TMED5

gene
On this page

Also known as CGI-100p24g2p24gamma2

Summary

TMED5 (transmembrane p24 trafficking protein 5, HGNC:24251) is a protein-coding gene on chromosome 1p22.1, encoding Transmembrane emp24 domain-containing protein 5 (Q9Y3A6). Potential role in vesicular protein trafficking, mainly in the early secretory pathway.

Involved in Golgi ribbon formation. Located in cis-Golgi network; endoplasmic reticulum exit site; and endoplasmic reticulum-Golgi intermediate compartment.

Source: NCBI Gene 50999 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 23 total
  • MANE Select transcript: NM_016040

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24251
Approved symbolTMED5
Nametransmembrane p24 trafficking protein 5
Location1p22.1
Locus typegene with protein product
StatusApproved
AliasesCGI-100, p24g2, p24gamma2
Ensembl geneENSG00000117500
Ensembl biotypeprotein_coding
OMIM616876
Entrez50999

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000370280, ENST00000370282, ENST00000370290, ENST00000479918, ENST00000483033, ENST00000909499, ENST00000909500, ENST00000909501, ENST00000909502, ENST00000935198

RefSeq mRNA: 3 — MANE Select: NM_016040 NM_001167830, NM_001410825, NM_016040

CCDS: CCDS53342, CCDS743, CCDS91003

Canonical transcript exons

ENST00000370282 — 4 exons

ExonStartEnd
ENSE000012850899318005493180413
ENSE000019453619314974293154888
ENSE000030680679316012993160226
ENSE000035035149315630093156483

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 98.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.7636 / max 371.8702, expressed in 1825 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1330045.51841824
132991.4329777
133020.7519363
133010.060411

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
skeletal muscle tissue of biceps brachiiUBERON:000450298.02gold quality
parietal pleuraUBERON:000240098.00gold quality
biceps brachiiUBERON:000150797.87gold quality
corpus epididymisUBERON:000435997.83gold quality
choroid plexus epitheliumUBERON:000391197.60gold quality
pleuraUBERON:000097797.56gold quality
spermCL:000001997.40gold quality
mucosa of sigmoid colonUBERON:000499397.15gold quality
jejunal mucosaUBERON:000039996.90gold quality
visceral pleuraUBERON:000240196.89gold quality
diaphragmUBERON:000110396.87gold quality
deciduaUBERON:000245096.87gold quality
pigmented layer of retinaUBERON:000178296.86gold quality
colonic mucosaUBERON:000031796.76gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451196.67gold quality
nephron tubuleUBERON:000123196.36gold quality
superficial temporal arteryUBERON:000161496.36gold quality
lower lobe of lungUBERON:000894996.33gold quality
renal glomerulusUBERON:000007496.30gold quality
cartilage tissueUBERON:000241896.27gold quality
pericardiumUBERON:000240796.21gold quality
heart right ventricleUBERON:000208096.20gold quality
metanephric glomerulusUBERON:000473696.14gold quality
male germ cellCL:000001595.93gold quality
cauda epididymisUBERON:000436095.90gold quality
bronchial epithelial cellCL:000232895.84gold quality
caput epididymisUBERON:000435895.67gold quality
palpebral conjunctivaUBERON:000181295.60gold quality
adrenal tissueUBERON:001830395.55gold quality
germinal epithelium of ovaryUBERON:000130495.48gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes13.55
E-CURD-112no2.55
E-MTAB-9543no2.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

220 targeting TMED5, 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-4795-3P100.0074.624024
HSA-MIR-3646100.0073.565283
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5692A100.0074.406850
HSA-MIR-3924100.0072.092394
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-548AW99.9972.573559
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-186-5P99.9970.833707
HSA-MIR-511-3P99.9968.851467
HSA-MIR-366299.9973.825684
HSA-MIR-450099.9972.722367
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-569699.9872.364487
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-433-3P99.9869.371203
HSA-MIR-806899.9873.852376
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-365899.9673.874379
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163

Literature-anchored findings (GeneRIF, showing 4)

  • Expression of cgi-100 mRNA decreased in a dose- and time-dependent manner in the K562 cells treated with matrine and over-expression of cgi-100 elevates the proliferation and the immaturity level of K562 cells. (PMID:18549622)
  • The luminal alpha-helical but not GOLD domain of p24gamma2 was required for efficient GPI-AP transport. (PMID:24778190)
  • Identification of a novel circ_0018289/miR-183-5p/TMED5 regulatory network in cervical cancer development. (PMID:34404391)
  • Silencing of TMED5 inhibits proliferation, migration and invasion, and enhances apoptosis of hepatocellular carcinoma cells. (PMID:36530030)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotmed5ENSDARG00000008765
mus_musculusTmed5ENSMUSG00000063406
rattus_norvegicusTmed5ENSRNOG00000000073
drosophila_melanogasterp24-1FBGN0030341
caenorhabditis_elegansWBGENE00011606

Paralogs (8): TMED2 (ENSG00000086598), TMED1 (ENSG00000099203), TMED7 (ENSG00000134970), TMED6 (ENSG00000157315), TMED4 (ENSG00000158604), TMED3 (ENSG00000166557), TMED10 (ENSG00000170348), TMED9 (ENSG00000184840)

Protein

Protein identifiers

Transmembrane emp24 domain-containing protein 5Q9Y3A6 (reviewed: Q9Y3A6)

Alternative names: p24 family protein gamma-2, p28

All UniProt accessions (3): B1AKT3, M0R072, Q9Y3A6

UniProt curated annotations — full annotation on UniProt →

Function. Potential role in vesicular protein trafficking, mainly in the early secretory pathway. Required for the maintenance of the Golgi apparatus; involved in protein exchange between Golgi stacks during assembly. Probably not required for COPI-vesicle-mediated retrograde transport.

Subunit / interactions. Interacts with TMED9 and TMED10.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus. cis-Golgi network membrane. Endoplasmic reticulum-Golgi intermediate compartment membrane.

Similarity. Belongs to the EMP24/GP25L family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y3A6-11yes
Q9Y3A6-22

RefSeq proteins (3): NP_001161302, NP_001397754, NP_057124* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009038GOLD_domDomain
IPR015720Emp24-likeFamily
IPR036598GOLD_dom_sfHomologous_superfamily

Pfam: PF01105

UniProt features (8 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y3A6-F182.830.57

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-3238698WNT ligand biogenesis and trafficking

MSigDB gene sets: 202 (showing top): HORIUCHI_WTAP_TARGETS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP, GOCC_COATED_VESICLE, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, SCHLOSSER_SERUM_RESPONSE_DN, GOBP_GOLGI_RIBBON_FORMATION, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN

GO Biological Process (4): intracellular protein transport (GO:0006886), endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), Golgi ribbon formation (GO:0090161), protein transport (GO:0015031)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (9): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), Golgi apparatus (GO:0005794), cis-Golgi network (GO:0005801), COPII-coated ER to Golgi transport vesicle (GO:0030134), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), endoplasmic reticulum exit site (GO:0070971), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by WNT1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm4
intracellular membrane-bounded organelle4
intracellular protein localization2
intracellular transport2
endomembrane system2
cellular anatomical structure2
protein transport1
intercellular transport1
Golgi vesicle transport1
Golgi organization1
transport1
establishment of protein localization1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
Golgi apparatus1
coated vesicle1
endoplasmic reticulum-Golgi intermediate compartment1
bounding membrane of organelle1
endoplasmic reticulum1

Protein interactions and networks

STRING

898 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMED5TMED9Q9BVK6944
TMED5TMED10P49755876
TMED5TMED2Q15363738
TMED5TMED4Q7Z7H5689
TMED5PIGCQ92535543
TMED5GRSF1Q12849448
TMED5OMA1Q96E52416
TMED5THAP6Q8TBB0394
TMED5TM9SF4Q92544383
TMED5MYSM1Q5VVJ2377
TMED5METTL13Q8N6R0371
TMED5MTF2Q9Y483368
TMED5SYPL1Q16563362
TMED5PGAP1Q75T13358
TMED5PLAGL2Q9UPG8353
TMED5HCKP08631353

IntAct

77 interactions, top by confidence:

ABTypeScore
CDK5RAP3UFL1psi-mi:“MI:0914”(association)0.870
TMED10TMED1psi-mi:“MI:0914”(association)0.730
TMED9TMED10psi-mi:“MI:0914”(association)0.730
DDRGK1UFL1psi-mi:“MI:0914”(association)0.710
TMED2ATP9Apsi-mi:“MI:0914”(association)0.640
CHST8CANXpsi-mi:“MI:0914”(association)0.640
CXCL9TMED5psi-mi:“MI:0915”(physical association)0.560
LIPGNRP1psi-mi:“MI:0914”(association)0.530
UBXN8psi-mi:“MI:0914”(association)0.530
CDK5RAP3PLD2psi-mi:“MI:0914”(association)0.530
CD70METTL15psi-mi:“MI:0914”(association)0.530
TMED5PRMT6psi-mi:“MI:0915”(physical association)0.510
TMED5psi-mi:“MI:0915”(physical association)0.370
TMED5iglC2psi-mi:“MI:0915”(physical association)0.370
DNAJC30TMED5psi-mi:“MI:0915”(physical association)0.370
Tmed10TARS3psi-mi:“MI:0914”(association)0.350
Tmed2psi-mi:“MI:0914”(association)0.350
KSR1DDX39Apsi-mi:“MI:0914”(association)0.350
KSR1FBLL1psi-mi:“MI:0914”(association)0.350
KSR1psi-mi:“MI:0914”(association)0.350
Prdm16ESYT2psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
PEBP1ANXA2P2psi-mi:“MI:0914”(association)0.350
GTMED5psi-mi:“MI:0914”(association)0.350
LHX1AIFM1psi-mi:“MI:0914”(association)0.350

BioGRID (96): TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Proximity Label-MS), TMED5 (Affinity Capture-MS), CXCL9 (Two-hybrid), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS), TMED5 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2KTI4, A0A7U2QYM2, A1CKN5, A5AAA1, A7SXK3, A8N0V8, B0CPJ0, B0WEV5, B2VVF0, F4JJJ3, O04015, O04226, O17528, P32296, P55014, P55015, P55016, P58421, P91926, Q0CNR4, Q13621, Q28BQ6, Q29N38, Q2KJ84, Q4HY20, Q5B5L5, Q5B971, Q5R809, Q69SA9, Q6AXN3, Q6AY25, Q78IS1, Q7QG73, Q870U4, Q948T9, Q949M9, Q94BV7, Q9CXE7, Q9DEB5, Q9HEK4

Diamond homologs: A7SXK3, D3ZTX0, O13770, O17528, P49020, Q13445, Q15363, Q28BQ6, Q2KJ84, Q2TBK5, Q3T133, Q3V009, Q54BN0, Q5BK85, Q5I0E7, Q5R7E6, Q5R809, Q63524, Q6AXN3, Q6AY25, Q769F9, Q78IS1, Q7Z7H5, Q99KF1, Q9BVK6, Q9CXE7, Q9R0Q3, Q9Y3A6, Q9Y3B3, Q9Y3Q3, P39704, B3MTS8, B3NZM5, B4GMC3, B4HJV5, B4JG34, B4KB41, B4LYB8, B4NKL0, B4PVC6

SIGNOR signaling

1 interactions.

AEffectBMechanism
TMED5“up-regulates activity”TMED10binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 95 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
COPI-dependent Golgi-to-ER retrograde traffic712.5×3e-04
COPI-mediated anterograde transport610.6×2e-03
Transport of small molecules114.5×2e-03

GO biological processes:

GO termPartnersFoldFDR
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum625.3×3e-05
endoplasmic reticulum to Golgi vesicle-mediated transport1017.0×3e-07
intracellular protein transport108.1×8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance13
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1168 predictions. Top by Δscore:

VariantEffectΔscore
1:93156294:A:ACdonor_gain1.0000
1:93156295:C:CCdonor_gain1.0000
1:93156296:TGA:Tdonor_loss1.0000
1:93156298:ACCAG:Adonor_loss1.0000
1:93156310:T:TAdonor_gain1.0000
1:93156479:CTACA:Cacceptor_gain1.0000
1:93156480:TACA:Tacceptor_gain1.0000
1:93156482:CA:Cacceptor_gain1.0000
1:93156484:C:CCacceptor_gain1.0000
1:93160123:ACTT:Adonor_loss1.0000
1:93160125:TTACG:Tdonor_loss1.0000
1:93160126:TACGT:Tdonor_loss1.0000
1:93160127:A:ACdonor_gain1.0000
1:93160127:A:Tdonor_loss1.0000
1:93160128:C:CAdonor_gain1.0000
1:93160128:CG:Cdonor_gain1.0000
1:93160128:CGT:Cdonor_gain1.0000
1:93160128:CGTG:Cdonor_gain1.0000
1:93160128:CGTGT:Cdonor_gain1.0000
1:93160225:AC:Aacceptor_gain1.0000
1:93160226:CC:Cacceptor_gain1.0000
1:93160227:C:CCacceptor_gain1.0000
1:93180052:A:ACdonor_gain1.0000
1:93180053:C:CTdonor_gain1.0000
1:93154692:T:Cdonor_gain0.9900
1:93154794:T:Adonor_gain0.9900
1:93156292:ATAC:Adonor_loss0.9900
1:93156293:TACT:Tdonor_loss0.9900
1:93156294:ACT:Adonor_loss0.9900
1:93156295:CTGA:Cdonor_gain0.9900

AlphaMissense

1522 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:93154806:C:GR185P1.000
1:93154816:C:GA182P1.000
1:93154812:C:GR183P0.999
1:93156441:A:CN110K0.999
1:93156441:A:TN110K0.999
1:93154697:A:CF221L0.998
1:93154697:A:TF221L0.998
1:93154698:A:CF221C0.998
1:93154699:A:GF221L0.998
1:93154743:A:CM206R0.998
1:93154765:A:GS199P0.998
1:93154809:T:AD184V0.998
1:93154825:C:GA179P0.998
1:93154850:A:CS170R0.998
1:93154850:A:TS170R0.998
1:93154852:T:GS170R0.998
1:93154860:A:GL167P0.998
1:93156408:G:CF121L0.998
1:93156408:G:TF121L0.998
1:93156410:A:GF121L0.998
1:93156417:C:AK118N0.998
1:93156417:C:GK118N0.998
1:93156432:G:CS113R0.998
1:93156432:G:TS113R0.998
1:93156434:T:GS113R0.998
1:93156442:T:AN110I0.998
1:93156448:A:GF108S0.998
1:93156451:C:GC107S0.998
1:93156451:C:TC107Y0.998
1:93156452:A:GC107R0.998

dbSNP variants (sampled 300 via entrez): RS1000097733 (1:93166418 C>T), RS1000173993 (1:93171555 T>C), RS1000270723 (1:93179014 C>G), RS1000439516 (1:93157742 C>T), RS1000444604 (1:93164988 G>A,C,T), RS1000479081 (1:93170371 G>A,C), RS1000506879 (1:93170528 T>C,G), RS1000749907 (1:93157051 A>G), RS1000880653 (1:93151326 A>G), RS1001120701 (1:93177099 A>T), RS1001150304 (1:93171309 A>C), RS1001188618 (1:93164090 A>G), RS1001359394 (1:93170969 G>A,C,T), RS1001473440 (1:93170796 A>C), RS1001530165 (1:93149539 C>T)

Disease associations

OMIM: gene MIM:616876 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006005_1High density lipoprotein cholesterol levels1.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases methylation, affects cotreatment, increases expression5
sodium arseniteaffects cotreatment, increases abundance, increases expression, decreases expression3
chloropicrindecreases expression, increases expression2
entinostatincreases expression, affects cotreatment2
Panobinostataffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutionincreases expression2
aristolochic acid Idecreases expression1
bisphenol Fincreases expression1
TAK-243decreases sumoylation1
methylmercuric chlorideincreases expression1
bisphenol Aaffects expression1
titanium dioxideaffects expression1
mono-(2-ethylhexyl)phthalateincreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
4-phenylbutyric aciddecreases expression, increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangdecreases expression1
Vorinostatincreases expression1
Acetaminophenincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Cisplatindecreases expression1
Clorgylineincreases expression1
Formaldehydedecreases expression1
Ivermectindecreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Plant Oilsincreases expression1
Dihydrotestosteroneincreases expression1
Tunicamycinincreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_TS72HAP1 TMED5 (-) 1Cancer cell lineMale
CVCL_XU33HAP1 TMED5 (-) 2Cancer cell lineMale

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.