Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51399
Gene name	Trafficking protein particle complex subunit 4
Gene symbol	TRAPPC4
Synonyms (NCBI Gene)	CGI-104HSPC172NEDESBAPTD009SBDNSYNBINDINTRS23
Chromosome	11
Chromosome location	11q23.3

198

Show/Hide all (198)

miRTarBase ID	miRNA	Experiments	Reference
MIRT642887	hsa-miR-8063	HITS-CLIP	23824327
MIRT642886	hsa-miR-4698	HITS-CLIP	23824327
MIRT642885	hsa-miR-6847-3p	HITS-CLIP	23824327
MIRT642884	hsa-miR-1206	HITS-CLIP	23824327
MIRT642883	hsa-miR-6853-3p	HITS-CLIP	23824327
MIRT642882	hsa-miR-3977	HITS-CLIP	23824327
MIRT573522	hsa-miR-4691-3p	PAR-CLIP	20371350
MIRT573521	hsa-miR-6884-3p	PAR-CLIP	20371350
MIRT642887	hsa-miR-8063	HITS-CLIP	23824327
MIRT642886	hsa-miR-4698	HITS-CLIP	23824327
MIRT642885	hsa-miR-6847-3p	HITS-CLIP	23824327
MIRT642884	hsa-miR-1206	HITS-CLIP	23824327
MIRT642883	hsa-miR-6853-3p	HITS-CLIP	23824327
MIRT642882	hsa-miR-3977	HITS-CLIP	23824327
MIRT573522	hsa-miR-4691-3p	PAR-CLIP	20371350
MIRT573521	hsa-miR-6884-3p	PAR-CLIP	20371350
MIRT1452067	hsa-miR-1179	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT1452069	hsa-miR-1252	CLIP-seq
MIRT1452070	hsa-miR-1276	CLIP-seq
MIRT1452071	hsa-miR-128	CLIP-seq
MIRT1452072	hsa-miR-1286	CLIP-seq
MIRT1452073	hsa-miR-1297	CLIP-seq
MIRT1452074	hsa-miR-150	CLIP-seq
MIRT1452075	hsa-miR-24	CLIP-seq
MIRT1452076	hsa-miR-26a	CLIP-seq
MIRT1452077	hsa-miR-26b	CLIP-seq
MIRT1452078	hsa-miR-3156-3p	CLIP-seq
MIRT1452079	hsa-miR-3167	CLIP-seq
MIRT1452080	hsa-miR-3664-3p	CLIP-seq
MIRT1452081	hsa-miR-3667-5p	CLIP-seq
MIRT1452082	hsa-miR-3692	CLIP-seq
MIRT1452083	hsa-miR-3978	CLIP-seq
MIRT1452084	hsa-miR-421	CLIP-seq
MIRT1452085	hsa-miR-4268	CLIP-seq
MIRT1452086	hsa-miR-4301	CLIP-seq
MIRT1452087	hsa-miR-4310	CLIP-seq
MIRT1452088	hsa-miR-4330	CLIP-seq
MIRT1452089	hsa-miR-4436b-5p	CLIP-seq
MIRT1452090	hsa-miR-4465	CLIP-seq
MIRT1452091	hsa-miR-4680-5p	CLIP-seq
MIRT1452092	hsa-miR-4684-3p	CLIP-seq
MIRT1452093	hsa-miR-4691-5p	CLIP-seq
MIRT1452094	hsa-miR-4709-5p	CLIP-seq
MIRT1452095	hsa-miR-4713-5p	CLIP-seq
MIRT1452096	hsa-miR-4722-5p	CLIP-seq
MIRT1452097	hsa-miR-4731-5p	CLIP-seq
MIRT1452098	hsa-miR-4797-5p	CLIP-seq
MIRT1452099	hsa-miR-498	CLIP-seq
MIRT1452100	hsa-miR-505	CLIP-seq
MIRT1452101	hsa-miR-519a	CLIP-seq
MIRT1452102	hsa-miR-519b-3p	CLIP-seq
MIRT1452103	hsa-miR-519c-3p	CLIP-seq
MIRT1452104	hsa-miR-532-3p	CLIP-seq
MIRT1452105	hsa-miR-548a-5p	CLIP-seq
MIRT1452106	hsa-miR-548ab	CLIP-seq
MIRT1452107	hsa-miR-548ak	CLIP-seq
MIRT1452108	hsa-miR-548b-5p	CLIP-seq
MIRT1452109	hsa-miR-548c-5p	CLIP-seq
MIRT1452110	hsa-miR-548d-5p	CLIP-seq
MIRT1452111	hsa-miR-548h	CLIP-seq
MIRT1452112	hsa-miR-548i	CLIP-seq
MIRT1452113	hsa-miR-548j	CLIP-seq
MIRT1452114	hsa-miR-548w	CLIP-seq
MIRT1452115	hsa-miR-548y	CLIP-seq
MIRT1452116	hsa-miR-559	CLIP-seq
MIRT1452117	hsa-miR-571	CLIP-seq
MIRT1452118	hsa-miR-578	CLIP-seq
MIRT1452119	hsa-miR-591	CLIP-seq
MIRT1452120	hsa-miR-630	CLIP-seq
MIRT1452121	hsa-miR-873	CLIP-seq
MIRT1452122	hsa-miR-876-5p	CLIP-seq
MIRT1452067	hsa-miR-1179	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT2135371	hsa-miR-1275	CLIP-seq
MIRT1452072	hsa-miR-1286	CLIP-seq
MIRT1452073	hsa-miR-1297	CLIP-seq
MIRT1452074	hsa-miR-150	CLIP-seq
MIRT1452076	hsa-miR-26a	CLIP-seq
MIRT1452077	hsa-miR-26b	CLIP-seq
MIRT1452078	hsa-miR-3156-3p	CLIP-seq
MIRT1452084	hsa-miR-421	CLIP-seq
MIRT2135372	hsa-miR-4260	CLIP-seq
MIRT1452086	hsa-miR-4301	CLIP-seq
MIRT1452087	hsa-miR-4310	CLIP-seq
MIRT1452088	hsa-miR-4330	CLIP-seq
MIRT1452090	hsa-miR-4465	CLIP-seq
MIRT2135373	hsa-miR-4665-5p	CLIP-seq
MIRT1452091	hsa-miR-4680-5p	CLIP-seq
MIRT1452092	hsa-miR-4684-3p	CLIP-seq
MIRT1452094	hsa-miR-4709-5p	CLIP-seq
MIRT1452095	hsa-miR-4713-5p	CLIP-seq
MIRT1452096	hsa-miR-4722-5p	CLIP-seq
MIRT1452099	hsa-miR-498	CLIP-seq
MIRT1452100	hsa-miR-505	CLIP-seq
MIRT1452101	hsa-miR-519a	CLIP-seq
MIRT1452102	hsa-miR-519b-3p	CLIP-seq
MIRT1452103	hsa-miR-519c-3p	CLIP-seq
MIRT1452104	hsa-miR-532-3p	CLIP-seq
MIRT1452118	hsa-miR-578	CLIP-seq
MIRT2135374	hsa-miR-615-5p	CLIP-seq
MIRT1452120	hsa-miR-630	CLIP-seq
MIRT1452121	hsa-miR-873	CLIP-seq
MIRT1452067	hsa-miR-1179	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT1452069	hsa-miR-1252	CLIP-seq
MIRT2135371	hsa-miR-1275	CLIP-seq
MIRT1452070	hsa-miR-1276	CLIP-seq
MIRT1452071	hsa-miR-128	CLIP-seq
MIRT1452072	hsa-miR-1286	CLIP-seq
MIRT1452073	hsa-miR-1297	CLIP-seq
MIRT1452074	hsa-miR-150	CLIP-seq
MIRT1452075	hsa-miR-24	CLIP-seq
MIRT1452076	hsa-miR-26a	CLIP-seq
MIRT1452077	hsa-miR-26b	CLIP-seq
MIRT1452078	hsa-miR-3156-3p	CLIP-seq
MIRT1452079	hsa-miR-3167	CLIP-seq
MIRT1452080	hsa-miR-3664-3p	CLIP-seq
MIRT1452081	hsa-miR-3667-5p	CLIP-seq
MIRT1452082	hsa-miR-3692	CLIP-seq
MIRT1452083	hsa-miR-3978	CLIP-seq
MIRT1452084	hsa-miR-421	CLIP-seq
MIRT2135372	hsa-miR-4260	CLIP-seq
MIRT1452086	hsa-miR-4301	CLIP-seq
MIRT1452087	hsa-miR-4310	CLIP-seq
MIRT1452088	hsa-miR-4330	CLIP-seq
MIRT1452089	hsa-miR-4436b-5p	CLIP-seq
MIRT1452090	hsa-miR-4465	CLIP-seq
MIRT2135373	hsa-miR-4665-5p	CLIP-seq
MIRT1452091	hsa-miR-4680-5p	CLIP-seq
MIRT1452092	hsa-miR-4684-3p	CLIP-seq
MIRT1452094	hsa-miR-4709-5p	CLIP-seq
MIRT1452095	hsa-miR-4713-5p	CLIP-seq
MIRT1452096	hsa-miR-4722-5p	CLIP-seq
MIRT1452097	hsa-miR-4731-5p	CLIP-seq
MIRT1452098	hsa-miR-4797-5p	CLIP-seq
MIRT1452099	hsa-miR-498	CLIP-seq
MIRT1452100	hsa-miR-505	CLIP-seq
MIRT1452101	hsa-miR-519a	CLIP-seq
MIRT1452102	hsa-miR-519b-3p	CLIP-seq
MIRT1452103	hsa-miR-519c-3p	CLIP-seq
MIRT1452104	hsa-miR-532-3p	CLIP-seq
MIRT1452105	hsa-miR-548a-5p	CLIP-seq
MIRT1452106	hsa-miR-548ab	CLIP-seq
MIRT1452107	hsa-miR-548ak	CLIP-seq
MIRT1452108	hsa-miR-548b-5p	CLIP-seq
MIRT1452109	hsa-miR-548c-5p	CLIP-seq
MIRT1452110	hsa-miR-548d-5p	CLIP-seq
MIRT1452111	hsa-miR-548h	CLIP-seq
MIRT1452112	hsa-miR-548i	CLIP-seq
MIRT1452113	hsa-miR-548j	CLIP-seq
MIRT1452114	hsa-miR-548w	CLIP-seq
MIRT1452115	hsa-miR-548y	CLIP-seq
MIRT1452116	hsa-miR-559	CLIP-seq
MIRT1452118	hsa-miR-578	CLIP-seq
MIRT1452119	hsa-miR-591	CLIP-seq
MIRT2135374	hsa-miR-615-5p	CLIP-seq
MIRT1452120	hsa-miR-630	CLIP-seq
MIRT1452121	hsa-miR-873	CLIP-seq
MIRT1452122	hsa-miR-876-5p	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT1452084	hsa-miR-421	CLIP-seq
MIRT1452094	hsa-miR-4709-5p	CLIP-seq
MIRT1452100	hsa-miR-505	CLIP-seq
MIRT1452118	hsa-miR-578	CLIP-seq
MIRT1452120	hsa-miR-630	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT1452079	hsa-miR-3167	CLIP-seq
MIRT1452082	hsa-miR-3692	CLIP-seq
MIRT1452089	hsa-miR-4436b-5p	CLIP-seq
MIRT1452097	hsa-miR-4731-5p	CLIP-seq
MIRT1452122	hsa-miR-876-5p	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT1452072	hsa-miR-1286	CLIP-seq
MIRT1452079	hsa-miR-3167	CLIP-seq
MIRT1452082	hsa-miR-3692	CLIP-seq
MIRT1452084	hsa-miR-421	CLIP-seq
MIRT1452088	hsa-miR-4330	CLIP-seq
MIRT1452089	hsa-miR-4436b-5p	CLIP-seq
MIRT1452091	hsa-miR-4680-5p	CLIP-seq
MIRT1452092	hsa-miR-4684-3p	CLIP-seq
MIRT1452094	hsa-miR-4709-5p	CLIP-seq
MIRT1452096	hsa-miR-4722-5p	CLIP-seq
MIRT1452097	hsa-miR-4731-5p	CLIP-seq
MIRT1452100	hsa-miR-505	CLIP-seq
MIRT1452118	hsa-miR-578	CLIP-seq
MIRT1452120	hsa-miR-630	CLIP-seq
MIRT1452121	hsa-miR-873	CLIP-seq
MIRT1452122	hsa-miR-876-5p	CLIP-seq
MIRT1452068	hsa-miR-122	CLIP-seq
MIRT1452079	hsa-miR-3167	CLIP-seq
MIRT1452082	hsa-miR-3692	CLIP-seq
MIRT1452084	hsa-miR-421	CLIP-seq
MIRT1452089	hsa-miR-4436b-5p	CLIP-seq
MIRT1452094	hsa-miR-4709-5p	CLIP-seq
MIRT1452097	hsa-miR-4731-5p	CLIP-seq
MIRT1452100	hsa-miR-505	CLIP-seq
MIRT1452122	hsa-miR-876-5p	CLIP-seq

Show/Hide all (37)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0005515	Function	Protein binding	IPI	17110339, 21826244
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	27066478
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005795	Component	Golgi stack	IEA
GO:0005795	Component	Golgi stack	ISS	11018053
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	IBA
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	IMP	31794024
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	NAS	27066478
GO:0006901	Process	Vesicle coating	NAS	27066478
GO:0006914	Process	Autophagy	IMP	31794024
GO:0008021	Component	Synaptic vesicle	IEA
GO:0008021	Component	Synaptic vesicle	ISS	11018053
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0016358	Process	Dendrite development	IEA
GO:0016358	Process	Dendrite development	ISS	11018053
GO:0030008	Component	TRAPP complex	IBA
GO:0030008	Component	TRAPP complex	IDA	21525244
GO:0030008	Component	TRAPP complex	IEA
GO:0030008	Component	TRAPP complex	IMP	31794024
GO:0030425	Component	Dendrite	IEA
GO:0030425	Component	Dendrite	ISS	11018053
GO:0031982	Component	Vesicle	IEA
GO:0045202	Component	Synapse	IEA
GO:0045202	Component	Synapse	ISS	11018053
GO:0045211	Component	Postsynaptic membrane	IEA
GO:0048208	Process	COPII vesicle coating	NAS	27066478
GO:0048786	Component	Presynaptic active zone	IEA
GO:0098839	Component	Postsynaptic density membrane	IEA
GO:0099022	Process	Vesicle tethering	NAS	27066478
GO:1990071	Component	TRAPPII protein complex	NAS	27066478
GO:1990072	Component	TRAPPIII protein complex	NAS	27066478

MIM	HGNC	e!Ensembl
610971	19943	ENSG00000196655

Q9Y296

Protein name

Trafficking protein particle complex subunit 4 (Hematopoietic stem/progenitor cell protein 172) (Synbindin) (TRS23 homolog)

Protein function

Core component of the TRAPP complexes which has a function of guanine nucleotide exchange factor activity for Rab1 GTPase (Probable). Plays a role in vesicular transport from endoplasmic reticulum to Golgi and autophagy (PubMed:31794024). May pl

PDB

2J3T , 2JSN , 2ZMV

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04099	Sybindin	3 → 209	Sybindin-like family	Family

Sequence

MAIFSVYVVNKAGGLIYQLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVG
HAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSNEKLMLASMFHSLFA
IGSQLSPEQGSSGIEMLETDTFKLHCYQTLTGIKFVVLADPRQAGIDSLLRKIYEIYSDF
ALKNPFYSLEMPIRCELFDQNLKLALEVAEKAGTFGPGS

Sequence length

219

Interactions

View interactions

	Reactome
			COPII-mediated vesicle transport RAB GEFs exchange GTP for GDP on RABs

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Neurodevelopmental disorder with epilepsy, spasticity, and brain atrophy	Likely pathogenic; Pathogenic	rs1943311987, rs375776811, rs1943450738	RCV003330168 RCV001003468 RCV001172280	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain anomalies	Likely pathogenic; Pathogenic	rs375776811	RCV001267711	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (10)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRAPPC4-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (25)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenoma	Adenoma	BEFREE	21826244		★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	32901138	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar Diseases	Cerebellar diseases	Pubtator	31794024	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	21826244, 23625650		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	21826244	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	31794024, 39787667	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	32901138	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	39787667	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glucose-6-phosphate transport defect	Glucose-6-Phosphate Transport Defect	CLINVAR_DG	10026167, 10323254, 10923042, 10940311, 12444104, 15953877, 18835800, 22899091, 24646511, 26913919, 28224773, 9758626		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen Storage Disease	CLINVAR_DG	10323254, 10923042, 9758626		★★★★★ ★☆☆☆☆ Found in Text Mining only
GLYCOGEN STORAGE DISEASE Ic	Glycogen Storage Disease	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	31794024		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	31794024		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	31794024, 39787667	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	32901138, 39787667	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	23625650		★★★★★ ★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	31794024		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-specific syndromic intellectual disability	Syndromic Mental Retardation	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Parkinson Disease	Parkinson disease	BEFREE	20035503		★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	20035503	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Psychomotor Disorders	Psychiatric disorders	Pubtator	32901138	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	GENOMICS_ENGLAND_DG	31794024		★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	31794024, 39787667	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Spastic tetraparesis	Spastic tetraparesis	GENOMICS_ENGLAND_DG	31794024		★★★★★ ★☆☆☆☆ Found in Text Mining only
Visual Cortex Disorder	Visual cortex disease	GENOMICS_ENGLAND_DG	31794024		★★★★★ ★☆☆☆☆ Found in Text Mining only

TRAPPC4 (trafficking protein particle complex subunit 4)