TRAPPC3L

Summary

TRAPPC3L (trafficking protein particle complex subunit 3L, HGNC:21090) is a protein-coding gene on chromosome 6q22.1, encoding Trafficking protein particle complex subunit 3-like protein (Q5T215). May play a role in vesicular transport from endoplasmic reticulum to Golgi.

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

Source: NCBI Gene 100128327 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_001139444

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21090
Approved symbol	TRAPPC3L
Name	trafficking protein particle complex subunit 3L
Location	6q22.1
Locus type	gene with protein product
Status	Approved
Aliases	bA259P20.2, FLJ11180
Ensembl gene	ENSG00000173626
Ensembl biotype	protein_coding
OMIM	614137
Entrez	100128327

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000356128, ENST00000368602, ENST00000437098

RefSeq mRNA: 1 — MANE Select: NM_001139444 NM_001139444

CCDS: CCDS47468

Canonical transcript exons

ENST00000368602 — 5 exons

Exon	Start	End
ENSE00001210145	116540363	116540462
ENSE00001210150	116543303	116543400
ENSE00001411589	116494989	116497073
ENSE00001447536	116545473	116545684
ENSE00003495274	116500481	116500666

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 94.44.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2684 / max 50.0958, expressed in 46 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
75263	0.1329	28
75265	0.0881	12
75264	0.0475	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	94.44	gold quality
dorsal root ganglion	UBERON:0000044	89.38	gold quality
monocyte	CL:0000576	82.86	gold quality
leukocyte	CL:0000738	81.52	gold quality
trigeminal ganglion	UBERON:0001675	78.63	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.82	gold quality
sperm	CL:0000019	69.00	silver quality
mucosa of paranasal sinus	UBERON:0005030	68.40	silver quality
spleen	UBERON:0002106	63.99	gold quality
placenta	UBERON:0001987	62.49	gold quality
calcaneal tendon	UBERON:0003701	60.79	gold quality
granulocyte	CL:0000094	60.19	gold quality
lower lobe of lung	UBERON:0008949	59.76	silver quality
hindlimb stylopod muscle	UBERON:0004252	57.51	gold quality
mucosa of transverse colon	UBERON:0004991	56.17	gold quality
right coronary artery	UBERON:0001625	54.78	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
pancreatic ductal cell	CL:0002079	54.20	silver quality
tendon	UBERON:0000043	54.07	gold quality
epithelial cell of pancreas	CL:0000083	53.95	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
cartilage tissue	UBERON:0002418	53.91	gold quality
lower esophagus mucosa	UBERON:0035834	53.79	gold quality
lymph node	UBERON:0000029	53.76	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
blood	UBERON:0000178	53.42	gold quality
gingival epithelium	UBERON:0001949	53.35	gold quality
right lung	UBERON:0002167	52.99	gold quality
heart left ventricle	UBERON:0002084	52.60	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.75

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting TRAPPC3L, 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-3134	100.00	66.43	777
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-7159-3P	99.51	70.17	1920
HSA-MIR-6833-5P	99.50	68.93	1161
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-4796-5P	99.34	70.06	810
HSA-MIR-3064-5P	99.26	66.13	1497
HSA-MIR-3085-3P	99.26	66.16	1490
HSA-MIR-6504-5P	99.26	65.95	1487
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-5583-3P	99.06	65.68	1018
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-3138	98.41	67.53	744
HSA-MIR-3921	97.81	67.45	1431
HSA-MIR-3173-5P	97.35	65.82	1282

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Trappc3l	ENSMUSG00000071340
rattus_norvegicus	Trappc3l	ENSRNOG00000031290
drosophila_melanogaster	Bet3	FBGN0260859
caenorhabditis_elegans		WBGENE00014222

Paralogs (1): TRAPPC3 (ENSG00000054116)

Protein

Protein identifiers

Trafficking protein particle complex subunit 3-like protein — Q5T215 (reviewed: Q5T215)

Alternative names: BET3-like protein

All UniProt accessions (2): Q5T215, A0A0A0MSL6

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Homodimer. 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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5T215-1	1	yes
Q5T215-2	2

RefSeq proteins (1): NP_001132916* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007194	TRAPP_component	Family
IPR016721	Bet3	Family
IPR024096	NO_sig/Golgi_transp_ligand-bd	Homologous_superfamily

Pfam: PF04051

UniProt features (3 total): chain 1, lipid moiety-binding region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T215-F1	86.53	0.65

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): 68

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_INTRA_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY, GOCC_CIS_GOLGI_NETWORK, GOBP_GOLGI_VESICLE_TRANSPORT, chr6q22, GOMF_NUCLEOSIDE_TRIPHOSPHATASE_REGULATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY, GOBP_INTRACELLULAR_TRANSPORT, FORTSCHEGGER_PHF8_TARGETS_UP, GOCC_TRAPP_COMPLEX, GOCC_CIS_GOLGI_NETWORK_MEMBRANE, GOCC_VESICLE_TETHERING_COMPLEX, PAX3_TARGET_GENES

GO Biological Process (4): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), intra-Golgi vesicle-mediated transport (GO:0006891), vesicle-mediated transport (GO:0016192), Golgi vesicle transport (GO:0048193)

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

GO Cellular Component (5): endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), TRAPP complex (GO:0030008), cis-Golgi network membrane (GO:0033106), Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
Golgi vesicle transport	2
endomembrane system	2
intracellular membrane-bounded organelle	2
intercellular transport	1
intracellular transport	1
transport	1
cellular process	1
vesicle-mediated transport	1
binding	1
cellular anatomical structure	1
vesicle tethering complex	1
intracellular protein-containing complex	1
cis-Golgi network	1
bounding membrane of organelle	1

Protein interactions and networks

STRING

394 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRAPPC3L	TRAPPC8	Q9Y2L5	744
TRAPPC3L	TRAPPC6B	Q86SZ2	721
TRAPPC3L	TRAPPC12	Q8WVT3	719
TRAPPC3L	TRAPPC4	Q9Y296	713
TRAPPC3L	TRAPPC2	P0DI81	674
TRAPPC3L	TRAPPC10	P48553	660
TRAPPC3L	TRAPPC2L	Q9UL33	539
TRAPPC3L	TRAPPC1	Q9Y5R8	406
TRAPPC3L	TRAPPC5	Q8IUR0	406
TRAPPC3L	SPINK13	Q1W4C9	348
TRAPPC3L	PPM1J	Q5JR12	347
TRAPPC3L	TRAPPC9	Q96Q05	346
TRAPPC3L	TRAPPC6A	O75865	341
TRAPPC3L	STARD5	P59094	336
TRAPPC3L	SKOR2	Q2VWA4	330

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GOLM1	RAB19	psi-mi:“MI:0914”(association)	0.350

BioGRID (18): TRAPPC3L (Two-hybrid), TRAPPC3L (Two-hybrid), TRAPPC4 (Two-hybrid), TRAPPC8 (Two-hybrid), TRAPPC9 (Two-hybrid), TRAPPC10 (Two-hybrid), TRAPPC11 (Two-hybrid), TRAPPC12 (Two-hybrid), TRAPPC5 (Two-hybrid), TRAPPC6A (Two-hybrid), TRAPPC6B (Two-hybrid), TRAPPC2L (Two-hybrid), TRAPPC2 (Two-hybrid), TRAPPC1 (Two-hybrid), TRAPPC3L (Two-hybrid)

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: O43617, O55013, P34605, P36149, Q4KL14, Q5T215, Q5U1Z2, Q5ZI57, Q61IU9, Q86K94, Q9P6P5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

990 predictions. Top by Δscore:

Variant	Effect	Δscore
6:116543296:CACTT:C	donor_loss	1.0000
6:116543297:ACTTA:A	donor_loss	1.0000
6:116543298:CTTA:C	donor_loss	1.0000
6:116543299:TTA:T	donor_loss	1.0000
6:116543300:T:TG	donor_loss	1.0000
6:116543301:A:AC	donor_gain	1.0000
6:116543301:ACA:A	donor_loss	1.0000
6:116543302:C:CC	donor_gain	1.0000
6:116543302:CA:C	donor_gain	1.0000
6:116543302:CAT:C	donor_gain	1.0000
6:116543399:TT:T	acceptor_gain	1.0000
6:116543401:C:CC	acceptor_gain	1.0000
6:116545471:A:AC	donor_gain	1.0000
6:116545472:C:CC	donor_gain	1.0000
6:116500427:AG:A	donor_gain	0.9900
6:116500557:T:TA	donor_gain	0.9900
6:116512232:CTCAG:C	donor_loss	0.9900
6:116512233:TCAG:T	donor_loss	0.9900
6:116512234:CAGGT:C	donor_loss	0.9900
6:116512235:AGGT:A	donor_loss	0.9900
6:116512236:GGTA:G	donor_loss	0.9900
6:116512237:GTAA:G	donor_loss	0.9900
6:116512238:T:G	donor_loss	0.9900
6:116540460:CCC:C	acceptor_gain	0.9900
6:116540461:CC:C	acceptor_gain	0.9900
6:116540461:CCC:C	acceptor_gain	0.9900
6:116540462:CC:C	acceptor_gain	0.9900
6:116543294:T:TA	donor_gain	0.9900
6:116543295:CCACT:C	donor_loss	0.9900
6:116543302:CATT:C	donor_gain	0.9900

AlphaMissense

1178 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:116543363:A:T	V27D	0.980
6:116540461:C:G	G48R	0.979
6:116540448:C:T	G52E	0.973
6:116500593:A:G	L105P	0.972
6:116543312:A:G	L44S	0.972
6:116540460:C:T	G48D	0.969
6:116540439:A:G	L55P	0.967
6:116543354:A:G	L30P	0.967
6:116500506:C:T	G134E	0.966
6:116540442:C:G	R54P	0.966
6:116500494:C:T	G138D	0.965
6:116500507:C:A	G134W	0.965
6:116500577:A:C	N110K	0.961
6:116500577:A:T	N110K	0.961
6:116500662:G:T	A82D	0.961
6:116543376:A:C	Y23D	0.961
6:116540461:C:A	G48C	0.960
6:116500492:C:G	A139P	0.959
6:116540448:C:A	G52V	0.955
6:116540427:A:G	F59S	0.954
6:116540449:C:G	G52R	0.954
6:116540449:C:T	G52R	0.954
6:116543366:A:G	L26P	0.953
6:116497054:A:T	V149D	0.952
6:116497009:A:T	I164K	0.951
6:116500593:A:T	L105Q	0.951
6:116543320:G:C	N41K	0.950
6:116543320:G:T	N41K	0.950
6:116500491:G:T	A139D	0.949
6:116500593:A:C	L105R	0.949

dbSNP variants (sampled 300 via entrez): RS1000057975 (6:116528385 G>A,T), RS1000082814 (6:116508554 T>C), RS1000148544 (6:116517635 G>A,T), RS1000343394 (6:116521338 G>A,T), RS1000354362 (6:116497095 G>A), RS1000378580 (6:116514237 A>G), RS1000403625 (6:116535765 C>G), RS1000409538 (6:116540966 C>T), RS1000459019 (6:116497779 A>G), RS1000461902 (6:116541290 T>C), RS1000467625 (6:116509107 A>C), RS1000543462 (6:116521197 A>G), RS1000627366 (6:116527257 C>T), RS1000641122 (6:116534015 C>A,G,T), RS1000861231 (6:116542408 G>A)

Disease associations

OMIM: gene MIM:614137 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004133_46	Ulcerative colitis	9.000000e-06
GCST010002_333	Refractive error	2.000000e-36

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	decreases expression	1
bisphenol A	decreases methylation	1
CGP 52608	affects binding, increases reaction	1
licochalcone B	decreases expression	1
Aflatoxins	decreases expression	1
Estradiol	increases expression	1
Zearalenone	increases expression	1

Clinical trials (associated diseases)

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