Seroatlas · Human Serome Atlas

PRDM4

PR domain zinc finger protein 4

Also known as: PFM1, PRDM4_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9UKN5
Gene: PRDM4
Ensembl: ENSG00000110851
Chromosome: 12
Canonical length: 801 aa
Protein class: Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

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. An elevated expression level of this gene has been observed in PC12 cells treated with nerve growth factor, beta polypeptide (NGF). This gene is located in a chromosomal region that is thought to contain tumor suppressor genes. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

801 residues, UniProt reviewed canonical sequence.

>Q9UKN5|PRDM4
     1  MHHRMNEMNL SPVGMEQLTS SSVSNALPVS GSHLGLAASP THSAIPAPGL PVAIPNLGPS
    61  LSSLPSALSL MLPMGIGDRG VMCGLPERNY TLPPPPYPHL ESSYFRTILP GILSYLADRP
   121  PPQYIHPNSI NVDGNTALSI TNNPSALDPY QSNGNVGLEP GIVSIDSRSV NTHGAQSLHP
   181  SDGHEVALDT AITMENVSRV TSPISTDGMA EELTMDGVAG EHSQIPNGSR SHEPLSVDSV
   241  SNNLAADAVG HGGVIPMHGN GLELPVVMET DHIASRVNGM SDSALSDSIH TVAMSTNSVS
   301  VALSTSHNLA SLESVSLHEV GLSLEPVAVS SITQEVAMGT GHVDVSSDSL SFVSPSLQME
   361  DSNSNKENMA TLFTIWCTLC DRAYPSDCPE HGPVTFVPDT PIESRARLSL PKQLVLRQSI
   421  VGAEVGVWTG ETIPVRTCFG PLIGQQSHSM EVAEWTDKAV NHIWKIYHNG VLEFCIITTD
   481  ENECNWMMFV RKARNREEQN LVAYPHDGKI FFCTSQDIPP ENELLFYYSR DYAQQIGVPE
   541  HPDVHLCNCG KECNSYTEFK AHLTSHIHNH LPTQGHSGSH GPSHSKERKW KCSMCPQAFI
   601  SPSKLHVHFM GHMGMKPHKC DFCSKAFSDP SNLRTHLKIH TGQKNYRCTL CDKSFTQKAH
   661  LESHMVIHTG EKNLKCDYCD KLFMRRQDLK QHVLIHTQER QIKCPKCDKL FLRTNHLKKH
   721  LNSHEGKRDY VCEKCTKAYL TKYHLTRHLK TCKGPTSSSS APEEEEEDDS EEEDLADSVG
   781  TEDCRINSAV YSADESLSAH K

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PRDM4 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): 0.58
Highest tissue expression: 42 nTPM

Expression across tissuesHPA

Tissue

parathyroid gland: 42 nTPM
kidney: 20 nTPM
retina: 19 nTPM
bone marrow: 16 nTPM
rectum: 15 nTPM
esophagus: 15 nTPM

Single-cell type

b-cells: 126 nCPM
renal collecting duct intercalated cells: 97 nCPM
distal convoluted tubule cells: 56 nCPM
esophageal apical cells: 52 nCPM
renal connecting tubule cells: 48 nCPM
epididymal clear cells: 45 nCPM

Immune cell

non-classical monocyte: 4.2 nTPM
intermediate monocyte: 3 nTPM
memory B-cell: 2.6 nTPM
myeloid DC: 2.3 nTPM
T-reg: 2.2 nTPM
naive B-cell: 2.1 nTPM

Brain region

thalamus: 28 nTPM
cerebellum: 27 nTPM
white matter: 26 nTPM
pons: 25 nTPM
cerebral cortex: 25 nTPM
basal ganglia: 24 nTPM

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): 0.61
gnomAD pLI: 0
gnomAD missense Z: 1.07
DepMap mean gene effect: 0.01
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

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
PR domain zinc finger protein 2, PR domain
PR-domain zinc finger protein PRDM4
PRDM4, zinc ribbon domain
PRDM4, PR/SET domain
PR zinc knuckle motif

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PRDM4 as an antibody target. Whether an autoantibody or antibody against PRDM4 could matter depends on whether native PRDM4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PRDM4 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PRDM4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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