TRAPPC1

Summary

TRAPPC1 (trafficking protein particle complex subunit 1, HGNC:19894) is a protein-coding gene on chromosome 17p13.1, encoding Trafficking protein particle complex subunit 1 (Q9Y5R8). May play a role in vesicular transport from endoplasmic reticulum to Golgi. It is a common-essential gene (DepMap: required in 98.7% of cancer cell lines).

This gene product plays a role in vesicular transport of proteins to the Golgi apparatus from the endoplasmic reticulum. The encoded protein is a component of the multisubunit transport protein particle (TRAPP) complex. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 58485 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 18 total
• Cancer dependency (DepMap): dependent in 98.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_021210

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19894
Approved symbol	TRAPPC1
Name	trafficking protein particle complex subunit 1
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Aliases	MUM2, BET5
Ensembl gene	ENSG00000170043
Ensembl biotype	protein_coding
OMIM	610969
Entrez	58485

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000303731, ENST00000540486, ENST00000571739, ENST00000571947, ENST00000572656, ENST00000573989, ENST00000575639, ENST00000924843, ENST00000924844, ENST00000924845, ENST00000968005, ENST00000968006

RefSeq mRNA: 2 — MANE Select: NM_021210 NM_001166621, NM_021210

CCDS: CCDS11125

Canonical transcript exons

ENST00000303731 — 4 exons

Exon	Start	End
ENSE00001144941	7931506	7931576
ENSE00001303169	7931731	7931946
ENSE00002679263	7930349	7930734
ENSE00003520520	7931011	7931149

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 99.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 92.0771 / max 584.3812, expressed in 1824 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164341	85.8658	1824
164340	2.1490	1278
164336	1.2246	787
164338	1.1323	757
164339	0.8461	581
164337	0.8437	576
164342	0.0155	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	99.10	gold quality
leukocyte	CL:0000738	99.08	gold quality
stromal cell of endometrium	CL:0002255	98.93	gold quality
granulocyte	CL:0000094	98.68	gold quality
islet of Langerhans	UBERON:0000006	98.16	gold quality
right adrenal gland	UBERON:0001233	98.09	gold quality
prefrontal cortex	UBERON:0000451	98.07	gold quality
right adrenal gland cortex	UBERON:0035827	98.06	gold quality
right coronary artery	UBERON:0001625	98.03	gold quality
bone marrow cell	CL:0002092	98.02	gold quality
adenohypophysis	UBERON:0002196	98.01	gold quality
right lung	UBERON:0002167	97.97	gold quality
left adrenal gland	UBERON:0001234	97.91	gold quality
mucosa of transverse colon	UBERON:0004991	97.91	gold quality
right frontal lobe	UBERON:0002810	97.88	gold quality
left adrenal gland cortex	UBERON:0035825	97.88	gold quality
left coronary artery	UBERON:0001626	97.87	gold quality
anterior cingulate cortex	UBERON:0009835	97.85	gold quality
apex of heart	UBERON:0002098	97.84	gold quality
smooth muscle tissue	UBERON:0001135	97.79	gold quality
vermiform appendix	UBERON:0001154	97.76	gold quality
thoracic aorta	UBERON:0001515	97.73	gold quality
ascending aorta	UBERON:0001496	97.71	gold quality
descending thoracic aorta	UBERON:0002345	97.71	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.70	gold quality
coronary artery	UBERON:0001621	97.69	gold quality
hypothalamus	UBERON:0001898	97.68	gold quality
metanephros cortex	UBERON:0010533	97.66	gold quality
lower esophagus	UBERON:0013473	97.61	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.61	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	17.62
E-CURD-88	yes	7.58
E-MTAB-10042	yes	6.96
E-MTAB-7316	yes	6.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting TRAPPC1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-548AZ-3P	99.82	70.56	3549
HSA-MIR-548BC	99.82	70.61	3524
HSA-MIR-548E-3P	99.82	70.59	3514
HSA-MIR-548F-3P	99.82	70.59	3540
HSA-MIR-548A-3P	99.76	70.58	3524
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-940	99.37	66.14	2064
HSA-MIR-6808-5P	99.31	66.23	2150
HSA-MIR-6893-5P	99.31	66.25	2119
HSA-MIR-4279	99.19	66.70	2437
HSA-MIR-4504	99.10	69.14	1328
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-4324	99.04	70.14	1569
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-4778-5P	97.96	68.06	1634
HSA-MIR-4715-5P	97.62	67.47	506
HSA-MIR-296-5P	97.61	64.02	851
HSA-MIR-1236-5P	96.62	66.38	856
HSA-MIR-4693-3P	95.23	65.92	735

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.7% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

• This paper studies human as well as yeast TRAPP subunits. (PMID:11805826)
• Mum2 binds to the alpha1-alpha2 loop of the Bet3-Tpc6B heterodimer. (PMID:16828797)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trappc1	ENSDARG00000039005
mus_musculus	Trappc1	ENSMUSG00000049299
rattus_norvegicus	Trappc1	ENSRNOG00000037627
drosophila_melanogaster	Bet5	FBGN0260860
caenorhabditis_elegans		WBGENE00077643

Paralogs (1): TRAPPC4 (ENSG00000196655)

Protein

Protein identifiers

Trafficking protein particle complex subunit 1 — Q9Y5R8 (reviewed: Q9Y5R8)

Alternative names: BET5 homolog, Multiple myeloma protein 2

All UniProt accessions (4): Q9Y5R8, I3L1R8, I3L3S0, I3L3V5

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Part of the multisubunit transport protein particle (TRAPP) complex. The heterodimer TRAPPC6B-TRAPPC3 interacts with TRAPPC1 likely providing a core for TRAPP complex formation.

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

Similarity. Belongs to the TRAPP small subunits family. BET5 subfamily.

RefSeq proteins (2): NP_001160093, NP_067033* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007233	TRAPPC	Family
IPR011012	Longin-like_dom_sf	Homologous_superfamily

Pfam: PF04099

UniProt features (2 total): chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y5R8-F1	95.64	0.96

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-204005	COPII-mediated vesicle transport
R-HSA-6798695	Neutrophil degranulation
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 185 (showing top): ATF_B, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_VESICLE_LOCALIZATION, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, CHANDRAN_METASTASIS_DN, GOLDRATH_ANTIGEN_RESPONSE, RICKMAN_METASTASIS_DN, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, ELK1_01, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, GOBP_MEMBRANE_ORGANIZATION

GO Biological Process (5): 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)

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

GO Cellular Component (9): extracellular region (GO:0005576), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), TRAPP complex (GO:0030008), azurophil granule lumen (GO:0035578), TRAPPII protein complex (GO:1990071), TRAPPIII protein complex (GO:1990072), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-3 pathways:

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
cellular anatomical structure	3
endomembrane system	2
intracellular membrane-bounded organelle	2
Golgi apparatus	2
TRAPP complex	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
binding	1
intracellular anatomical structure	1
vesicle tethering complex	1
intracellular protein-containing complex	1
vacuolar lumen	1
secretory granule lumen	1
azurophil granule	1
endosome	1

Protein interactions and networks

STRING

1110 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRAPPC1	TRAPPC6A	O75865	998
TRAPPC1	TRAPPC3	O43617	998
TRAPPC1	TRAPPC2	P0DI81	998
TRAPPC1	TRAPPC5	Q8IUR0	998
TRAPPC1	TRAPPC4	Q9Y296	991
TRAPPC1	TRAPPC8	Q9Y2L5	966
TRAPPC1	TRAPPC9	Q96Q05	896
TRAPPC1	RAB1A	P11476	888
TRAPPC1	TRAPPC10	P48553	838
TRAPPC1	TRAPPC13	A5PLN9	804
TRAPPC1	TRAPPC12	Q8WVT3	768
TRAPPC1	TRAPPC11	Q7Z392	751
TRAPPC1	RYR2	Q92736	717
TRAPPC1	TRAPPC2L	Q9UL33	717
TRAPPC1	USO1	O60763	645

IntAct

66 interactions, top by confidence:

A	B	Type	Score
TRAPPC6A	TRAPPC3	psi-mi:“MI:0914”(association)	0.850
TRAPPC3	TRAPPC1	psi-mi:“MI:0915”(physical association)	0.840
RUFY4	NDC80	psi-mi:“MI:0914”(association)	0.830
RAB3IP	TRAPPC3	psi-mi:“MI:0914”(association)	0.700
KANK4	TRAPPC3	psi-mi:“MI:0914”(association)	0.640
TRAPPC2L	TRAPPC13	psi-mi:“MI:0914”(association)	0.560
TRAPPC1	TRAPPC13	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
Trappc11	TRAPPC3	psi-mi:“MI:0914”(association)	0.350
Trappc8	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC3	TRAPPC6B	psi-mi:“MI:0914”(association)	0.350
BCL2L14		psi-mi:“MI:0914”(association)	0.350
TAFA3	FUOM	psi-mi:“MI:0914”(association)	0.350
	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC5	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TBC1D14		psi-mi:“MI:0914”(association)	0.350
TRAPPC1	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
KANK4		psi-mi:“MI:0914”(association)	0.350
CABS1		psi-mi:“MI:0914”(association)	0.350
STMN4		psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
ITM2B	ILVBL	psi-mi:“MI:0914”(association)	0.350
TRAPPC11	TRAPPC13	psi-mi:“MI:0914”(association)	0.350

BioGRID (120): TRAPPC1 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC12 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), TRAPPC11 (Affinity Capture-MS), TRAPPC6A (Affinity Capture-MS), TRAPPC6B (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC4 (Affinity Capture-MS), TRAPPC8 (Affinity Capture-MS), C7orf43 (Affinity Capture-MS)

ESM2 similar proteins: A0JN39, D2SW95, O08810, O22715, O23140, P23514, P35602, P35603, P49661, P53618, P84091, P84092, P91926, Q0DJ99, Q0DJA0, Q15029, Q15437, Q17QI1, Q29N38, Q2KMM2, Q3SZN2, Q3ZC13, Q4R706, Q54HS9, Q5F3X4, Q5NCF2, Q5NVF7, Q5R4A0, Q5R5G2, Q5R922, Q5ZIA5, Q5ZK03, Q5ZL57, Q5ZMP6, Q66HV4, Q6NWK2, Q6P856, Q7QG73, Q7ZVX6, Q7ZW98

Diamond homologs: Q03630, Q17QI1, Q2KMM2, Q557G3, Q5NCF2, Q9UT70, Q9Y5R8, Q2TBL9, Q5R9J9, Q69BT7, Q9ES56, Q9Y296, O43041, Q54UU1

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
TRAPPC1	“form complex”	“TRAPP III complex, TRAPPC2 variant”	binding
TRAPPC1	“form complex”	“TRAPP III complex, TRAPPC2B variant”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 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	13	47.5×	6e-17
COPII-mediated vesicle transport	9	43.2×	5e-11

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle tethering	11	259.6×	2e-23
COPII vesicle coat assembly	7	117.0×	8e-12
endoplasmic reticulum to Golgi vesicle-mediated transport	12	38.8×	1e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

506 predictions. Top by Δscore:

Variant	Effect	Δscore
17:7930732:CAG:C	acceptor_gain	1.0000
17:7930735:C:CC	acceptor_gain	1.0000
17:7931006:CTGA:C	donor_loss	1.0000
17:7931007:TGA:T	donor_loss	1.0000
17:7931008:GACC:G	donor_loss	1.0000
17:7931009:A:AC	donor_gain	1.0000
17:7931009:A:AG	donor_loss	1.0000
17:7931010:C:CC	donor_gain	1.0000
17:7931010:CCG:C	donor_gain	1.0000
17:7931010:CCGCA:C	donor_gain	1.0000
17:7931014:A:AC	donor_gain	1.0000
17:7931015:C:CC	donor_gain	1.0000
17:7931146:CTTC:C	acceptor_gain	1.0000
17:7931147:TTC:T	acceptor_gain	1.0000
17:7931148:TC:T	acceptor_gain	1.0000
17:7931149:CC:C	acceptor_gain	1.0000
17:7931150:C:CC	acceptor_gain	1.0000
17:7931150:CTGC:C	acceptor_loss	1.0000
17:7931475:T:TA	donor_gain	1.0000
17:7931478:T:TA	donor_gain	1.0000
17:7931486:T:TA	donor_gain	1.0000
17:7931504:A:AC	donor_gain	1.0000
17:7931505:C:CC	donor_gain	1.0000
17:7931505:CATGT:C	donor_gain	1.0000
17:7931732:T:TA	donor_gain	1.0000
17:7931735:T:TA	donor_gain	1.0000
17:7930730:TACAG:T	acceptor_gain	0.9900
17:7930733:AGC:A	acceptor_loss	0.9900
17:7930734:GC:G	acceptor_loss	0.9900
17:7930736:T:G	acceptor_loss	0.9900

AlphaMissense

943 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:7931557:C:T	G40E	1.000
17:7931558:C:G	G40R	1.000
17:7931558:C:T	G40R	1.000
17:7931566:A:G	L37P	1.000
17:7930643:A:T	V134D	0.999
17:7931063:G:A	T86I	0.999
17:7931072:A:T	V83D	0.999
17:7931108:A:G	L71P	0.999
17:7931545:G:A	S44F	0.999
17:7931557:C:A	G40V	0.999
17:7931558:C:A	G40W	0.999
17:7931767:C:A	W21C	0.999
17:7931767:C:G	W21C	0.999
17:7931769:A:G	W21R	0.999
17:7931769:A:T	W21R	0.999
17:7931792:C:A	G13V	0.999
17:7931792:C:T	G13E	0.999
17:7931803:A:C	F9L	0.999
17:7931803:A:T	F9L	0.999
17:7931804:A:G	F9S	0.999
17:7931805:A:G	F9L	0.999
17:7931822:A:T	V3D	0.999
17:7931065:A:C	N85K	0.998
17:7931065:A:T	N85K	0.998
17:7931108:A:T	L71H	0.998
17:7931115:A:C	Y69D	0.998
17:7931123:G:A	T66I	0.998
17:7931129:A:G	F64S	0.998
17:7931530:A:T	V49D	0.998
17:7931537:A:G	S47P	0.998

dbSNP variants (sampled 300 via entrez): RS1000040924 (17:7933149 C>A,T), RS1000162751 (17:7932392 C>T), RS1000433162 (17:7932804 G>C,T), RS1001142904 (17:7930848 A>T), RS1002822579 (17:7930937 T>C), RS1003827624 (17:7932260 G>A,T), RS1005044258 (17:7932000 AG>A,AGG), RS1005971911 (17:7930180 G>A,C), RS1006045394 (17:7930521 G>A,T), RS1006218020 (17:7933843 G>A), RS1006718792 (17:7930479 G>A), RS1006957716 (17:7930247 A>G), RS1007909181 (17:7931405 C>A,G,T), RS1007927501 (17:7933651 T>C), RS1008004332 (17:7931745 T>C)

Disease associations

OMIM: gene MIM:610969 | 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: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects expression, increases expression	4
sodium arsenite	increases expression, decreases expression, increases abundance	3
Cyclosporine	decreases expression, decreases methylation	3
Tobacco Smoke Pollution	decreases expression, increases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Lipopolysaccharides	affects response to substance, affects expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tunicamycin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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