RNF39

gene
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Also known as HZFw1LIRFFAP216

Summary

RNF39 (ring finger protein 39, HGNC:18064) is a protein-coding gene on chromosome 6p22.1, encoding RING finger protein 39 (Q9H2S5). Plays an inhibitory role in anti-RNA viral innate immunity by targeting the adapter DDX3X and promoting its ‘Lys-48’-linked polyubiquitination.

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.

Source: NCBI Gene 80352 — RefSeq curated summary.

At a glance

  • GWAS associations: 30
  • Clinical variants (ClinVar): 72 total
  • MANE Select transcript: NM_025236

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18064
Approved symbolRNF39
Namering finger protein 39
Location6p22.1
Locus typegene with protein product
StatusApproved
AliasesHZFw1, LIRF, FAP216
Ensembl geneENSG00000204618
Ensembl biotypeprotein_coding
OMIM607524
Entrez80352

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000244360, ENST00000376751

RefSeq mRNA: 2 — MANE Select: NM_025236 NM_025236, NM_170769

CCDS: CCDS4673, CCDS4674

Canonical transcript exons

ENST00000244360 — 4 exons

ExonStartEnd
ENSE000017040483007315730073248
ENSE000017411143007345630073478
ENSE000018255103007522330075769
ENSE000018936103007027030071691

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 92.67.

Top tissues by expression

133 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
skin of abdomenUBERON:000141692.67gold quality
zone of skinUBERON:000001492.27gold quality
skin of legUBERON:000151192.23gold quality
lower esophagus mucosaUBERON:003583488.21gold quality
esophagus mucosaUBERON:000246982.43gold quality
minor salivary glandUBERON:000183082.37gold quality
saliva-secreting glandUBERON:000104482.19gold quality
vaginaUBERON:000099679.91gold quality
olfactory segment of nasal mucosaUBERON:000538676.99gold quality
prostate glandUBERON:000236772.95gold quality
right uterine tubeUBERON:000130272.28gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047371.73gold quality
body of stomachUBERON:000116170.26gold quality
ectocervixUBERON:001224970.06gold quality
esophagusUBERON:000104369.90gold quality
stromal cell of endometriumCL:000225569.58gold quality
cortical plateUBERON:000534368.98gold quality
mammary glandUBERON:000191168.96gold quality
thoracic mammary glandUBERON:000520068.96gold quality
uterine cervixUBERON:000000268.69gold quality
tonsilUBERON:000237268.52gold quality
stomachUBERON:000094567.14gold quality
islet of LangerhansUBERON:000000665.43gold quality
fundus of stomachUBERON:000116065.22gold quality
endocervixUBERON:000045864.99gold quality
right lungUBERON:000216764.98gold quality
urinary bladderUBERON:000125563.35gold quality
pancreasUBERON:000126463.24gold quality
ganglionic eminenceUBERON:000402363.20gold quality
fallopian tubeUBERON:000388963.03gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes3.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting RNF39, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-4481100.0066.421669
HSA-MIR-4455100.0065.481587
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-314899.9775.066478
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-211099.9666.681930
HSA-MIR-767-5P99.9570.85993
HSA-MIR-568299.8972.561005
HSA-MIR-427199.8868.322244
HSA-MIR-137-3P99.8774.742401
HSA-MIR-197699.7465.481127
HSA-MIR-430699.7270.503630
HSA-MIR-472999.6972.184233
HSA-MIR-317599.6566.302031
HSA-MIR-451699.6167.783390
HSA-MIR-1213199.4868.721673
HSA-MIR-6871-3P99.4368.85741
HSA-MIR-94099.3766.142064
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-806599.1970.381289
HSA-MIR-478499.1567.411733
HSA-MIR-3152-3P99.1066.35678
HSA-MIR-443499.1067.011984
HSA-MIR-570399.1067.092053

Literature-anchored findings (GeneRIF, showing 3)

  • these findings suggest that RNF39 and TRIM39 are involved in the etiology of Behcet’s disease. (PMID:20875797)
  • Results identified RNF39 as cis methylation quantitative trait loci in both allergic rhinitis and asthma. (PMID:28149331)
  • The findings provide evidence that hypermethylation in an independent MHC locus, RNF39, is also associated with relapsing-remitting multiple sclerosis. (PMID:28729889)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusRnf39ENSMUSG00000036492
rattus_norvegicusRnf39ENSRNOG00000000781
rattus_norvegicusENSRNOG00000079068

Paralogs (80): MID2 (ENSG00000080561), TRIM9 (ENSG00000100505), MID1 (ENSG00000101871), MEFV (ENSG00000103313), TRIM35 (ENSG00000104228), TRIM14 (ENSG00000106785), TRIM37 (ENSG00000108395), TRIM2 (ENSG00000109654), TRIM3 (ENSG00000110171), TRIM38 (ENSG00000112343), TRIM62 (ENSG00000116525), TRIM67 (ENSG00000119283), TRIM32 (ENSG00000119401), BSPRY (ENSG00000119411), TRIM25 (ENSG00000121060), TRIM6 (ENSG00000121236), TRIM24 (ENSG00000122779), TRIM51 (ENSG00000124900), TRIM28 (ENSG00000130726), TRIM21 (ENSG00000132109), TRIM5 (ENSG00000132256), TRIM22 (ENSG00000132274), TRIM47 (ENSG00000132481), TRIM45 (ENSG00000134253), TRIM29 (ENSG00000137699), TRIM54 (ENSG00000138100), PML (ENSG00000140464), TRIM65 (ENSG00000141569), TRIM43B (ENSG00000144010), TRIM43 (ENSG00000144015), TRIM7 (ENSG00000146054), TRIM41 (ENSG00000146063), TRIM50 (ENSG00000146755), TRIM4 (ENSG00000146833), TRIM55 (ENSG00000147573), TRIM48 (ENSG00000150244), TRIM36 (ENSG00000152503), TRIM11 (ENSG00000154370), TRIM74 (ENSG00000155428), TRIM42 (ENSG00000155890)

Protein

Protein identifiers

RING finger protein 39Q9H2S5 (reviewed: Q9H2S5)

Alternative names: Protein HZFw

All UniProt accessions (1): Q9H2S5

UniProt curated annotations — full annotation on UniProt →

Function. Plays an inhibitory role in anti-RNA viral innate immunity by targeting the adapter DDX3X and promoting its ‘Lys-48’-linked polyubiquitination. Alternatively, enhances the cGAS-STING pathway activation by promoting ‘Lys-63’-linked ubiquitination of STING1, facilitating the STING1-TBK1 complex formation and STING1 activation. (Microbial infection) Plays a positive role in human immunodeficiency virus (HIV-1) replication.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in testis.

Pathway. Protein modification; protein ubiquitination.

Isoforms (3)

UniProt IDNamesCanonical?
Q9H2S5-11, HZFW1yes
Q9H2S5-22, HZFW2
Q9H2S5-33, HZFW3

RefSeq proteins (2): NP_079512, NP_739575 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR001870B30.2/SPRYDomain
IPR003877SPRY_domDomain
IPR003879Butyrophylin_SPRYDomain
IPR006574PRYDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR017907Znf_RING_CSConserved_site
IPR027370Znf-RING_eukDomain
IPR043136B30.2/SPRY_sfHomologous_superfamily
IPR050143TRIM/RBCCFamily

Pfam: PF00622, PF13445, PF13765

UniProt features (11 total): sequence variant 4, splice variant 3, chain 1, domain 1, mutagenesis site 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H2S5-F166.270.25

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (1):

PositionPhenotype
108complete loss of e3 ligase activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 122 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, XU_GH1_AUTOCRINE_TARGETS_UP, NKX25_02, CHX10_01, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, GOBP_REGULATION_OF_IMMUNE_RESPONSE, SRF_C, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION

GO Biological Process (7): negative regulation of cytoplasmic pattern recognition receptor signaling pathway (GO:0039532), innate immune response (GO:0045087), protein K63-linked ubiquitination (GO:0070534), positive regulation of cGAS/STING signaling pathway (GO:0141111), cytoplasmic pattern recognition receptor signaling pathway (GO:0002753), positive regulation of type I interferon production (GO:0032481), cGAS/STING signaling pathway (GO:0140896)

GO Molecular Function (5): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasmic pattern recognition receptor signaling pathway2
regulation of cytoplasmic pattern recognition receptor signaling pathway2
positive regulation of cytokine production2
negative regulation of immune system process1
negative regulation of intracellular signal transduction1
immune response1
defense response to symbiont1
protein polyubiquitination1
positive regulation of pattern recognition receptor signaling pathway1
cGAS/STING signaling pathway1
positive regulation of intracellular signal transduction1
pattern recognition receptor signaling pathway1
intracellular receptor signaling pathway1
regulation of type I interferon production1
type I interferon production1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

761 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RNF39HLA-FP30511796
RNF39POLR1HQ9P1U0708
RNF39HLA-AP01891682
RNF39C10orf105Q8TEF2578
RNF39TCF19Q9Y242560
RNF39CFAP92Q9ULG3515
RNF39TRIM31Q9BZY9513
RNF39CDSNQ15517494
RNF39CCHCR1Q8TD31491
RNF39ZFP57Q9NU63447
RNF39ABCF1Q8NE71440
RNF39PPP1R11O60927435
RNF39PSMC5P47210433
RNF39ZNF57Q68EA5428
RNF39PRKACAP17612421
RNF39PRKACGP22612421

IntAct

22 interactions, top by confidence:

ABTypeScore
RNF39DNAAF6psi-mi:“MI:0915”(physical association)0.560
KRT27RNF39psi-mi:“MI:0915”(physical association)0.560
GOLGA6L9RNF39psi-mi:“MI:0915”(physical association)0.560
RABEP1RNF39psi-mi:“MI:0915”(physical association)0.560
AP1B1RNF39psi-mi:“MI:0915”(physical association)0.560
MORN3RNF39psi-mi:“MI:0915”(physical association)0.560
RINT1RNF39psi-mi:“MI:0915”(physical association)0.560
RNF39DNAAF6psi-mi:“MI:0915”(physical association)0.000
RNF39KRT27psi-mi:“MI:0915”(physical association)0.000
RNF39GOLGA6L9psi-mi:“MI:0915”(physical association)0.000
RNF39RABEP1psi-mi:“MI:0915”(physical association)0.000
RNF39AP1B1psi-mi:“MI:0915”(physical association)0.000
RNF39MORN3psi-mi:“MI:0915”(physical association)0.000
RNF39RINT1psi-mi:“MI:0915”(physical association)0.000

BioGRID (10): RNF39 (Two-hybrid), RNF39 (Two-hybrid), RNF39 (Two-hybrid), RNF39 (Two-hybrid), RNF39 (Two-hybrid), RNF39 (Two-hybrid), RNF39 (Two-hybrid), RNF39 (Affinity Capture-Western), RNF39 (Affinity Capture-Western), TP53 (Affinity Capture-Western)

ESM2 similar proteins: A0A0U1RR11, A0A0U1RRI6, A6NCS6, A6NJG2, B0BN44, D3YXK1, E9PY61, E9Q0B3, F5H4A9, O00220, O00221, P09038, P0DPI3, P22083, P98077, Q08AU9, Q2M2W7, Q2M3V2, Q2TBI2, Q5F267, Q5FW56, Q5IS69, Q5R866, Q5T4W7, Q5TM52, Q5U4P2, Q5VTJ3, Q659K9, Q673H1, Q69ZB3, Q6AYE8, Q6IPT2, Q6PJ61, Q7RTU4, Q7TSX9, Q7YR31, Q80SU3, Q86SH2, Q86Y97, Q8NBR0

Diamond homologs: A0A3B3IT33, A0JN74, A2XK56, A4QPC6, A6NCK2, A6NDI0, A6NGJ6, A6NI03, A6NLI5, A6NLU0, B1H278, B8B5U8, C9J1S8, D3YY23, D3Z8N2, F8VTS6, I1YAP6, O00478, O00481, O13033, O54952, O60106, O76064, P0CI25, P0CI26, P18892, P19474, P38398, P48754, P82456, P86448, P86449, Q14258, Q14527, Q1XHT8, Q28DS3, Q2HJ46, Q3C1V9, Q3TL54, Q4KLN8

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RNF39ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

72 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance55
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

740 predictions. Top by Δscore:

VariantEffectΔscore
6:30073151:CCTTA:Cdonor_loss1.0000
6:30073152:CTTA:Cdonor_loss1.0000
6:30073153:TTACC:Tdonor_loss1.0000
6:30073154:TA:Tdonor_loss1.0000
6:30073155:A:AGdonor_loss1.0000
6:30073156:C:CTdonor_loss1.0000
6:30073156:CCTGT:Cdonor_gain1.0000
6:30073244:CAAAT:Cacceptor_gain1.0000
6:30073245:AAAT:Aacceptor_gain1.0000
6:30073246:AAT:Aacceptor_gain1.0000
6:30073247:AT:Aacceptor_gain1.0000
6:30073249:C:CCacceptor_gain1.0000
6:30073250:T:Aacceptor_loss1.0000
6:30073254:C:CTacceptor_gain1.0000
6:30073489:C:CTacceptor_gain1.0000
6:30073490:A:Tacceptor_gain1.0000
6:30071689:CGG:Cacceptor_gain0.9900
6:30071692:C:CCacceptor_gain0.9900
6:30071699:C:CTacceptor_gain0.9900
6:30073155:A:ACdonor_gain0.9900
6:30073156:C:CCdonor_gain0.9900
6:30073246:AATCT:Aacceptor_gain0.9900
6:30073247:ATCT:Aacceptor_gain0.9900
6:30073255:A:Tacceptor_gain0.9900
6:30073257:A:ACacceptor_gain0.9900
6:30073257:A:Cacceptor_gain0.9900
6:30073451:CTCA:Cdonor_loss0.9900
6:30073452:TCA:Tdonor_loss0.9900
6:30073453:CA:Cdonor_loss0.9900
6:30073454:A:ACdonor_gain0.9900

AlphaMissense

2654 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:30071204:G:CF390L0.993
6:30071204:G:TF390L0.993
6:30071206:A:GF390L0.993
6:30071516:C:AW286C0.993
6:30071516:C:GW286C0.993
6:30071240:G:CF378L0.991
6:30071240:G:TF378L0.991
6:30071242:A:GF378L0.991
6:30071573:G:CF267L0.991
6:30071573:G:TF267L0.991
6:30071575:A:GF267L0.991
6:30075528:A:GC88R0.991
6:30071518:A:GW286R0.990
6:30071518:A:TW286R0.990
6:30075467:C:TC108Y0.989
6:30071241:A:GF378S0.988
6:30075469:G:CF107L0.988
6:30075469:G:TF107L0.988
6:30075471:A:GF107L0.988
6:30075352:A:CN146K0.986
6:30075352:A:TN146K0.986
6:30075468:A:GC108R0.986
6:30071280:A:GI365T0.985
6:30075497:G:TP98Q0.984
6:30075326:A:GI155T0.983
6:30075466:G:CC108W0.983
6:30075527:C:TC88Y0.983
6:30075472:G:CS106R0.982
6:30075472:G:TS106R0.982
6:30075474:T:GS106R0.982

dbSNP variants (sampled 300 via entrez): RS1000209541 (6:30074167 C>G), RS1000302971 (6:30074377 G>A), RS1000417246 (6:30071585 G>A), RS1000542037 (6:30072388 A>G), RS1000750123 (6:30072941 C>A), RS1001215432 (6:30075423 C>G,T), RS1001589928 (6:30071047 T>G), RS1001768790 (6:30077159 T>C), RS1003057991 (6:30072281 G>A), RS1003366347 (6:30071494 C>A,T), RS1003387282 (6:30070680 A>G), RS1004735656 (6:30076395 T>G), RS1006168389 (6:30071919 G>A), RS1006211776 (6:30076803 C>A,T), RS1006829034 (6:30070188 C>T)

Disease associations

OMIM: gene MIM:607524 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

30 associations (top):

StudyTraitp-value
GCST000308_3AIDS progression5.000000e-07
GCST000549_24HIV-1 control2.000000e-08
GCST002324_6Anger8.000000e-07
GCST004521_12Autism spectrum disorder or schizophrenia2.000000e-12
GCST004521_121Autism spectrum disorder or schizophrenia3.000000e-13
GCST004521_171Autism spectrum disorder or schizophrenia4.000000e-14
GCST004521_177Autism spectrum disorder or schizophrenia3.000000e-12
GCST004521_2Autism spectrum disorder or schizophrenia2.000000e-16
GCST004521_210Autism spectrum disorder or schizophrenia5.000000e-15
GCST004521_216Autism spectrum disorder or schizophrenia5.000000e-13
GCST004521_218Autism spectrum disorder or schizophrenia5.000000e-11
GCST004521_247Autism spectrum disorder or schizophrenia4.000000e-09
GCST004521_263Autism spectrum disorder or schizophrenia7.000000e-17
GCST004521_268Autism spectrum disorder or schizophrenia7.000000e-12
GCST004521_269Autism spectrum disorder or schizophrenia7.000000e-11
GCST004521_295Autism spectrum disorder or schizophrenia6.000000e-18
GCST004521_3Autism spectrum disorder or schizophrenia2.000000e-15
GCST004521_44Autism spectrum disorder or schizophrenia2.000000e-17
GCST004521_51Autism spectrum disorder or schizophrenia9.000000e-14
GCST004521_56Autism spectrum disorder or schizophrenia1.000000e-22
GCST004521_58Autism spectrum disorder or schizophrenia1.000000e-17
GCST004521_59Autism spectrum disorder or schizophrenia1.000000e-11
GCST004521_70Autism spectrum disorder or schizophrenia8.000000e-20
GCST004521_79Autism spectrum disorder or schizophrenia1.000000e-16
GCST004521_80Autism spectrum disorder or schizophrenia1.000000e-15
GCST004521_92Autism spectrum disorder or schizophrenia1.000000e-11
GCST004623_17Neutrophil percentage of granulocytes2.000000e-30
GCST006269_1232General cognitive ability5.000000e-08
GCST008436_1Nonobstructive coronary artery disease7.000000e-07
GCST009391_776Metabolite levels7.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0000180HIV-1 infection
EFO:0003015aggressive behavior
EFO:0007994neutrophil percentage of granulocytes
EFO:0004337intelligence
EFO:1001483non-obstructive coronary artery disease
EFO:0010393sphingomyelin 18:0 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Phthalic Acidsaffects methylation, decreases methylation, increases abundance2
Silicon Dioxideincreases expression2
aristolochic acid Iincreases expression1
aminomethylphosphonic acid (AMPA)affects methylation, increases abundance1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases methylation1
mono-(2-ethylhexyl)phthalatedecreases methylation, increases abundance1
1-hydroxypyreneaffects cotreatment, decreases methylation1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
Decitabineaffects expression1
Fulvestrantaffects cotreatment, increases methylation1
Glyphosateincreases abundance, affects methylation1
Atrazineincreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Cadmiumdecreases expression1
Calcitriolincreases expression1
Cisplatinaffects expression1
Estradiolaffects cotreatment, decreases expression1
Nickeldecreases expression1
Smokeincreases expression1
Sodium Dodecyl Sulfateincreases expression1
Tobacco Smoke Pollutionincreases expression1
Asbestos, Crocidoliteincreases expression1
Metals, Heavyaffects cotreatment, decreases methylation1
Cadmium Chloridedecreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): AIDS