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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	83696
Gene name	Trafficking protein particle complex subunit 9
Gene symbol	TRAPPC9
Synonyms (NCBI Gene)	IBPIKBKBBPMRT13NIBPT1TRS120
Chromosome	8
Chromosome location	8q24.3
Summary	This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb

Show/Hide all (16)

SNP ID	Visualize variation	Clinical significance	Consequence
rs146235874	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, synonymous variant
rs267607136	G>A,C	Pathogenic	Genic upstream transcript variant, non coding transcript variant, stop gained, missense variant, coding sequence variant
rs267607137	G>A	Pathogenic, likely-pathogenic	Genic upstream transcript variant, non coding transcript variant, stop gained, intron variant, coding sequence variant
rs373701249	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs539016732	C>T	Likely-pathogenic	Genic downstream transcript variant, splice donor variant
rs587780486	C>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, genic upstream transcript variant
rs755371528	T>G	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs786205595	G>A	Likely-pathogenic	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, stop gained
rs1174482090	->GATC	Pathogenic	Non coding transcript variant, genic upstream transcript variant, frameshift variant, coding sequence variant
rs1465738840	C>T	Likely-pathogenic	Splice acceptor variant
rs1554632235	GTAGTT>TTAGTC	Likely-pathogenic	Coding sequence variant, downstream transcript variant, stop gained, genic downstream transcript variant, non coding transcript variant
rs1554689877	->A	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant, non coding transcript variant
rs1554689964	GGCCAGT>-	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant, non coding transcript variant
rs1587520018	T>G	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1588295226	TT>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant
rs1588397346	->CCTCACGGTACCCCCGTGAC	Pathogenic	5 prime UTR variant, frameshift variant, upstream transcript variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant

Show/Hide all (62)

miRTarBase ID	miRNA	Experiments	Reference
MIRT048179	hsa-miR-196a-5p	CLASH	23622248
MIRT044131	hsa-miR-30e-5p	CLASH	23622248
MIRT495659	hsa-miR-583	PAR-CLIP	22291592
MIRT495658	hsa-miR-6873-5p	PAR-CLIP	22291592
MIRT495657	hsa-miR-3126-5p	PAR-CLIP	22291592
MIRT495656	hsa-miR-6875-5p	PAR-CLIP	22291592
MIRT495659	hsa-miR-583	PAR-CLIP	22291592
MIRT495658	hsa-miR-6873-5p	PAR-CLIP	22291592
MIRT495657	hsa-miR-3126-5p	PAR-CLIP	22291592
MIRT495656	hsa-miR-6875-5p	PAR-CLIP	22291592
MIRT495659	hsa-miR-583	PAR-CLIP	22291592
MIRT495658	hsa-miR-6873-5p	PAR-CLIP	22291592
MIRT495657	hsa-miR-3126-5p	PAR-CLIP	22291592
MIRT495656	hsa-miR-6875-5p	PAR-CLIP	22291592
MIRT495659	hsa-miR-583	PAR-CLIP	22291592
MIRT495658	hsa-miR-6873-5p	PAR-CLIP	22291592
MIRT495657	hsa-miR-3126-5p	PAR-CLIP	22291592
MIRT495656	hsa-miR-6875-5p	PAR-CLIP	22291592
MIRT1452252	hsa-miR-1273f	CLIP-seq
MIRT1452253	hsa-miR-1275	CLIP-seq
MIRT1452254	hsa-miR-3150b-3p	CLIP-seq
MIRT1452255	hsa-miR-3675-5p	CLIP-seq
MIRT1452256	hsa-miR-4283	CLIP-seq
MIRT1452257	hsa-miR-4489	CLIP-seq
MIRT1452258	hsa-miR-4525	CLIP-seq
MIRT1452259	hsa-miR-4665-5p	CLIP-seq
MIRT1452260	hsa-miR-4723-5p	CLIP-seq
MIRT1452261	hsa-miR-4784	CLIP-seq
MIRT1452262	hsa-miR-625	CLIP-seq
MIRT1452263	hsa-miR-637	CLIP-seq
MIRT1452264	hsa-miR-765	CLIP-seq
MIRT1452254	hsa-miR-3150b-3p	CLIP-seq
MIRT1452265	hsa-miR-3928	CLIP-seq
MIRT1452266	hsa-miR-4446-3p	CLIP-seq
MIRT1452267	hsa-miR-4459	CLIP-seq
MIRT1452268	hsa-miR-4492	CLIP-seq
MIRT1452269	hsa-miR-4498	CLIP-seq
MIRT1452270	hsa-miR-4700-3p	CLIP-seq
MIRT1452271	hsa-miR-4721	CLIP-seq
MIRT1452261	hsa-miR-4784	CLIP-seq
MIRT1452272	hsa-miR-762	CLIP-seq
MIRT1452264	hsa-miR-765	CLIP-seq
MIRT2356525	hsa-miR-1291	CLIP-seq
MIRT2356526	hsa-miR-221	CLIP-seq
MIRT2356527	hsa-miR-222	CLIP-seq
MIRT2356528	hsa-miR-3176	CLIP-seq
MIRT2356529	hsa-miR-328	CLIP-seq
MIRT2356530	hsa-miR-3689a-3p	CLIP-seq
MIRT2356531	hsa-miR-3689c	CLIP-seq
MIRT2356532	hsa-miR-3922-3p	CLIP-seq
MIRT1452265	hsa-miR-3928	CLIP-seq
MIRT2356533	hsa-miR-4455	CLIP-seq
MIRT1452267	hsa-miR-4459	CLIP-seq
MIRT2356534	hsa-miR-4520a-5p	CLIP-seq
MIRT2356535	hsa-miR-4520b-5p	CLIP-seq
MIRT2356536	hsa-miR-4648	CLIP-seq
MIRT2356537	hsa-miR-4654	CLIP-seq
MIRT1452270	hsa-miR-4700-3p	CLIP-seq
MIRT2356538	hsa-miR-4728-5p	CLIP-seq
MIRT2356539	hsa-miR-4769-5p	CLIP-seq
MIRT2356540	hsa-miR-545	CLIP-seq
MIRT2356541	hsa-miR-548v	CLIP-seq

Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21525244, 21858081, 33961781
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	27066478
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005802	Component	Trans-Golgi network	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	NAS	27066478
GO:0006901	Process	Vesicle coating	NAS	27066478
GO:0021987	Process	Cerebral cortex development	IMP	20004763
GO:0030008	Component	TRAPP complex	IDA	21525244
GO:0030154	Process	Cell differentiation	IEA
GO:0030182	Process	Neuron differentiation	IEA
GO:0099022	Process	Vesicle tethering	NAS	27066478
GO:1990071	Component	TRAPPII protein complex	NAS	27066478

MIM	HGNC	e!Ensembl
611966	30832	ENSG00000167632

Q96Q05

Protein name

Trafficking protein particle complex subunit 9 (NIK- and IKBKB-binding protein) (Tularik gene 1 protein)

Protein function

Functions as an activator of NF-kappa-B through increased phosphorylation of the IKK complex. May function in neuronal cells differentiation. May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:1595144

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08626	TRAPPC9-Trs120	158 → 357	Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit	Family
PF08626	TRAPPC9-Trs120	346 → 673	Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed at high levels in muscle and kidney and to a lower extent in brain, heart and placenta. {ECO:0000269|PubMed:15951441}.

Sequence

MSVPDYMQCAEDHQTLLVVVQPVGIVSEENFFRIYKRICSVSQISVRDSQRVLYIRYRHH
YPPENNEWGDFQTHRKVVGLITITDCFSAKDWPQTFEKFHVQKEIYGSTLYDSRLFVFGL
QGEIVEQPRTDVAFYPNYEDCQTVEKRIEDFIESLFIVLESKRLDRATDKSGDKIPLLCV
PFEKKDFVGLDTDSRHYKKRCQGRMRKHVGDLCLQAGMLQDSLVHYHMSVELLRSVNDFL
WLGAALEGLCSASVIYHYPGGTGGKSGARRFQGSTLPAEAANRHRPGAQEVLIDPGALTT
NGINPDTSTEIGRAKNCLSPEDIIDKYKEAISYYSKYKNAGVIELEACIKAVRVLAIQKR
SMEASEFLQNAVYINLRQLSEEEKIQRYSILSELYELIGFHRKSAFFKRVAAMQCVAPSI
AEPGWRACYKLLLETLPGYSLSLDPKDFSRGTHRGWAAVQMRLLHELVYASRRMGNPALS
VRHLSFLLQTMLDFLSDQEKKDVAQSLENYTSKCPGTMEPIALPGGLTLPPVPFTKLPIV
RHVKLLNLPASLRPHKMKSLLGQNVSTKSPFIYSPIIAHNRGEERNKKIDFQWVQGDVCE
VQLMVYNPMPFELRVENMGLLTSGVEFESLPAALSLPAESGLYPVTLVGVPQTTGTITVN
GYHTTVFGVFSDCLLDNLPGIKTSGSTVEVIPALPRLQISTSLPRSAHSLQPSSGDEIST
NVSVQLYNGESQQLIIKLENIGMEPLEKLEVTSKVLTTKEKLYGDFLSWKLEETLAQFPL
QPGKVATFTINIKVKLDFSCQENLLQDLSDDGISVSGFPLSSPFRQVVRPRVEGKPVNPP
ESNKAGDYSHVKTLEAVLNFKYSGGPGHTEGYYRNLSLGLHVEVEPSVFFTRVSTLPATS
TRQCHLLLDVFNSTEHELTVSTRSSEALILHAGECQRMAIQVDKFNFESFPESPGEKGQF
ANPKQLEEERREARGLEIHSKLGICWRIPSLKRSGEASVEGLLNQLVLEHLQLAPLQWDV
LVDGQPCDREAVAACQVGDPVRLEVRLTNRSPRSVGPFALTVVPFQDHQNGVHNYDLHDT
VSFVGSSTFYLDAVQPSGQSACLGALLFLYTGDFFLHIRFHEDSTSKELPPSWFCLPSVH
VCALEAQA

Sequence length

1148

Interactions

View interactions

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

313

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Likely pathogenic; Pathogenic	rs2131117340, rs267607136, rs373701249	RCV001814413 RCV001813926 RCV001836911
Autism spectrum disorder	Pathogenic	rs752040819	RCV003127735
Autosomal recessive non-syndromic intellectual disability	Pathogenic	rs2131714597	RCV002243541
Intellectual disability	Likely pathogenic; Pathogenic	rs2071449158	RCV001260866
Intellectual disability, autosomal recessive 13	Pathogenic; Likely pathogenic	rs765943218, rs587780486, rs781469639, rs267607136, rs267607137, rs2131714307, rs2131922149, rs1489634479, rs2065638761, rs779744636, rs774787025, rs786205595, rs2539628652, rs2489805216, rs2539378745 View all (16 more)	RCV001785082 RCV000118683 RCV005238107 RCV000000794 RCV000000795 RCV000000796 RCV002227923 RCV002246785 RCV002289409 RCV002308532 RCV002471718 RCV003984824 RCV003226044 RCV003226102 RCV003336627 RCV003405213 RCV004690449 RCV003988328 RCV003988934 RCV004577426 RCV004585208 RCV000499511 RCV000501638 RCV001336731 RCV000034319 RCV004029278 RCV000985089 RCV001255732 RCV001255740 RCV001328632 RCV001374749
Intellectual disability-obesity-brain malformations-facial dysmorphism syndrome	Pathogenic	rs889624353	RCV001252379
Malignant tumor of esophagus	Likely pathogenic; Pathogenic	rs2071449158	RCV005909270
TRAPPC9-related disorder	Likely pathogenic; Pathogenic	rs2540231164, rs1554689964	RCV003896290 RCV003419847

Show/Hide Unknown Diseases (26)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs1563908442, rs539016732	-
Acute myeloid leukemia	Benign; Uncertain significance; Likely benign	rs113072129, rs143778652, rs2614718	RCV005916819 RCV005889359 RCV005889368
Adrenocortical carcinoma, hereditary	Benign; Likely benign	rs11166965, rs2614718	RCV005889360 RCV005889371
Cervical cancer	Benign	rs113072129	RCV005916820
Cholangiocarcinoma	Benign	rs11166965	RCV005889366
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign; Likely benign	rs2614718	RCV005889380
Colon adenocarcinoma	Benign; Likely benign	rs2614718	RCV005889367
Colorectal cancer	Benign	rs11166965	RCV005889363
Familial cancer of breast	Likely benign; Benign	rs547773428, rs9792174	RCV005929786 RCV005899347
Familial pancreatic carcinoma	Benign; Likely benign	rs2614718	RCV005889373
Gastric cancer	Benign; Likely benign	rs2614718	RCV005889374
Hepatocellular carcinoma	Benign; Likely benign	rs2614718	RCV005889369
History of neurodevelopmental disorder	Benign	rs367682297	RCV000716597
Intellectual Disability, Recessive	Uncertain significance; Benign; Likely benign; Conflicting classifications of pathogenicity	rs143778652, rs148523016, rs117632905, rs146235874, rs35578974, rs34179337, rs12549048, rs117685875, rs11166965, rs114949291, rs2614718, rs58740567, rs112551069, rs3735801, rs3735802 View all (54 more)	RCV000286252 RCV000278340 RCV000331735 RCV000262428 RCV000311757 RCV000261001 RCV000319877 RCV000359487 RCV000347198 RCV000376511 RCV000323246 RCV000351447 RCV000298928 RCV000322051 RCV000384914 RCV000325741 RCV000369913 RCV000334004 RCV000274208 RCV000300177 RCV000390442 RCV000291897 RCV000344704 RCV000397285 RCV000356435 RCV000271592 RCV000367806 RCV000275408 RCV000385240 RCV000390346 RCV000307775 RCV000332605 RCV000389509 RCV000402129 RCV000377332 RCV000280516 RCV000337927 RCV000368670 RCV000310370 RCV000398698 RCV000360152 RCV000393647 RCV000293136 RCV000383902 RCV000343506 RCV000341679 RCV000315440 RCV000379425 RCV000338962 RCV000353516 RCV000368886 RCV000270574 RCV000372954 RCV000338119 RCV000276379 RCV000328134 RCV000269789 RCV000327095 RCV000286322 RCV000271805 RCV000362706 RCV000265509 RCV000318247 RCV000375192 RCV000278570 RCV000317335 RCV000302369 RCV000390307 RCV000376722
Lung cancer	Benign; Likely benign	rs2614718	RCV005889379
Lymphoma	Benign; Likely benign	rs2614718	RCV005889375
Malignant lymphoma, large B-cell, diffuse	Benign	rs11166965	RCV005889362
Nonpapillary renal cell carcinoma	Benign; Likely benign	rs2614718	RCV005889370
Ovarian cancer	Benign; Likely benign	rs2614718	RCV005889372
Ovarian serous cystadenocarcinoma	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	rs114562350, rs2614718, rs112551069, rs374826041, rs757482428	RCV005916413 RCV005889376 RCV005931815 RCV005899346 RCV005899348
Sarcoma	Uncertain significance	rs768169759, rs745348155	RCV005924217 RCV005930105
Thymoma	Benign; Likely benign	rs11166965, rs2614718	RCV005889365 RCV005889378
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs757482428	RCV005899349
Uterine carcinosarcoma	Benign; Likely benign	rs11166965, rs2614718	RCV005889364 RCV005889377
Uterine corpus endometrial carcinoma	Likely benign	rs201180771	RCV005930507
Uveal melanoma	Benign	rs11166965	RCV005889361

Show/Hide Text Mining Associations (40)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Agenesis of Corpus Callosum	Associate	27108886
Alcohol Related Disorders	Associate	36348459
Alzheimer Disease	Associate	34440432
Ataxia	Associate	27108886
Autistic Disorder	Associate	24776741
Brain Diseases	Associate	22549410, 29187737, 33513295
Carcinogenesis	Associate	19034969
Cerebellar Hypoplasia	Associate	27108886
Cognition Disorders	Associate	22549410
Congenital Disorders of Glycosylation	Associate	35042660
Coronary Disease	Associate	34937574
Craniosynostoses	Associate	27108886
Dental Caries	Associate	36348459
Developmental Disabilities	Associate	29391579, 33513295
Diastrophic dysplasia	Associate	27108886
Emphysema	Associate	27669027
Facial Dysmorphism with Multiple Malformations	Associate	27108886
Fibrosis	Associate	28918882
Glucose Intolerance	Associate	35914803
Idiopathic Hypogonadotropic Hypogonadism	Associate	33208564
Immunologic Deficiency Syndromes	Associate	32162493
Immunologic Deficiency Syndromes	Inhibit	32162493
Intellectual Disability	Associate	20004764, 20004765, 21513506, 21629298, 22549410, 24776741, 27108886, 29187737, 29391579, 32162493, 33513295, 35042660, 36348459, 36672789
Language Disorders	Associate	29187737
Leukoencephalopathies	Associate	20004764, 20004765, 23412934
Mental Retardation X Linked Nonsyndromic	Associate	20004765
Microcephaly	Associate	20004764, 20004765, 27108886, 29187737, 33513295
Multiple Sclerosis	Associate	23412934
Muscle Hypotonia	Associate	22549410
Musculoskeletal Abnormalities	Associate	29391579
Neoplasms	Associate	19034969
Netherton Syndrome	Associate	20004765, 21629298
Non alcoholic Fatty Liver Disease	Associate	28918882
Nonsyndromic Deafness	Associate	22549410
Obesity	Associate	22549410, 29187737
Overweight	Associate	27108886
Pulmonary Disease Chronic Obstructive	Associate	27669027
Schaaf Yang syndrome	Associate	22549410
Speech Disorders	Associate	29391579
Usher Syndrome Type ID	Associate	27108886

TRAPPC9 (trafficking protein particle complex subunit 9)