TRAPPC2B

Summary

TRAPPC2B (trafficking protein particle complex subunit 2B, HGNC:10710) is a protein-coding gene on chromosome 19q13.43, encoding Trafficking protein particle complex subunit 2B (P0DI82). Prevents transcriptional repression and induction of cell death by ENO1.

Enables transcription corepressor binding activity; transcription regulator inhibitor activity; and transmembrane transporter binding activity. Involved in positive regulation of gene expression and skeletal system development. Located in endoplasmic reticulum; nucleus; and perinuclear region of cytoplasm. Part of TRAPP complex.

Source: NCBI Gene 10597 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001355204

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10710
Approved symbol	TRAPPC2B
Name	trafficking protein particle complex subunit 2B
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	SEDLP1, MIP-2A
Ensembl gene	ENSG00000256060
Ensembl biotype	protein_coding
OMIM	620472
Entrez	10597

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000543226, ENST00000596755

RefSeq mRNA: 1 — MANE Select: NM_001355204 NM_001355204

CCDS: CCDS86812

Canonical transcript exons

ENST00000543226 — 2 exons

Exon	Start	End
ENSE00002267434	57363551	57363703
ENSE00002277150	57364815	57365405

Expression profiles

Bgee: expression breadth ubiquitous, 148 present calls, max score 88.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.6705 / max 113.8635, expressed in 1801 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177769	18.6705	1801

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	88.97	gold quality
muscle of leg	UBERON:0001383	88.28	gold quality
adrenal tissue	UBERON:0018303	87.90	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.40	gold quality
left adrenal gland cortex	UBERON:0035825	86.26	gold quality
left testis	UBERON:0004533	85.94	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.90	gold quality
left adrenal gland	UBERON:0001234	85.80	gold quality
testis	UBERON:0000473	85.71	gold quality
right adrenal gland	UBERON:0001233	85.65	gold quality
right testis	UBERON:0004534	85.59	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.34	gold quality
right adrenal gland cortex	UBERON:0035827	85.32	gold quality
islet of Langerhans	UBERON:0000006	85.22	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.16	gold quality
skeletal muscle tissue	UBERON:0001134	85.14	gold quality
adrenal gland	UBERON:0002369	85.13	gold quality
heart left ventricle	UBERON:0002084	85.11	gold quality
heart	UBERON:0000948	84.54	gold quality
right atrium auricular region	UBERON:0006631	84.44	gold quality
muscle tissue	UBERON:0002385	84.28	gold quality
omental fat pad	UBERON:0010414	84.20	gold quality
adenohypophysis	UBERON:0002196	83.91	gold quality
adipose tissue	UBERON:0001013	83.73	gold quality
tibial artery	UBERON:0007610	83.45	gold quality
popliteal artery	UBERON:0002250	83.43	gold quality
subcutaneous adipose tissue	UBERON:0002190	83.42	gold quality
placenta	UBERON:0001987	83.37	gold quality
pituitary gland	UBERON:0000007	82.96	gold quality
muscle layer of sigmoid colon	UBERON:0035805	82.81	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-10	yes	44.32
E-ANND-3	yes	6.10

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• MBP-1 interacting protein-2A (MIP-2A) preferentially expresses in certain tissues, including the pituitary gland, and negatively regulates the LHbeta gene transcription (MBP-1 interacting protein-2A) (PMID:12700240)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Trappc2	ENSRNOG00000042276
drosophila_melanogaster	Trs20	FBGN0266724

Paralogs (2): TRAPPC2L (ENSG00000167515), TRAPPC2 (ENSG00000196459)

Protein

Protein identifiers

Trafficking protein particle complex subunit 2B — P0DI82 (reviewed: P0DI82)

Alternative names: MBP-1-interacting protein 2A

All UniProt accessions (2): P0DI82, Q6IBE5

UniProt curated annotations — full annotation on UniProt →

Function. Prevents transcriptional repression and induction of cell death by ENO1. May play a role in vesicular transport from endoplasmic reticulum to Golgi.

Subunit / interactions. Can homodimerize. Part of the multisubunit TRAPP (transport protein particle) complex. Interacts with ENO1 and TRAPPC2L. Interacts with PITX1, SF1 and TRAPPC3.

Subcellular location. Nucleus. Cytoplasm. Perinuclear region. Endoplasmic reticulum-Golgi intermediate compartment.

Tissue specificity. Expressed in brain, heart, kidney, liver, lung, pancreas, placenta, skeletal muscle, fetal cartilage, fibroblasts, placenta and lymphocytes.

Miscellaneous. The gene encoding this protein appears to have arisen by retrotransposition of a cDNA from the X-linked locus TRAPPC2. The site of integration of this retrotransposed cDNA appears to lie within an intron of the ZNF547 gene, which provides a promoter and non-coding 5’ exon. TRAPPC2 and this protein are indistinguishable at protein level, and both proteins have been identified and functionally characterized.

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

RefSeq proteins (1): NP_001342133* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006722	Sedlin	Family
IPR011012	Longin-like_dom_sf	Homologous_superfamily

Pfam: PF04628

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DI82-F1	92.51	0.85

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): 119

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GOBP_VESICLE_LOCALIZATION, GOBP_VESICLE_ORGANIZATION, GOBP_VESICLE_TARGETING, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOBP_MEMBRANE_ORGANIZATION, GOBP_ORGANELLE_LOCALIZATION, HEIDENBLAD_AMPLICON_12P11_12_DN, GOCC_NUCLEAR_ENVELOPE, GOCC_NUCLEAR_OUTER_MEMBRANE, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENT, GOCC_NUCLEAR_MEMBRANE, GOBP_GOLGI_VESICLE_TRANSPORT, GOMF_TRANSCRIPTION_COREGULATOR_BINDING

GO Biological Process (6): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle coat assembly (GO:0006901), positive regulation of gene expression (GO:0010628), COPII vesicle coat assembly (GO:0048208), obsolete vesicle tethering (GO:0099022), vesicle-mediated transport (GO:0016192)

GO Molecular Function (3): transcription corepressor binding (GO:0001222), transcription regulator inhibitor activity (GO:0140416), protein binding (GO:0005515)

GO Cellular Component (10): nucleus (GO:0005634), nuclear outer membrane (GO:0005640), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), TRAPP complex (GO:0030008), perinuclear region of cytoplasm (GO:0048471), TRAPPII protein complex (GO:1990071), TRAPPIII protein complex (GO:1990072)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
intracellular membrane-bounded organelle	3
cellular anatomical structure	3
regulation of gene expression	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
gene expression	1
positive regulation of macromolecule biosynthetic process	1
vesicle coat assembly	1
protein-containing complex assembly	1
COPII-coated vesicle budding	1
transport	1
cellular process	1
transcription coregulator binding	1
transcription regulator activity	1
molecular function inhibitor activity	1
binding	1
nuclear membrane	1
organelle outer membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
nuclear lumen	1
intracellular anatomical structure	1
endomembrane system	1
vesicle tethering complex	1
intracellular protein-containing complex	1
endosome	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

7 interactions, top by confidence:

A	B	Type	Score
TRAPPC1	TRAPPC13	psi-mi:“MI:0914”(association)	0.530
TRAPPC2B	ZBED1	psi-mi:“MI:0915”(physical association)	0.370
Trappc8	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
TGOLN2	BLTP3B	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (238): PITX1 (Affinity Capture-Western), NR5A1 (Affinity Capture-Western), TRAPPC2 (Affinity Capture-Western), TRAPPC2 (Two-hybrid), TRAPPC2 (Two-hybrid), TRAPPC2 (Two-hybrid), TRAPPC2 (Affinity Capture-Western), MBL2 (Affinity Capture-Western), TRAPPC2 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS)

ESM2 similar proteins: A7RJI7, B0G185, D3ZVF4, E2QV03, F1SRI0, O02173, O13732, O17901, O23685, O43041, O74891, P0DI81, P0DI82, P35181, P35604, P38334, P53600, P56377, P61923, P61924, P61966, P61967, Q03630, Q08CN0, Q0VD30, Q1JQ98, Q28HU2, Q28IG8, Q3T0F2, Q3ZBS3, Q4S4I5, Q54CU7, Q54RV6, Q54UU1, Q5R5F2, Q5RES6, Q5ZKP4, Q5ZLN2, Q74ZD2, Q7T102

Diamond homologs: A7RVK7, D3ZVF4, E2QV03, F1SRI0, O02173, P0DI81, P0DI82, P38334, Q08CN0, Q28IG8, Q3T0F2, Q54RV6, Q5RES6, Q5ZKP4, Q9CQP2, Q9USZ5, Q9VUZ1, B5FXJ6, Q54CU7, A6H7F7, B2RYU6, Q5M8X5, Q9JME7, Q9UL33, B5XGE7, Q5RBK9

SIGNOR signaling

1 interactions.

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

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

260 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57364799:C:A	acceptor_gain	1.0000
19:57363700:CGAGG:C	donor_loss	0.9900
19:57363701:GAGGT:G	donor_loss	0.9900
19:57363702:AGGT:A	donor_loss	0.9900
19:57363703:GGTG:G	donor_loss	0.9900
19:57363704:G:GA	donor_loss	0.9900
19:57363705:T:A	donor_loss	0.9900
19:57363701:GAG:G	donor_gain	0.9800
19:57364800:G:A	acceptor_gain	0.9800
19:57365024:TGGAC:T	donor_gain	0.9800
19:57365308:A:T	donor_gain	0.9800
19:57364813:A:AG	acceptor_gain	0.9700
19:57364814:G:GG	acceptor_gain	0.9700
19:57363611:G:GT	donor_gain	0.9600
19:57363704:G:GG	donor_gain	0.9600
19:57364807:C:A	acceptor_gain	0.9600
19:57364814:GGA:G	acceptor_gain	0.9600
19:57365040:GTG:G	donor_gain	0.9600
19:57365307:G:GT	donor_gain	0.9600
19:57364810:TGCAG:T	acceptor_loss	0.9500
19:57364811:GCAGG:G	acceptor_loss	0.9500
19:57364812:CAG:C	acceptor_loss	0.9500
19:57364809:CTGCA:C	acceptor_loss	0.9400
19:57363565:T:TA	donor_gain	0.9300
19:57363566:A:AA	donor_gain	0.9300
19:57365042:G:GA	donor_gain	0.9300
19:57365107:G:GT	donor_gain	0.9200
19:57365235:G:T	donor_gain	0.9200
19:57365009:T:G	donor_gain	0.9100
19:57365025:GGACA:G	donor_gain	0.9100

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000872006 (19:57362631 A>T), RS1002242746 (19:57361838 T>A), RS1003415761 (19:57364215 A>G), RS1004253977 (19:57363788 C>G,T), RS1004598120 (19:57363228 G>A,C), RS1004823774 (19:57363372 T>G), RS1006088961 (19:57362066 A>G), RS1006680846 (19:57361670 T>C), RS1007857454 (19:57364769 C>A,T), RS1008346997 (19:57365099 T>C), RS1008726714 (19:57363411 T>C,G), RS1009364431 (19:57364453 T>C), RS1009743086 (19:57364240 G>A), RS1010225948 (19:57362576 T>C), RS1010404280 (19:57362181 G>A)

Disease associations

OMIM: gene MIM:620472 | 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

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	increases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	affects cotreatment, decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Selenium	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Zinc	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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