TRAPPC5

Summary

TRAPPC5 (trafficking protein particle complex subunit 5, HGNC:23067) is a protein-coding gene on chromosome 19p13.2, encoding Trafficking protein particle complex subunit 5 (Q8IUR0). May play a role in vesicular transport from endoplasmic reticulum to Golgi. It is a common-essential gene (DepMap: required in 94.5% of cancer cell lines).

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Part of TRAPP complex.

Source: NCBI Gene 126003 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 23 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 94.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_001042462

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23067
Approved symbol	TRAPPC5
Name	trafficking protein particle complex subunit 5
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC52424, TRS31
Ensembl gene	ENSG00000181029
Ensembl biotype	protein_coding
Entrez	126003

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000317378, ENST00000426877, ENST00000595985, ENST00000596148, ENST00000944764

RefSeq mRNA: 3 — MANE Select: NM_001042462 NM_001042461, NM_001042462, NM_174894

CCDS: CCDS42490

Canonical transcript exons

ENST00000596148 — 2 exons

Exon	Start	End
ENSE00003027165	7680833	7680878
ENSE00003493590	7682242	7687703

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 98.20.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 91.2116 / max 521.7233, expressed in 1828 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173596	90.3263	1828
208677	0.8853	588

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.20	gold quality
right testis	UBERON:0004534	98.04	gold quality
stromal cell of endometrium	CL:0002255	97.70	gold quality
superior frontal gyrus	UBERON:0002661	97.61	gold quality
prefrontal cortex	UBERON:0000451	97.48	gold quality
primary visual cortex	UBERON:0002436	97.45	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.43	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.01	gold quality
lower esophagus mucosa	UBERON:0035834	96.85	gold quality
granulocyte	CL:0000094	96.78	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.48	gold quality
testis	UBERON:0000473	96.02	gold quality
frontal cortex	UBERON:0001870	95.41	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.72	gold quality
cerebral cortex	UBERON:0000956	94.58	gold quality
blood	UBERON:0000178	94.48	gold quality
putamen	UBERON:0001874	94.34	gold quality
bone marrow cell	CL:0002092	94.20	gold quality
apex of heart	UBERON:0002098	94.10	gold quality
leukocyte	CL:0000738	93.87	gold quality
temporal lobe	UBERON:0001871	93.78	gold quality
monocyte	CL:0000576	93.71	gold quality
amygdala	UBERON:0001876	93.68	gold quality
Ammon’s horn	UBERON:0001954	93.68	gold quality
nucleus accumbens	UBERON:0001882	93.67	gold quality
caudate nucleus	UBERON:0001873	93.50	gold quality
anterior cingulate cortex	UBERON:0009835	93.48	gold quality
brain	UBERON:0000955	93.29	gold quality
bone marrow	UBERON:0002371	93.24	gold quality
cortex of kidney	UBERON:0001225	93.14	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	179.42
E-MTAB-7037	yes	115.26
E-HCAD-6	yes	38.86
E-CURD-112	yes	20.17
E-ANND-3	yes	11.32

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 94.5% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trappc5	ENSDARG00000026068
mus_musculus	Trappc5	ENSMUSG00000040236
rattus_norvegicus	Trappc5	ENSRNOG00000001003
drosophila_melanogaster	Trs31	FBGN0266723
caenorhabditis_elegans		WBGENE00013259

Protein

Protein identifiers

Trafficking protein particle complex subunit 5 — Q8IUR0 (reviewed: Q8IUR0)

All UniProt accessions (2): Q8IUR0, M0QZQ8

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Subunit / interactions. Component of the multisubunit TRAPP (transport protein particle) complex, which includes at least TRAPPC2, TRAPPC2L, TRAPPC3, TRAPPC3L, TRAPPC4, TRAPPC5, TRAPPC8, TRAPPC9, TRAPPC10, TRAPPC11 and TRAPPC12.

Subcellular location. Golgi apparatus. cis-Golgi network. Endoplasmic reticulum.

Similarity. Belongs to the TRAPP small subunits family. BET3 subfamily.

RefSeq proteins (3): NP_001035926, NP_001035927, NP_777554 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007194	TRAPP_component	Family
IPR016696	TRAPP-I_su5	Family
IPR024096	NO_sig/Golgi_transp_ligand-bd	Homologous_superfamily

Pfam: PF04051

UniProt features (3 total): chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IUR0-F1	85.79	0.57

Functional residue map

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

Post-translational modifications (1): 10

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-204005	COPII-mediated vesicle transport
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 109 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GOBP_VESICLE_LOCALIZATION, GOBP_VESICLE_ORGANIZATION, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP, GOBP_MEMBRANE_ORGANIZATION, BURTON_ADIPOGENESIS_PEAK_AT_24HR, GOBP_ORGANELLE_LOCALIZATION, LEE_AGING_CEREBELLUM_UP, MARSON_BOUND_BY_FOXP3_STIMULATED, GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENT, chr19p13

GO Biological Process (6): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle coat assembly (GO:0006901), COPII vesicle coat assembly (GO:0048208), obsolete vesicle tethering (GO:0099022), vesicle-mediated transport (GO:0016192), Golgi vesicle transport (GO:0048193)

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

GO Cellular Component (8): cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), TRAPP complex (GO:0030008), TRAPPI protein complex (GO:1990070), TRAPPII protein complex (GO:1990071), TRAPPIII protein complex (GO:1990072), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
ER to Golgi Anterograde Transport	1
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
TRAPP complex	3
cellular anatomical structure	2
endomembrane system	2
intracellular membrane-bounded organelle	2
Golgi apparatus	2
intercellular transport	1
intracellular transport	1
Golgi vesicle transport	1
vesicle budding from membrane	1
vesicle organization	1
vesicle coat assembly	1
protein-containing complex assembly	1
COPII-coated vesicle budding	1
transport	1
cellular process	1
vesicle-mediated transport	1
binding	1
intracellular anatomical structure	1
vesicle tethering complex	1
intracellular protein-containing complex	1
endoplasmic reticulum-Golgi intermediate compartment	1
endosome	1

Protein interactions and networks

STRING

1150 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRAPPC5	TRAPPC6A	O75865	998
TRAPPC5	TRAPPC1	Q9Y5R8	998
TRAPPC5	TRAPPC4	Q9Y296	998
TRAPPC5	TRAPPC2	P0DI81	997
TRAPPC5	TRAPPC3	O43617	997
TRAPPC5	TRAPPC8	Q9Y2L5	980
TRAPPC5	TRAPPC9	Q96Q05	938
TRAPPC5	TRAPPC10	P48553	882
TRAPPC5	TRAPPC13	A5PLN9	775
TRAPPC5	TRAPPC12	Q8WVT3	766
TRAPPC5	RAB1A	P11476	761
TRAPPC5	TRAPPC11	Q7Z392	744
TRAPPC5	TRAPPC6B	Q86SZ2	676
TRAPPC5	TRAPPC2L	Q9UL33	667
TRAPPC5	SETX	Q7Z333	505

IntAct

116 interactions, top by confidence:

A	B	Type	Score
MED20	MED19	psi-mi:“MI:0914”(association)	0.840
RUFY4	NDC80	psi-mi:“MI:0914”(association)	0.830
CCNDBP1	TRAPPC5	psi-mi:“MI:0915”(physical association)	0.780
TRAPPC5	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.780
TRAPPC3	TRAPPC5	psi-mi:“MI:0915”(physical association)	0.740
TUBA1C	TXNDC9	psi-mi:“MI:0914”(association)	0.730
RAB3IP	TRAPPC3	psi-mi:“MI:0914”(association)	0.700
KANK4	TRAPPC3	psi-mi:“MI:0914”(association)	0.640
PTGR3	DBT	psi-mi:“MI:0914”(association)	0.640
IL13RA2	CHEK1	psi-mi:“MI:0914”(association)	0.640
TRAPPC5	HMG20A	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2	TRAPPC5	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	TRAPPC13	psi-mi:“MI:0914”(association)	0.560
IL13RA2	METTL15	psi-mi:“MI:0914”(association)	0.530
NPY2R	RTL8C	psi-mi:“MI:0914”(association)	0.530
BTBD1	TRAPPC10	psi-mi:“MI:0914”(association)	0.530
TRAPPC1	TRAPPC13	psi-mi:“MI:0914”(association)	0.530
TPCN2	AP3B1	psi-mi:“MI:0914”(association)	0.530
BCL2L14	CHEK1	psi-mi:“MI:0914”(association)	0.530
CABS1	TRAPPC10	psi-mi:“MI:0914”(association)	0.530
PRAMEF17	CUL2	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530

BioGRID (189): TRAPPC5 (Two-hybrid), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC3 (Co-fractionation), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS)

ESM2 similar proteins: A7RWP6, B4GW22, B4NC41, F1QMV3, F4JWP9, O43617, O55013, P34605, P36149, P45437, Q02880, Q08DS5, Q29G21, Q29G82, Q2NL13, Q32L78, Q4KL14, Q5BLF0, Q5F359, Q5R7L4, Q5RC82, Q5T215, Q5U1Z2, Q5ZI57, Q61IU9, Q62991, Q6GNS3, Q6P2Z0, Q6P2Z6, Q803N9, Q86K94, Q86SZ2, Q8AVM7, Q8BRF7, Q8IUR0, Q8K224, Q8WVM8, Q96D46, Q98SP7, Q99MH9

Diamond homologs: P15847, Q03337, Q2NL13, Q54YG5, Q5F359, Q7KQM2, Q8IUR0, Q9CQA1, Q9P7N9, Q8SU25

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
TRAPPC5	“form complex”	“TRAPP III complex, TRAPPC2 variant”	binding
TRAPPC5	“form complex”	“TRAPP III complex, TRAPPC2B variant”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 108 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:

Pathway	Partners	Fold	FDR
RAB GEFs exchange GTP for GDP on RABs	8	14.2×	3e-05

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle tethering	7	78.0×	1e-09
COPII vesicle coat assembly	5	39.5×	2e-05
endoplasmic reticulum to Golgi vesicle-mediated transport	9	13.7×	4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	21
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

464 predictions. Top by Δscore:

Variant	Effect	Δscore
19:7682236:CCGCA:C	acceptor_loss	1.0000
19:7682237:CGCAG:C	acceptor_loss	1.0000
19:7682238:GCA:G	acceptor_loss	1.0000
19:7682238:GCAGG:G	acceptor_loss	1.0000
19:7682239:CA:C	acceptor_loss	1.0000
19:7682240:A:AC	acceptor_loss	1.0000
19:7682240:A:AG	acceptor_gain	1.0000
19:7682240:AG:A	acceptor_gain	1.0000
19:7682240:AGGGT:A	acceptor_gain	1.0000
19:7682241:G:GG	acceptor_gain	1.0000
19:7682241:GG:G	acceptor_gain	1.0000
19:7682241:GGGT:G	acceptor_gain	1.0000
19:7682241:GGGTG:G	acceptor_gain	1.0000
19:7682838:GA:G	donor_gain	1.0000
19:7682237:C:CA	acceptor_gain	0.9900
19:7682240:AGG:A	acceptor_gain	0.9900
19:7682241:G:GT	acceptor_gain	0.9900
19:7682241:GGG:G	acceptor_gain	0.9900
19:7682832:A:G	donor_gain	0.9900
19:7680878:GGTGA:G	donor_loss	0.9800
19:7680879:G:GA	donor_loss	0.9800
19:7680880:T:A	donor_loss	0.9800
19:7682779:G:GT	donor_gain	0.9800
19:7682782:G:GT	donor_gain	0.9800
19:7682899:A:AG	donor_gain	0.9800
19:7682900:G:GG	donor_gain	0.9800
19:7680881:G:GT	donor_loss	0.9700
19:7680879:G:GG	donor_gain	0.9600
19:7681012:G:GT	donor_gain	0.9600
19:7682829:GAGA:G	donor_gain	0.9600

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000083785 (19:7680485 C>T), RS1000136938 (19:7681974 G>A,C,T), RS1000190338 (19:7687348 G>A), RS1000464639 (19:7682298 C>T), RS1001069294 (19:7683587 G>C,T), RS1001094088 (19:7679301 CGTGT>C,CGT), RS1001289345 (19:7684049 G>A), RS1001541746 (19:7683313 G>A,T), RS1001734944 (19:7681232 G>A), RS1001967496 (19:7679156 T>C), RS1002110087 (19:7684568 C>T), RS1002482388 (19:7684859 T>G), RS1002579530 (19:7678903 C>A,G,T), RS1002969179 (19:7680321 C>T), RS1003001701 (19:7680079 G>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295892 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Cadmium Chloride	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
arsenite	affects binding, increases reaction	1
diallyl trisulfide	increases expression	1
ICG 001	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Carcinogens	decreases expression	1
Mutagens	decreases expression	1
Smoke	decreases expression	1
Lactic Acid	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4118950	Binding	Binding affinity to TRAPPC5 in human NCI-H358 cells at 1 uM by mass spectrometry based pull down assay	Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. — Bioorg Med Chem

Clinical trials (associated diseases)

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