRS LHVRVQKSKA
  1621  VLQSKSTLAS KKRTDRFNIK SRERSGGPVT RSLQLAAAAD LSENKREDGS AKQELKDFSY
  1681  SLRLASRCSP PAAPYITRQY RKVKAPAAAQ FQGPFFKE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PRDM2 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)

0.61

Highest tissue expression

75 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PRDM2.

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 304 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Flexion contracture

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)

0.22

gnomAD pLI

1

gnomAD missense Z

1.08

DepMap mean gene effect

0.02

DepMap dependency class

none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• determination of adult lifespan
• methylation
• negative regulation of transcription by RNA polymerase II
• positive regulation of transcription by RNA polymerase II
• regulation of DNA-templated transcription
• regulation of transcription by RNA polymerase II

Molecular functions

• DNA-binding transcription activator activity, RNA polymerase II-specific
• DNA-binding transcription factor activity
• DNA-binding transcription factor activity, RNA polymerase II-specific
• DNA-binding transcription repressor activity, RNA polymerase II-specific
• histone H3K9 trimethyltransferase activity
• RNA polymerase II transcription regulatory region sequence-specific DNA binding
• sequence-specific DNA binding
• zinc ion binding

Cellular components

• Golgi apparatus
• 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
• C2H2-type zinc finger
• PR domain zinc finger protein 2, PR domain
• PR domain zinc finger protein 2
• PRDM2, PR/SET domain

KeywordsUniProt

• Activator
• Alternative initiation
• DNA-binding
• Isopeptide bond
• Metal-binding
• Methyltransferase
• Nucleus
• Phosphoprotein
• Repeat
• S-adenosyl-L-methionine
• Transcription
• Transcription regulation
• Transferase
• Ubl conjugation
• Zinc
• Zinc-finger

InteractionsUniProt · HPA

Protein binding partners of PRDM2 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• GATA3