TRAPPC13

Summary

TRAPPC13 (trafficking protein particle complex subunit 13, HGNC:25828) is a protein-coding gene on chromosome 5q12.3, encoding Trafficking protein particle complex subunit 13 (A5PLN9).

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; vesicle coating; and vesicle tethering. Predicted to be located in cytosol. Predicted to be part of TRAPPIII protein complex.

Source: NCBI Gene 80006 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 63 total
• MANE Select transcript: NM_024941

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25828
Approved symbol	TRAPPC13
Name	trafficking protein particle complex subunit 13
Location	5q12.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13611, MGC48585
Ensembl gene	ENSG00000113597
Ensembl biotype	protein_coding
Entrez	80006

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 6 retained_intron, 5 protein_coding, 2 nonsense_mediated_decay

ENST00000231526, ENST00000399438, ENST00000415825, ENST00000438419, ENST00000504243, ENST00000504751, ENST00000505108, ENST00000505553, ENST00000508304, ENST00000509234, ENST00000512009, ENST00000520525, ENST00000715762

RefSeq mRNA: 6 — MANE Select: NM_024941 NM_001093755, NM_001093756, NM_001243737, NM_001365342, NM_001365343, NM_024941

CCDS: CCDS47221, CCDS47222, CCDS47223, CCDS58950

Canonical transcript exons

ENST00000399438 — 13 exons

Exon	Start	End
ENSE00002042978	65664504	65666233
ENSE00003462713	65664237	65664384
ENSE00003469689	65652501	65652545
ENSE00003513676	65662050	65662150
ENSE00003556314	65660699	65660897
ENSE00003595652	65650810	65650882
ENSE00003596532	65658368	65658501
ENSE00003628087	65635301	65635369
ENSE00003640981	65635944	65636043
ENSE00003657123	65655636	65655653
ENSE00003675807	65637696	65637780
ENSE00003685875	65647055	65647182
ENSE00004027847	65625027	65625106

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 93.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.9337 / max 215.3042, expressed in 1721 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
56693	9.9337	1721
56692	2.4155	1299

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	93.01	gold quality
calcaneal tendon	UBERON:0003701	89.90	gold quality
secondary oocyte	CL:0000655	89.35	gold quality
rectum	UBERON:0001052	88.31	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.28	gold quality
cortical plate	UBERON:0005343	88.21	gold quality
ganglionic eminence	UBERON:0004023	88.18	gold quality
ventricular zone	UBERON:0003053	87.60	gold quality
prefrontal cortex	UBERON:0000451	87.59	gold quality
islet of Langerhans	UBERON:0000006	87.56	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.35	gold quality
monocyte	CL:0000576	86.70	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.68	gold quality
adrenal tissue	UBERON:0018303	86.67	gold quality
mononuclear cell	CL:0000842	86.37	gold quality
leukocyte	CL:0000738	86.26	gold quality
right adrenal gland cortex	UBERON:0035827	86.06	gold quality
adenohypophysis	UBERON:0002196	85.96	gold quality
metanephros cortex	UBERON:0010533	85.91	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.86	gold quality
anterior cingulate cortex	UBERON:0009835	85.43	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	85.41	gold quality
cingulate cortex	UBERON:0003027	85.29	gold quality
right adrenal gland	UBERON:0001233	85.25	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.22	gold quality
cerebellar hemisphere	UBERON:0002245	85.16	gold quality
pituitary gland	UBERON:0000007	85.13	gold quality
cerebellar cortex	UBERON:0002129	85.10	gold quality
muscle of leg	UBERON:0001383	85.08	gold quality
stromal cell of endometrium	CL:0002255	85.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting TRAPPC13, 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-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-7845-5P	99.88	64.88	771
HSA-LET-7A-2-3P	99.87	70.53	1921

Literature-anchored findings (GeneRIF, showing 1)

• Results lend support for the existence of a mammalian TRAPPIII complex containing TRAPPC13, which is important for autophagic flux under certain stress conditions. (PMID:28536105)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trappc13	ENSDARG00000033768
mus_musculus	Trappc13	ENSMUSG00000021711
rattus_norvegicus	Trappc13	ENSRNOG00000012124
drosophila_melanogaster	CG4953	FBGN0032204
caenorhabditis_elegans		WBGENE00016964

Protein

Protein identifiers

Trafficking protein particle complex subunit 13 — A5PLN9 (reviewed: A5PLN9)

All UniProt accessions (3): A5PLN9, D6RB83, H0YBF8

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Part of the multisubunit TRAPP (transport protein particle) complex.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the TRAPPC13 family.

Isoforms (5)

UniProt ID	Names	Canonical?
A5PLN9-1	1	yes
A5PLN9-2	2
A5PLN9-4	3
A5PLN9-5	4
A5PLN9-7	5

RefSeq proteins (6): NP_001087224, NP_001087225, NP_001230666, NP_001352271, NP_001352272, NP_079217* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010378	TRAPPC13	Family
IPR055427	TRAPPC13_N	Domain
IPR055428	TRAPPC13_C	Domain
IPR055429	TRAPPC13_M	Domain

Pfam: PF06159, PF23643, PF23647

UniProt features (8 total): splice variant 4, sequence conflict 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A5PLN9-F1	87.10	0.60

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8876198	RAB GEFs exchange GTP for GDP on RABs

MSigDB gene sets: 133 (showing top): GOBP_VESICLE_LOCALIZATION, GOBP_VESICLE_ORGANIZATION, GCANCTGNY_MYOD_Q6, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, ONKEN_UVEAL_MELANOMA_UP, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, IRF1_Q6, MODULE_301, GFI1_01, GOBP_MEMBRANE_ORGANIZATION, chr5q12, GOBP_ORGANELLE_LOCALIZATION

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle coat assembly (GO:0006901), obsolete vesicle tethering (GO:0099022)

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

GO Cellular Component (4): cytoplasm (GO:0005737), cytosol (GO:0005829), TRAPPII protein complex (GO:1990071), TRAPPIII protein complex (GO:1990072)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Rab regulation of trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
cellular anatomical structure	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
binding	1
intracellular anatomical structure	1
endosome	1

Protein interactions and networks

STRING

1152 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRAPPC13	TRAPPC8	Q9Y2L5	973
TRAPPC13	TRAPPC11	Q7Z392	964
TRAPPC13	TRAPPC12	Q8WVT3	955
TRAPPC13	TRAPPC9	Q96Q05	881
TRAPPC13	TRAPPC10	P48553	858
TRAPPC13	TRAPPC2L	Q9UL33	815
TRAPPC13	TRAPPC1	Q9Y5R8	804
TRAPPC13	TRAPPC5	Q8IUR0	775
TRAPPC13	TRAPPC4	Q9Y296	768
TRAPPC13	TRAPPC3	O43617	763
TRAPPC13	TRAPPC2	P0DI81	735
TRAPPC13	TRAPPC6A	O75865	680
TRAPPC13	TRAPPC6B	Q86SZ2	664
TRAPPC13	RAB1A	P11476	447
TRAPPC13	RIC1	Q4ADV7	437

IntAct

40 interactions, top by confidence:

A	B	Type	Score
	TRAPPC13	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC2L	TRAPPC13	psi-mi:“MI:0914”(association)	0.560
TRAPPC2L	TRAPPC13	psi-mi:“MI:0915”(physical association)	0.560
TRAPPC1	TRAPPC13	psi-mi:“MI:0914”(association)	0.530
TRAPPC13	RPSA2	psi-mi:“MI:0915”(physical association)	0.400
TRAPPC3	TRAPPC13	psi-mi:“MI:0915”(physical association)	0.400
TRAPPC13	TRAPPC8	psi-mi:“MI:0915”(physical association)	0.400
TRAPPC8	TRAPPC13	psi-mi:“MI:0915”(physical association)	0.400
TRAPPC13		psi-mi:“MI:0915”(physical association)	0.370
FOS	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
ARL3	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC11	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC2	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
trappc2_trappc2b_human	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
ZBTB3	VWA8	psi-mi:“MI:0914”(association)	0.350
DNAJC10	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC5	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
CMBL	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TBC1D14	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
RAB43	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
OTUB2	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
GAB2	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC6B	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
TRAPPC13	UBB	psi-mi:“MI:0914”(association)	0.350

BioGRID (123): UBB (Affinity Capture-MS), COG6 (Affinity Capture-MS), TRAPPC12 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS), TRAPPC13 (Affinity Capture-MS)

ESM2 similar proteins: A2VE14, A5PLN9, B1WC68, D3Z7P3, O54865, O89050, O94925, P13264, P16068, P20595, P38024, P51583, P97834, Q02153, Q0VCB2, Q0VCJ8, Q13042, Q13098, Q3TIR1, Q4R4U1, Q4ZHR9, Q5F450, Q5M887, Q5NVN7, Q5R5F8, Q5RB35, Q5RB59, Q5RBN9, Q5RKN4, Q5ZJB7, Q5ZMH6, Q67FW5, Q6AXQ0, Q6NRT5, Q86TJ2, Q8R349, Q8VH37, Q91YQ7, Q99LD4, Q99PV3

Diamond homologs: A5PLN9, A7MB76, A8WX89, Q0VFT9, Q3TIR1, Q55EX6, Q5M887, Q5RCG0, Q6GPR5, Q6PBY7, Q95QQ2, Q95TN1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 25 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	9	53.2×	7e-12
COPII-mediated vesicle transport	6	46.6×	3e-07

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle tethering	9	405.5×	5e-21
COPII vesicle coat assembly	8	255.3×	9e-17
endoplasmic reticulum to Golgi vesicle-mediated transport	10	61.8×	8e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2116 predictions. Top by Δscore:

Variant	Effect	Δscore
5:65635292:A:AG	acceptor_gain	1.0000
5:65635293:C:G	acceptor_gain	1.0000
5:65635299:A:AG	acceptor_gain	1.0000
5:65635300:G:GA	acceptor_gain	1.0000
5:65635370:G:GG	donor_gain	1.0000
5:65635938:A:AG	acceptor_gain	1.0000
5:65635939:T:G	acceptor_gain	1.0000
5:65635940:TCA:T	acceptor_loss	1.0000
5:65635942:A:AG	acceptor_gain	1.0000
5:65635942:AG:A	acceptor_gain	1.0000
5:65635943:G:GC	acceptor_gain	1.0000
5:65635943:GG:G	acceptor_gain	1.0000
5:65635943:GGA:G	acceptor_gain	1.0000
5:65635943:GGAGA:G	acceptor_gain	1.0000
5:65635993:TGCAG:T	donor_gain	1.0000
5:65636042:GG:G	donor_gain	1.0000
5:65636043:GG:G	donor_gain	1.0000
5:65636044:G:GC	donor_loss	1.0000
5:65636044:G:GG	donor_gain	1.0000
5:65636045:T:G	donor_loss	1.0000
5:65647041:A:AG	acceptor_gain	1.0000
5:65647042:A:G	acceptor_gain	1.0000
5:65647180:CAT:C	donor_gain	1.0000
5:65647181:AT:A	donor_gain	1.0000
5:65647183:G:GG	donor_gain	1.0000
5:65647188:GAT:G	donor_gain	1.0000
5:65624948:TTGA:T	donor_gain	0.9900
5:65635285:C:G	acceptor_gain	0.9900
5:65635297:A:AG	acceptor_gain	0.9900
5:65635297:ACAGT:A	acceptor_gain	0.9900

AlphaMissense

2745 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:65625101:T:A	L14Q	1.000
5:65625101:T:C	L14P	1.000
5:65635304:T:C	M17T	1.000
5:65635305:G:A	M17I	1.000
5:65635305:G:C	M17I	1.000
5:65635305:G:T	M17I	1.000
5:65635310:T:C	L19P	1.000
5:65635319:C:A	P22H	1.000
5:65636039:T:C	F71L	1.000
5:65636041:T:A	F71L	1.000
5:65636041:T:G	F71L	1.000
5:65637701:T:A	I74K	1.000
5:65637709:G:A	G77R	1.000
5:65637709:G:C	G77R	1.000
5:65637710:G:A	G77E	1.000
5:65637710:G:T	G77V	1.000
5:65637718:T:C	F80L	1.000
5:65637719:T:C	F80S	1.000
5:65637719:T:G	F80C	1.000
5:65637720:T:A	F80L	1.000
5:65637720:T:G	F80L	1.000
5:65637724:A:C	S82R	1.000
5:65637726:T:A	S82R	1.000
5:65637726:T:G	S82R	1.000
5:65637737:T:A	V86D	1.000
5:65637744:T:A	N88K	1.000
5:65637744:T:G	N88K	1.000
5:65647062:T:A	L103H	1.000
5:65647062:T:C	L103P	1.000
5:65647149:T:A	I132K	1.000

dbSNP variants (sampled 300 via entrez): RS1000045690 (5:65632847 T>G), RS1000077933 (5:65626539 C>T), RS1000103542 (5:65638703 G>C), RS1000131004 (5:65659439 C>G), RS1000155940 (5:65626758 T>C,G), RS1000228522 (5:65644093 A>G), RS1000301604 (5:65652145 G>A,C), RS1000472319 (5:65658765 A>G,T), RS1000580566 (5:65643773 T>C), RS1000581914 (5:65633213 A>T), RS1000613167 (5:65659793 G>A), RS1000647913 (5:65631298 A>T), RS1000669998 (5:65638240 A>G), RS1000790050 (5:65627107 G>A,C), RS1000821510 (5:65658399 A>G,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

3 associations (top):

Study	Trait	p-value
GCST010701_121	Cortical surface area (MOSTest)	6.000000e-11
GCST010702_62	Subcortical volume (MOSTest)	6.000000e-12
GCST010703_77	Brain morphology (MOSTest)	2.000000e-16

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Hydrogen Peroxide	affects expression, increases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	decreases expression	1
corosolic acid	increases expression	1
K 7174	increases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Formaldehyde	decreases expression	1
Lead	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Thimerosal	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Aflatoxin M1	decreases expression	1
Gold Compounds	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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