TMX3

gene
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Also known as FLJ20793KIAA1830PDIA13

Summary

TMX3 (thioredoxin related transmembrane protein 3, HGNC:24718) is a protein-coding gene on chromosome 18q22.1, encoding Protein disulfide-isomerase TMX3 (Q96JJ7). Probable disulfide isomerase, which participates in the folding of proteins containing disulfide bonds.

This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange reactions. The canonical protein encoded by this gene has an N-terminal ER-signal sequence, a catalytically active thioredoxin domain, one transmembrane domain and a C-terminal ER-retention sequence. This gene is expressed in many tissues but has its highest expression in heart and skeletal muscle. It is expressed in the retinal neuroepithelium and lens epithelium in the developing murine eye and haploinsufficiency of this gene in humans and zebrafish is associated with microphthalmia. Alternative splicing results in multiple transcript variants encoding distinct isoforms.

Source: NCBI Gene 54495 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 113 total
  • MANE Select transcript: NM_019022

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24718
Approved symbolTMX3
Namethioredoxin related transmembrane protein 3
Location18q22.1
Locus typegene with protein product
StatusApproved
AliasesFLJ20793, KIAA1830, PDIA13
Ensembl geneENSG00000166479
Ensembl biotypeprotein_coding
OMIM616102
Entrez54495

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 9 protein_coding, 5 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000299608, ENST00000443099, ENST00000544714, ENST00000562706, ENST00000564008, ENST00000564631, ENST00000565918, ENST00000566135, ENST00000566887, ENST00000569053, ENST00000569982, ENST00000578765, ENST00000578816, ENST00000580785, ENST00000903506, ENST00000903507, ENST00000915516, ENST00000915517, ENST00000961335, ENST00000961336

RefSeq mRNA: 7 — MANE Select: NM_019022 NM_001350512, NM_001350513, NM_001350514, NM_001350515, NM_001350516, NM_001350517, NM_019022

CCDS: CCDS32840, CCDS86679, CCDS86680

Canonical transcript exons

ENST00000299608 — 16 exons

ExonStartEnd
ENSE000011033566871136468711403
ENSE000011033926871002168710144
ENSE000012897186867368868677193
ENSE000026136836871493668715108
ENSE000035029536868292568682981
ENSE000035128486867946368679531
ENSE000035261426868098168681110
ENSE000035371386868766768687765
ENSE000035502566870174568701790
ENSE000035771176870040568700485
ENSE000035953786871384668713900
ENSE000036037316868442868684485
ENSE000036076766869722668697303
ENSE000036207176868419068684243
ENSE000036678976869793268698031
ENSE000036866286869129568691361

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 98.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.2893 / max 358.8404, expressed in 1808 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
17232025.90671803
1723194.32961470
1723180.052916

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370198.22gold quality
endothelial cellCL:000011596.79gold quality
Brodmann (1909) area 23UBERON:001355496.24gold quality
stromal cell of endometriumCL:000225596.06gold quality
deciduaUBERON:000245095.88gold quality
oviduct epitheliumUBERON:000480495.88gold quality
vermiform appendixUBERON:000115495.72gold quality
visceral pleuraUBERON:000240195.61gold quality
epithelial cell of pancreasCL:000008395.30silver quality
parietal pleuraUBERON:000240095.06gold quality
cardiac muscle of right atriumUBERON:000337995.05gold quality
secondary oocyteCL:000065594.72gold quality
tibiaUBERON:000097994.57gold quality
monocyteCL:000057694.53gold quality
rectumUBERON:000105294.31gold quality
lymph nodeUBERON:000002994.30gold quality
tendonUBERON:000004394.12gold quality
smooth muscle tissueUBERON:000113594.05gold quality
leukocyteCL:000073894.03gold quality
right uterine tubeUBERON:000130294.03gold quality
oocyteCL:000002393.78gold quality
caecumUBERON:000115393.67gold quality
epithelium of nasopharynxUBERON:000195193.64gold quality
germinal epithelium of ovaryUBERON:000130493.57gold quality
adrenal tissueUBERON:001830393.38gold quality
endometriumUBERON:000129593.36gold quality
small intestine Peyer’s patchUBERON:000345493.17gold quality
nerveUBERON:000102193.15gold quality
tibial nerveUBERON:000132393.15gold quality
gall bladderUBERON:000211092.94gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.44
E-MTAB-2983no733.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

187 targeting TMX3, 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-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3646100.0073.565283
HSA-MIR-4262100.0073.263931
HSA-MIR-8485100.0077.574731
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-150-5P99.9966.691976
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-1213699.9872.815713
HSA-MIR-548P99.9872.253784
HSA-MIR-569699.9872.364487
HSA-MIR-806899.9873.852376
HSA-MIR-480399.9871.993117
HSA-MIR-433-3P99.9869.371203

Literature-anchored findings (GeneRIF, showing 4)

  • TMX3 is a thioredoxin-related transmembrane protein of the endoplasmic reticulum (PMID:15623505)
  • analysis of TMX3 interdomain stabilization of the N-terminal redox-active domain (PMID:17881353)
  • Haploinsufficiency for TMX3 results in a small eye phenotype and represents a novel genetic cause of microphthalmia and coloboma. (PMID:20485507)
  • Data show that TMX3 expression is upregulated in melanoma cell lines and patient samples. TMX knockdown altered mitochondrial organization, enhanced bioenergetics, and elevated mitochondrial- and NOX4-derived ROS. The TMX-knockdown-induced oxidative stress suppressed melanoma proliferation, migration, and xenograft tumor growth by inhibiting NFAT1. TMX1 is associated with poor disease outcome. (PMID:31304984)

Cross-species orthologs

12 orthologs

OrganismSymbolGene ID
danio_reriotmx3aENSDARG00000038894
danio_reriotmx3bENSDARG00000088466
mus_musculusTmx3ENSMUSG00000024614
rattus_norvegicusTmx3ENSRNOG00000045740
drosophila_melanogasterERp60FBGN0033663
drosophila_melanogasterTmx3FBGN0036579
drosophila_melanogasterPdiFBGN0286818
caenorhabditis_elegansWBGENE00003962
caenorhabditis_elegansWBGENE00003963
caenorhabditis_eleganspdi-3WBGENE00003964
caenorhabditis_elegansM04D5.1WBGENE00014807
caenorhabditis_elegansZK973.11WBGENE00022836

Paralogs (13): ERP44 (ENSG00000023318), PDIA5 (ENSG00000065485), TMX4 (ENSG00000125827), ERP27 (ENSG00000139055), TMX1 (ENSG00000139921), PDIA6 (ENSG00000143870), TXNDC11 (ENSG00000153066), PDIA4 (ENSG00000155660), PDIA3 (ENSG00000167004), PDILT (ENSG00000169340), PDIA2 (ENSG00000185615), P4HB (ENSG00000185624), TXNDC5 (ENSG00000239264)

Protein

Protein identifiers

Protein disulfide-isomerase TMX3Q96JJ7 (reviewed: Q96JJ7)

Alternative names: Thioredoxin domain-containing protein 10, Thioredoxin-related transmembrane protein 3

All UniProt accessions (6): B4DIE3, Q96JJ7, H3BPB3, H3BRY0, H3BT89, H3BVI1

UniProt curated annotations — full annotation on UniProt →

Function. Probable disulfide isomerase, which participates in the folding of proteins containing disulfide bonds. May act as a dithiol oxidase. Acts as a regulator of endoplasmic reticulum-mitochondria contact sites via its ability to regulate redox signals.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed. Expressed in brain, testis, lung, skin, kidney, uterus, bone, stomach, liver, prostate, placenta, eye and muscle.

Post-translational modifications. N-glycosylated.

Domain organisation. The di-lysine motif confers endoplasmic reticulum localization for type I membrane proteins.

Induction. Not up-regulated by unfolded protein response (UPR).

Similarity. Belongs to the protein disulfide isomerase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96JJ7-11yes
Q96JJ7-22

RefSeq proteins (7): NP_001337441, NP_001337442, NP_001337443, NP_001337444, NP_001337445, NP_001337446, NP_061895* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013766Thioredoxin_domainDomain
IPR017937Thioredoxin_CSConserved_site
IPR036249Thioredoxin-like_sfHomologous_superfamily
IPR052250PDI_TMX3Family

Pfam: PF00085, PF13848

UniProt features (19 total): sequence variant 3, active site 2, glycosylation site 2, splice variant 2, topological domain 2, signal peptide 1, chain 1, disulfide bond 1, transmembrane region 1, domain 1, region of interest 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96JJ7-F185.680.65

Functional residue map

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

Catalytic / active sites (2): 56 (nucleophile); 53 (nucleophile)

Disulfide bonds (1): 53–56

Glycosylation sites (2): 258, 313

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-114608Platelet degranulation

MSigDB gene sets: 122 (showing top): GOCC_SECRETORY_GRANULE, REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION, GOCC_CELL_SURFACE, chr18q22, DURCHDEWALD_SKIN_CARCINOGENESIS_DN, SENESE_HDAC3_TARGETS_DN, GOCC_PLATELET_ALPHA_GRANULE, GOCC_PLATELET_ALPHA_GRANULE_MEMBRANE, GOCC_SECRETORY_VESICLE, NUYTTEN_EZH2_TARGETS_DN, GOCC_SECRETORY_GRANULE_MEMBRANE, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_DISULFIDE_OXIDOREDUCTASE_ACTIVITY, GOMF_INTRAMOLECULAR_OXIDOREDUCTASE_ACTIVITY

GO Biological Process (0):

GO Molecular Function (4): protein disulfide isomerase activity (GO:0003756), protein-disulfide reductase activity (GO:0015035), protein binding (GO:0005515), isomerase activity (GO:0016853)

GO Cellular Component (6): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), cell surface (GO:0009986), platelet alpha granule membrane (GO:0031092), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Response to elevated platelet cytosolic Ca2+1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
catalytic activity, acting on a protein2
cellular anatomical structure2
intramolecular oxidoreductase activity, transposing S-S bonds1
disulfide oxidoreductase activity1
binding1
catalytic activity1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
secretory granule membrane1
platelet alpha granule1

Protein interactions and networks

STRING

1547 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMX3UNC50Q53HI1677
TMX3TMX4Q9H1E5661
TMX3TMX2Q9Y320634
TMX3ERP29P30040578
TMX3RIC3Q7Z5B4572
TMX3ERP27Q96DN0568
TMX3DSELQ8IZU8542
TMX3SCCPDHQ8NBX0467
TMX3TXNP10599460
TMX3EMC6Q9BV81455
TMX3FAM240BA0A1B0GVZ2451
TMX3AGR3Q8TD06450
TMX3PCF11O94913423
TMX3CCT7Q99832414
TMX3RBM5P52756412

IntAct

81 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
TMX3FHL3psi-mi:“MI:0915”(physical association)0.560
FHL3TMX3psi-mi:“MI:0915”(physical association)0.560
CANXTMX3psi-mi:“MI:0403”(colocalization)0.530
ZW10psi-mi:“MI:0914”(association)0.350
psi-mi:“MI:0914”(association)0.350
ESYT2psi-mi:“MI:0914”(association)0.350
E5ESYT2psi-mi:“MI:0914”(association)0.350
PGRMC1psi-mi:“MI:0914”(association)0.350
HAX1psi-mi:“MI:0914”(association)0.350
BVLF1VWA8psi-mi:“MI:0914”(association)0.350
M2IPO5psi-mi:“MI:0914”(association)0.350
HSCBRBP5psi-mi:“MI:0914”(association)0.350
TSPOpsi-mi:“MI:0914”(association)0.350
EHD4DNAJA2psi-mi:“MI:0914”(association)0.350
MS4A4AMON2psi-mi:“MI:0914”(association)0.350
P2RY6ESYT2psi-mi:“MI:0914”(association)0.350
SLC15A3psi-mi:“MI:0914”(association)0.350
UNC93B1psi-mi:“MI:0914”(association)0.350
VAMP5ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (150): TMX3 (Two-hybrid), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), TMX3 (Proximity Label-MS), TMX3 (Proximity Label-MS), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-RNA), TMX3 (Affinity Capture-MS), TMX3 (Affinity Capture-MS), TMX3 (Synthetic Lethality), TMX3 (Co-fractionation)

ESM2 similar proteins: A0A8M1N5Y4, F1R520, O09161, O09165, O14958, O18934, P07221, P08003, P12637, P13667, P14211, P15253, P18418, P19204, P19633, P20942, P27797, P28491, P30040, P30101, P31231, P31235, P31415, P38657, P38659, P51868, P52193, P52555, P57759, P81623, P81628, Q01H84, Q14554, Q29RV1, Q2HWU3, Q2KIL5, Q4R6K8, Q4VIT4, Q4VIT5, Q5I0H9

Diamond homologs: A0A8M1N5Y4, A3KPF5, D4B2L8, O13704, O13811, O22022, O22263, O48773, O83889, P05307, P07591, P07887, P08003, P09103, P0A4L1, P0A4L2, P0AGG4, P0AGG5, P0AGG6, P0AGG7, P11598, P12243, P12865, P13667, P17967, P21195, P23400, P27773, P30101, P33791, P34329, P37395, P38657, P38658, P38659, P38660, P38661, P46843, P50254, P50338

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign6
Benign37

Top pathogenic / likely-pathogenic (0)

SpliceAI

3770 predictions. Top by Δscore:

VariantEffectΔscore
18:68677189:ATAGA:Aacceptor_gain1.0000
18:68677190:TAGA:Tacceptor_gain1.0000
18:68677191:AGA:Aacceptor_gain1.0000
18:68677191:AGACT:Aacceptor_loss1.0000
18:68677192:GA:Gacceptor_gain1.0000
18:68677193:ACTG:Aacceptor_loss1.0000
18:68677194:C:Aacceptor_loss1.0000
18:68677194:C:CCacceptor_gain1.0000
18:68677195:T:Gacceptor_loss1.0000
18:68679456:AACTT:Adonor_loss1.0000
18:68679457:ACTTA:Adonor_loss1.0000
18:68679458:CTTAC:Cdonor_loss1.0000
18:68679459:TTA:Tdonor_loss1.0000
18:68679460:TA:Tdonor_loss1.0000
18:68679461:A:ACdonor_gain1.0000
18:68679462:C:Adonor_loss1.0000
18:68679462:C:CCdonor_gain1.0000
18:68679462:CCA:Cdonor_gain1.0000
18:68679531:CCT:Cacceptor_loss1.0000
18:68679532:C:CAacceptor_loss1.0000
18:68679532:C:CCacceptor_gain1.0000
18:68679535:C:CTacceptor_gain1.0000
18:68679536:A:Tacceptor_gain1.0000
18:68680137:A:Cdonor_gain1.0000
18:68680979:A:ACdonor_gain1.0000
18:68680980:C:CCdonor_gain1.0000
18:68680980:CTT:Cdonor_gain1.0000
18:68681109:CA:Cacceptor_gain1.0000
18:68682923:A:ACdonor_gain1.0000
18:68682923:ACT:Adonor_gain1.0000

AlphaMissense

3002 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:68677128:A:CS390R1.000
18:68677128:A:TS390R1.000
18:68677130:T:GS390R1.000
18:68700422:A:CF125L1.000
18:68700422:A:TF125L1.000
18:68700424:A:GF125L1.000
18:68701757:G:TP100Q1.000
18:68701758:G:AP100S1.000
18:68677144:G:CP385R0.999
18:68677150:C:TG383D0.999
18:68697284:G:TA171D0.999
18:68700423:A:GF125S0.999
18:68700460:A:CY113D0.999
18:68701745:A:GL104P0.999
18:68701757:G:AP100L0.999
18:68701757:G:CP100R0.999
18:68701758:G:CP100A0.999
18:68701758:G:TP100T0.999
18:68701769:A:TV96D0.999
18:68710056:A:TV77D0.999
18:68710097:C:AW63C0.999
18:68710097:C:GW63C0.999
18:68710099:A:GW63R0.999
18:68710099:A:TW63R0.999
18:68710118:A:CC56W0.999
18:68710119:C:AC56F0.999
18:68710119:C:GC56S0.999
18:68710119:C:TC56Y0.999
18:68710120:A:GC56R0.999
18:68710120:A:TC56S0.999

dbSNP variants (sampled 300 via entrez): RS1000003885 (18:68701684 T>C), RS1000096842 (18:68702108 C>A,T), RS1000129206 (18:68693333 G>A), RS1000323214 (18:68687452 T>C), RS1000326405 (18:68707669 C>T), RS1000386671 (18:68681558 G>A,C), RS1000417727 (18:68681858 C>A), RS1000455422 (18:68713028 C>T), RS1000465915 (18:68694199 CAAG>C), RS1000475483 (18:68673804 T>A,C), RS1000543499 (18:68688574 C>CTCT), RS1000611697 (18:68687080 C>A), RS1000677162 (18:68707416 T>A), RS1000832082 (18:68713792 A>G,T), RS1000884229 (18:68714035 C>T)

Disease associations

OMIM: gene MIM:616102 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST002048_1Attention deficit hyperactivity disorder3.000000e-06
GCST002699_4Suicide in bipolar disorder4.000000e-06
GCST003074_20Cerebral amyloid deposition in APOEe4 non-carriers (PET imaging)8.000000e-08
GCST009391_1934Metabolite levels8.000000e-07

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004321attempted suicide
EFO:0007707cerebral amyloid deposition measurement
EFO:0009766asparagine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, decreases methylation5
entinostatdecreases expression, affects cotreatment2
Cyclosporinedecreases expression, increases expression2
dicrotophosdecreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
deoxynivalenolincreases expression1
sodium arsenatedecreases expression1
arseniteaffects binding, decreases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation1
Cadmiumincreases abundance, increases expression1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Ivermectindecreases expression1
Quercetinincreases expression1
Rotenoneincreases expression1
Testosteronedecreases expression1
Dronabinolincreases expression1
Theophyllineincreases expression1
Aflatoxin B1affects expression1
Cadmium Chlorideincreases abundance, increases expression1
Copper Sulfateincreases expression1
Lactic Aciddecreases expression1
Particulate Matterincreases abundance, decreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.