TRAF3IP3

gene
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Also known as T3JAM

Summary

TRAF3IP3 (TRAF3 interacting protein 3, HGNC:30766) is a protein-coding gene on chromosome 1q32.2, encoding TRAF3-interacting JNK-activating modulator (Q9Y228). Adapter protein that plays essential roles in both innate and adaptive immunity.

The gene encodes a protein that mediates cell growth by modulating the c-Jun N-terminal kinase signal transduction pathway. The encoded protein may also interact with a large multi-protein assembly containing the phosphatase 2A catalytic subunit. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 80342 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 67 total
  • MANE Select transcript: NM_025228

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30766
Approved symbolTRAF3IP3
NameTRAF3 interacting protein 3
Location1q32.2
Locus typegene with protein product
StatusApproved
AliasesT3JAM
Ensembl geneENSG00000009790
Ensembl biotypeprotein_coding
OMIM608255
Entrez80342

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 14 protein_coding, 3 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000367023, ENST00000367024, ENST00000367025, ENST00000367026, ENST00000400959, ENST00000460314, ENST00000467830, ENST00000468672, ENST00000471368, ENST00000474496, ENST00000476050, ENST00000477431, ENST00000478359, ENST00000479796, ENST00000487271, ENST00000488702, ENST00000884880, ENST00000884881, ENST00000884882, ENST00000884883, ENST00000884884, ENST00000957589

RefSeq mRNA: 4 — MANE Select: NM_025228 NM_001287754, NM_001320143, NM_001320144, NM_025228

CCDS: CCDS1490, CCDS73023, CCDS81422

Canonical transcript exons

ENST00000367025 — 17 exons

ExonStartEnd
ENSE00000792126209780470209780606
ENSE00001248122209779315209779374
ENSE00001443283209759034209759134
ENSE00001900931209756053209756309
ENSE00001913729209782056209782310
ENSE00002213174209762813209762870
ENSE00002221582209775599209775736
ENSE00002262885209763363209763392
ENSE00002267091209762515209762662
ENSE00002284279209763492209763587
ENSE00002302242209759982209760384
ENSE00002320911209763068209763092
ENSE00003479474209777352209777487
ENSE00003500170209781345209781458
ENSE00003516467209772948209773019
ENSE00003679353209778111209778173
ENSE00003694681209775349209775489

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 99.12.

FANTOM5 (CAGE): breadth broad, TPM avg 18.0491 / max 706.3126, expressed in 490 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
83564.4034355
83663.7747316
83553.4173314
83672.7284218
83572.5598260
83650.5581209
83680.331798
83630.152651
83640.083146
83540.040019

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.12gold quality
leukocyteCL:000073897.98gold quality
monocyteCL:000057697.94gold quality
mononuclear cellCL:000084297.91gold quality
bloodUBERON:000017897.40gold quality
spleenUBERON:000210696.53gold quality
lymph nodeUBERON:000002996.39gold quality
vermiform appendixUBERON:000115495.23gold quality
bone marrow cellCL:000209294.24gold quality
thymusUBERON:000237094.03gold quality
bone marrowUBERON:000237192.79gold quality
epithelium of nasopharynxUBERON:000195190.33gold quality
caecumUBERON:000115389.99gold quality
trabecular bone tissueUBERON:000248388.96gold quality
tonsilUBERON:000237288.87gold quality
small intestine Peyer’s patchUBERON:000345488.85gold quality
gall bladderUBERON:000211086.19gold quality
rectumUBERON:000105286.16gold quality
small intestineUBERON:000210886.14gold quality
mucosa of transverse colonUBERON:000499183.37gold quality
superficial temporal arteryUBERON:000161482.71gold quality
upper lobe of left lungUBERON:000895282.68gold quality
right lungUBERON:000216782.48gold quality
buccal mucosa cellCL:000233682.46gold quality
amniotic fluidUBERON:000017382.07gold quality
upper lobe of lungUBERON:000894881.26gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099180.56gold quality
colonic epitheliumUBERON:000039779.51gold quality
right coronary arteryUBERON:000162579.06gold quality
body of stomachUBERON:000116177.13gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 9.

ExperimentMarker?Max mean expression
E-MTAB-6701yes74.77
E-CURD-122yes37.32
E-MTAB-10287yes31.34
E-MTAB-8410yes21.86
E-HCAD-10yes21.47
E-HCAD-1yes18.13
E-CURD-112yes7.93
E-GEOD-130148yes3.69
E-MTAB-7606no1224.07
E-MTAB-6379no1046.64
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting TRAF3IP3, 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-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-63699.8069.581500
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-6832-3P99.5270.441726
HSA-MIR-203A-3P99.4970.562806
HSA-MIR-94099.3766.142064
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-4777-3P99.1568.92626
HSA-MIR-42198.9067.041883
HSA-MIR-3144-3P98.1567.34677
HSA-MIR-473697.9665.891287
HSA-MIR-1910-5P97.4266.36844
HSA-MIR-875-5P96.7466.48579
HSA-MIR-3059-3P96.7167.08606

Literature-anchored findings (GeneRIF, showing 8)

  • This paper provides an alignment of the mouse and human proteins. (PMID:14572659)
  • TRAF3IP3 stimulated cell growth by modulating the c-Jun N-terminal kinase (JNK) pathway (PMID:17868742)
  • Tumor microarray analysis on 23 primary melanoma and nine positive lymph nodes revealed that 70% of human primary melanoma and 66% of lymph node metastases were positive for TRAF3IP3. Immunohistochemistry analysis of the tumors revealed that TRAF3IP3-shRNA tumors had increased apoptosis and reduced microvascular density. (PMID:29553967)
  • Findings uncover TRAF3IP3 as an important regulator for RIG-I-MAVS signaling, which bridges MAVS and TRAF3 for an effective antiviral innate immune response. (PMID:31390091)
  • Secondary Genome-Wide Association Study Using Novel Analytical Strategies Disentangle Genetic Components of Cleft Lip and/or Cleft Palate in 1q32.2. (PMID:33137956)
  • High TRAF3IP3 Level Predicts Poor Prognosis of Patients with Gliomas. (PMID:33444836)
  • Novel germline TRAF3IP3 mutation in a dyad with familial acute B lymphoblastic leukemia. (PMID:33503336)
  • The variants in PTPRB, TRAF3IP3, and DISC1 genes were associated with Graves’ disease in the Chinese population. (PMID:36397361)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusTraf3ip3ENSMUSG00000037318
rattus_norvegicusTraf3ip3ENSRNOG00000005565
drosophila_melanogasterSlmapFBGN0040011
caenorhabditis_elegansWBGENE00019766

Paralogs (2): CCDC136 (ENSG00000128596), SLMAP (ENSG00000163681)

Protein

Protein identifiers

TRAF3-interacting JNK-activating modulatorQ9Y228 (reviewed: Q9Y228)

Alternative names: TRAF3-interacting protein 3

All UniProt accessions (7): Q9Y228, B1AJU2, C9J0C0, C9JBA0, C9JXB3, E2QRE5, H0YF09

UniProt curated annotations — full annotation on UniProt →

Function. Adapter protein that plays essential roles in both innate and adaptive immunity. Plays a crucial role in the regulation of thymocyte development. Mechanistically, mediates TCR-stimulated activation through recruiting MAP2K1/MEK1 to the Golgi and, thereby, facilitating the interaction of MAP2K1/MEK1 with its activator BRAF. Also plays an essential role in regulatory T-cell stability and function by recruiting the serine-threonine phosphatase catalytic subunit (PPP2CA) to the lysosome, thereby facilitating the interaction of PP2Ac with the mTORC1 component RPTOR and restricting glycolytic metabolism. Positively regulates TLR4 signaling activity in macrophage-mediated inflammation by acting as a molecular clamp to facilitate LPS-induced translocation of TLR4 to lipid rafts. In response to viral infection, facilitates the recruitment of TRAF3 to MAVS within mitochondria leading to IRF3 activation and interferon production. However, participates in the maintenance of immune homeostasis and the prevention of overzealous innate immunity by promoting ‘Lys-48’-dependent ubiquitination of TBK1.

Subunit / interactions. Interacts (via its coiled-coil domain) with TRAF3 (via isoleucine zipper). Interacts with MAP2K1. Interacts with PPP2CA; this interaction targets PPP2CA to the lysosomes. Interacts with TLR4. Interacts with MAVS. Interacts with TBK1.

Subcellular location. Cell membrane. Golgi apparatus membrane. Lysosome membrane. Mitochondrion outer membrane.

Isoforms (3)

UniProt IDNamesCanonical?
Q9Y228-11yes
Q9Y228-22
Q9Y228-33

RefSeq proteins (4): NP_001274683, NP_001307072, NP_001307073, NP_079504* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR051176Cent_Immune-Sig_ModFamily

UniProt features (13 total): splice variant 3, topological domain 2, sequence variant 2, region of interest 2, coiled-coil region 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y228-F174.770.43

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 215 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, MULLIGHAN_NPM1_SIGNATURE_3_UP, GNF2_CASP8, GOBP_POSITIVE_REGULATION_OF_TYPE_I_INTERFERON_PRODUCTION, GOBP_RESPONSE_TO_PEPTIDE, GOCC_VACUOLAR_MEMBRANE, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, GOBP_RESPONSE_TO_INTERFERON_BETA, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS, BROWNE_HCMV_INFECTION_48HR_DN, GOBP_REGULATION_OF_IMMUNE_RESPONSE, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, GOBP_POSITIVE_REGULATION_OF_INTERFERON_BETA_PRODUCTION, SU_THYMUS

GO Biological Process (5): cytoplasmic pattern recognition receptor signaling pathway (GO:0002753), positive regulation of type I interferon production (GO:0032481), positive regulation of interferon-beta production (GO:0032728), cellular response to interferon-beta (GO:0035458), antiviral innate immune response (GO:0140374)

GO Molecular Function (4): protein-macromolecule adaptor activity (GO:0030674), zf-TRAF domain binding (GO:0044198), molecular adaptor activity (GO:0060090), protein binding (GO:0005515)

GO Cellular Component (10): Golgi membrane (GO:0000139), mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), lysosomal membrane (GO:0005765), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), mitochondrial membrane (GO:0031966), lysosome (GO:0005764), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
positive regulation of cytokine production2
binding2
cytoplasm2
intracellular membrane-bounded organelle2
organelle membrane2
pattern recognition receptor signaling pathway1
intracellular receptor signaling pathway1
regulation of type I interferon production1
type I interferon production1
positive regulation of type I interferon production1
interferon-beta production1
regulation of interferon-beta production1
response to interferon-beta1
cellular response to cytokine stimulus1
innate immune response1
defense response to virus1
protein binding1
molecular adaptor activity1
protein domain specific binding1
molecular_function1
Golgi apparatus1
bounding membrane of organelle1
mitochondrial membrane1
organelle outer membrane1
lysosome1
lytic vacuole membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
mitochondrion1
mitochondrial envelope1
lytic vacuole1
endomembrane system1
cellular anatomical structure1

Protein interactions and networks

STRING

1566 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TRAF3IP3TRAF3Q13114974
TRAF3IP3FGFR1OP2Q9NVK5572
TRAF3IP3OTUD5Q96G74549
TRAF3IP3C1orf74Q96LT6544
TRAF3IP3TBK1Q9UHD2497
TRAF3IP3IKBKEQ14164496
TRAF3IP3RDXP35241469
TRAF3IP3ATG16L1Q676U5458
TRAF3IP3TRAF1Q13077450
TRAF3IP3LTBRP36941445
TRAF3IP3CRNKL1Q9BZJ0430
TRAF3IP3MSNP26038429
TRAF3IP3SLC7A6Q92536426
TRAF3IP3TRILQ7L0X0422
TRAF3IP3FAM170AA1A519416

IntAct

198 interactions, top by confidence:

ABTypeScore
EMDTRAF3IP3psi-mi:“MI:0915”(physical association)0.810
TRAF3IP3EMDpsi-mi:“MI:0915”(physical association)0.810
KASH5TRAF3IP3psi-mi:“MI:0915”(physical association)0.720
FATE1TRAF3IP3psi-mi:“MI:0915”(physical association)0.720
TRAF3IP3NDEL1psi-mi:“MI:0915”(physical association)0.720
NDEL1TRAF3IP3psi-mi:“MI:0915”(physical association)0.720
TRAF3IP3FATE1psi-mi:“MI:0915”(physical association)0.720
TRAF3IP3SP100psi-mi:“MI:0915”(physical association)0.670
TFIP11TRAF3IP3psi-mi:“MI:0915”(physical association)0.670
SP100TRAF3IP3psi-mi:“MI:0915”(physical association)0.670
TRAF3IP3TFIP11psi-mi:“MI:0915”(physical association)0.670
TRAF3IP3STRNpsi-mi:“MI:0915”(physical association)0.620
STRIP1TRAF3IP3psi-mi:“MI:0915”(physical association)0.620
TRAF3IP3STRN3psi-mi:“MI:0915”(physical association)0.620

BioGRID (128): TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), TRAF3IP3 (Two-hybrid), NDEL1 (Two-hybrid), FATE1 (Two-hybrid), CCDC155 (Two-hybrid), TRAF3IP3 (Two-hybrid), FGFR1OP2 (Affinity Capture-MS), SIKE1 (Affinity Capture-MS), STRIP2 (Affinity Capture-MS)

ESM2 similar proteins: A1L443, A2IDD5, A4IFI1, A6NJZ7, A6NNL0, A6NNM3, A8MT33, B1AL46, D3Z5T1, O95153, Q2M3G4, Q2T9R2, Q3TVI4, Q3TYX8, Q49AM3, Q4KLY2, Q569K6, Q5JTD0, Q5JXC2, Q5SSQ6, Q5SW24, Q5VT03, Q5VZR2, Q6ZNE9, Q7TN08, Q7TNF8, Q7Z591, Q80VJ8, Q810H6, Q811T9, Q86SX3, Q8C963, Q8CB62, Q8CII8, Q8IVF1, Q8IXR5, Q8N0S2, Q8N137, Q8N205, Q8N6L0

Diamond homologs: A6ZRW7, O74388, P0C219, P38823, P53924, Q03944, Q06001, Q10322, Q14BN4, Q28623, Q3URD3, Q8C0G2, Q9Y228, Q3TVA9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance57
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2517 predictions. Top by Δscore:

VariantEffectΔscore
1:209756307:G:GTdonor_gain1.0000
1:209759033:GCA:Gacceptor_gain1.0000
1:209759969:T:Aacceptor_gain1.0000
1:209760240:G:GTdonor_gain1.0000
1:209763393:G:GGdonor_gain1.0000
1:209775336:A:AGacceptor_gain1.0000
1:209775337:T:Gacceptor_gain1.0000
1:209775347:A:AGacceptor_gain1.0000
1:209775348:G:GGacceptor_gain1.0000
1:209775348:GAA:Gacceptor_gain1.0000
1:209775488:AGGT:Adonor_loss1.0000
1:209775489:GGTA:Gdonor_loss1.0000
1:209775490:GTATG:Gdonor_loss1.0000
1:209775491:T:Gdonor_loss1.0000
1:209775594:CTCA:Cacceptor_loss1.0000
1:209775595:TCA:Tacceptor_loss1.0000
1:209775596:CAG:Cacceptor_loss1.0000
1:209775597:A:AGacceptor_gain1.0000
1:209775597:AGC:Aacceptor_gain1.0000
1:209775598:G:GGacceptor_gain1.0000
1:209775598:G:GTacceptor_loss1.0000
1:209775598:GC:Gacceptor_gain1.0000
1:209775598:GCG:Gacceptor_gain1.0000
1:209775598:GCGAT:Gacceptor_gain1.0000
1:209775736:GGTA:Gdonor_loss1.0000
1:209777347:TACA:Tacceptor_loss1.0000
1:209777348:ACAG:Aacceptor_gain1.0000
1:209777350:AG:Aacceptor_gain1.0000
1:209777351:GG:Gacceptor_gain1.0000
1:209777351:GGGA:Gacceptor_gain1.0000

AlphaMissense

3606 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:209763388:T:CL201P0.996
1:209763495:G:CA204P0.995
1:209775421:G:CA283P0.994
1:209763376:T:CL197P0.993
1:209763517:T:CL211P0.992
1:209763547:T:CL221P0.991
1:209763506:G:CR207S0.990
1:209763506:G:TR207S0.990
1:209763538:T:CL218P0.990
1:209763499:T:CL205P0.989
1:209763526:A:TK214I0.989
1:209773003:T:CL253P0.988
1:209775434:T:CL287P0.988
1:209763559:T:CL225P0.987
1:209772982:T:CL246P0.986
1:209772970:T:CL242P0.985
1:209775476:T:CL301P0.985
1:209763508:A:TE208V0.984
1:209763567:G:CA228P0.982
1:209775614:G:CA311P0.981
1:209763388:T:AL201H0.979
1:209775711:T:CL343P0.979
1:209763378:T:CS198P0.978
1:209763508:A:CE208A0.977
1:209775720:T:CL346P0.977
1:209763376:T:AL197H0.976
1:209773000:A:CQ252P0.976
1:209775430:T:CS286P0.976
1:209775732:T:CL350P0.976
1:209763527:A:CK214N0.975

dbSNP variants (sampled 300 via entrez): RS1000231099 (1:209758833 C>T), RS1000330841 (1:209755875 A>G), RS1000846417 (1:209772021 G>A,C), RS1000940950 (1:209770491 G>A), RS1000990256 (1:209757062 A>G), RS1001172374 (1:209766470 T>C), RS1001192790 (1:209778792 T>C), RS1001317061 (1:209776958 G>A), RS1001478446 (1:209759520 G>A), RS1001598924 (1:209778258 G>A), RS1001637753 (1:209770533 G>A,C), RS1001687214 (1:209766247 G>A), RS1001773527 (1:209771332 T>C), RS1001866391 (1:209779629 A>C), RS1001944322 (1:209758379 A>T)

Disease associations

OMIM: gene MIM:608255 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

StudyTraitp-value
GCST004601_10Red blood cell count6.000000e-10
GCST004602_25Mean corpuscular volume9.000000e-10
GCST004630_19Mean corpuscular hemoglobin5.000000e-09
GCST004866_6Alopecia areata2.000000e-06
GCST006946_20Worry too long after an embarrassing experience4.000000e-08
GCST011088_2Orofacial clefts5.000000e-09
GCST90002390_336Mean corpuscular hemoglobin2.000000e-18
GCST90002392_250Mean corpuscular volume6.000000e-23
GCST90002396_161Mean reticulocyte volume3.000000e-17
GCST90002397_744Mean spheric corpuscular volume3.000000e-16
GCST90002403_60Red blood cell count8.000000e-18

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004305erythrocyte count
EFO:0004527mean corpuscular hemoglobin
EFO:0009589worry measurement
EFO:0010701mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionaffects expression, decreases expression3
sodium arseniteincreases expression, decreases expression2
Benzo(a)pyrenedecreases expression, increases methylation2
Nickeldecreases expression, increases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
GSK-J4decreases expression1
triphenyl phosphateaffects expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
CGP 52608affects binding, increases reaction1
Grape Seed Proanthocyanidinsdecreases expression, affects cotreatment1
Acetaminophenincreases expression1
Air Pollutants, Occupationaldecreases expression1
Arsenicaffects methylation1
Cadmiumdecreases expression, increases abundance1
Catechinaffects cotreatment, decreases expression1
Diurondecreases expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression1
Methyl Methanesulfonatedecreases expression1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Thiramincreases expression1
Vincristinedecreases expression1
Isotretinoinincreases expression1
Aflatoxin B1increases methylation1
Asbestos, Crocidoliteincreases expression1
Antirheumatic Agentsdecreases 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): alopecia areata