Seroatlas · Human Serome Atlas

RNF39

RING finger protein 39

Also known as: FAP216, HZFw1, LIRF, RNF39_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q9H2S5
Gene: RNF39
Ensembl: ENSG00000204618
Chromosome: 6
Canonical length: 420 aa
Protein class: Predicted intracellular proteins
Subcellular location: Vesicles,Plasma membrane,Centrosome

OverviewNCBI Gene

This gene lies within the major histocompatibility complex class I region on chromosome 6. Studies of a similar rat protein suggest that this gene encodes a protein that plays a role in an early phase of synaptic plasticity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

420 residues, UniProt reviewed canonical sequence.

>Q9H2S5|RNF39
     1  MWWRDLTRLR LWLKREAIPG EGRKAAKVNA GVGEKGIYTA SSRGGPPSAR SKAVTVVAEG
    61  AASRSWLSMD APELGPGLVE RLEQLATCPL CGGSFEDPVL LACEHSFCRA CLARRWGTPP
   121  ATGTEASPTA CPCCGLPCPR RSLRSNVRLA VEVRISRELR EKLAEPGARA GRRRGGRIPT
   181  MGCLDLPGED MRKTWRRFEV PTSKSSNSED DLPEDYPVVK KMLHRLTADL TLDPGTAHRR
   241  LLISADRRSV QLAPPGTPAP PDGPKRFDQL PAVLGAQGFG AGRHCWEVET ADAASCRDSS
   301  GEDADDEESH YAVGAAGESV QRKGCVRLCP AGAVWAVEGR GGRLWALTAP EPTLLGGVEP
   361  PPRRIRVDLD WERGRVAFYD GRSLDLLYAF QAPGPLGERI FPLFCTCDPR APLRIVPAES

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against RNF39 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): 0.43
Highest tissue expression: 64 nTPM

Expression across tissuesHPA

Tissue

skin: 64 nTPM
esophagus: 24 nTPM
vagina: 23 nTPM
cervix: 22 nTPM
salivary gland: 16 nTPM
stomach: 8.9 nTPM

Single-cell type

urothelial cells: 3.3 nCPM
ocular epithelial cells: 2.9 nCPM
papillary tip epithelial cells: 2.7 nCPM
prostatic club cells: 2.2 nCPM
endometrial secretory cells: 1.9 nCPM
prostatic hillock cells: 1.2 nCPM

Immune cell

neutrophil: 0.5 nTPM
eosinophil: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

cerebral cortex: 1.8 nTPM
basal ganglia: 1.4 nTPM
medulla oblongata: 1.4 nTPM
white matter: 1.3 nTPM
hippocampal formation: 1.2 nTPM
thalamus: 1.2 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): 1.19
gnomAD pLI: 0
gnomAD missense Z: 1.34
DepMap mean gene effect: -0.18
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

cytoplasm

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads RNF39 as an antibody target. Whether an autoantibody or antibody against RNF39 could matter depends on whether native RNF39 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

RNF39 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 RNF39 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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