TRAPPC11 (trafficking protein particle complex subunit 11)

Gene

• Entrez ID: 60684
• Gene name: Trafficking protein particle complex subunit 11
• Gene symbol: TRAPPC11
• Synonyms (NCBI Gene): C4orf41, FOIGR, GRY, LGMD2S, LGMDR18
• Chromosome: 4
• Chromosome location: 4q35.1
• Summary: The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alte

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140403642	C>T	Likely-pathogenic, pathogenic	Intron variant, stop gained, non coding transcript variant, coding sequence variant
rs143990563	C>A,G	Likely-pathogenic, benign-likely-benign	Missense variant, non coding transcript variant, coding sequence variant
rs146441514	C>G	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs148833310	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant, missense variant, 5 prime UTR variant, non coding transcript variant
rs150331292	C>G,T	Pathogenic	Stop gained, coding sequence variant, missense variant, 5 prime UTR variant, non coding transcript variant
rs150593522	T>-,TT	Conflicting-interpretations-of-pathogenicity, benign	Intron variant
rs151021715	A>C,G	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs200466260	C>G,T	Conflicting-interpretations-of-pathogenicity	Downstream transcript variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant, missense variant
rs201868142	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs397509417	G>A	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic downstream transcript variant
rs397509418	G>A	Pathogenic, pathogenic-likely-pathogenic	Intron variant
rs569565392	C>T	Likely-pathogenic	Stop gained, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs750976634	C>G,T	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, stop gained, non coding transcript variant
rs758227044	A>G	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs769785004	TCAG>-	Likely-pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, frameshift variant
rs778742385	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs780139133	C>T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs868721699	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, missense variant
rs886041052	G>T	Pathogenic	Splice acceptor variant
rs886041053	A>G	Pathogenic	Intron variant
rs1180079162	G>A,C	Likely-pathogenic	Splice acceptor variant
rs1186858080	G>A,T	Likely-pathogenic	Splice donor variant
rs1483190866	C>T	Likely-pathogenic	5 prime UTR variant, stop gained, coding sequence variant, non coding transcript variant
rs1554008865	->A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554008866	A>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1554009901	->T	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1579207748	AT>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT049471	hsa-miR-92a-3p	CLASH	23622248
MIRT037147	hsa-miR-877-3p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21525244
GO:0005737	Component	Cytoplasm	NAS	27066478
GO:0005794	Component	Golgi apparatus	IDA	27862579
GO:0005794	Component	Golgi apparatus	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	IMP	21525244
GO:0006888	Process	Endoplasmic reticulum to Golgi vesicle-mediated transport	NAS	27066478
GO:0007030	Process	Golgi organization	IMP	21525244
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0030008	Component	TRAPP complex	IMP	21525244
GO:0045054	Process	Constitutive secretory pathway	IMP	19942856
GO:0048208	Process	COPII vesicle coating	NAS	27066478
GO:0061635	Process	Regulation of protein complex stability	IMP	21525244
GO:0099022	Process	Vesicle tethering	NAS	27066478
GO:1990072	Component	TRAPPIII protein complex	NAS	27066478

Other IDs

• MIM: 614138
• HGNC: 25751
• e!Ensembl: ENSG00000168538

Protein

• UniProt ID: Q7Z392
• Protein name: Trafficking protein particle complex subunit 11
• Protein function: Involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF11817	Foie-gras_1	263 → 522	Foie gras liver health family 1	Family
  PF12742	Gryzun-like	1036 → 1095	Gryzun, putative Golgi trafficking	Domain

• Sequence:

  MSPTQWDFPVELCCRPMAFVTLTGLDVVYNAVHRAVWDAFCANRRADRVPISFKVLPGDH
  EYPKCRPKRTSYEWYIPKGILKTGWMNKHLNLVPALVVVFYELDWDEPQWKEKQSECATR
  VEIVRQSLQGRNTKVAVVLIQKKTPLPPGEDVIASERAAALCNACELSGKSLFVLPHTDH
  LVGYIIRLENAFYEHAQTYYYTEIRRVKSHKEFLNKTTHQLLFVRHQFKIAFFSELKQDT
  QNALKNYRTAYNLVHELRAHETNILEIKTMAGFINYKICRLCFQHNTPLDAIAQFRKHID
  LCKKKIGSAELSFEHDAWMSKQFQAFGDLFDEAIKLGLTAIQTQNPGFYYQQAAYYAQER
  KQLAKTLCNHEASVMYPNPDPLETQTGVLDFYGQRSWRQGILSFDLSDPEKEKVGILAIQ
  LKERNVVHSEIIITLLSNAVAQFKKYKCPRMKSHLMVQMGEEYYYAKDYTKALKLLDYVM
  CDYRSEGWWTLLTSVLTTALKCSYLMAQLKDYITYSLELLGRASTLKDDQKSRIEKNLIN
  VLMNESPDPEPDCDILAVKTAQKLWADRISLAGSNIFTIGVQDFVPFVQCKAKFHAPSFH
  VDVPVQFDIYLKADCPHPIRFSKLCVSFNNQEYNQFCVIEEASKANEVLENLTQGKMCLV
  PGKTRKLLFKFVAKTEDVGKKIEITSVDLALGNETGRCVVLNWQGGGGDAASSQEALQAA
  RSFKRRPKLPDNEVHWDSIIIQASTMIISRVPNISVHLLHEPPALTNEMYCLVVTVQSHE
  KTQIRDVKLTAGLKPGQDANLTQKTHVTLHGTELCDESYPALLTDIPVGDLHPGEQLEKM
  LYVRCGTVGSRMFLVYVSYLINTTVEEKEIVCKCHKDETVTIETVFPFDVAVKFVSTKFE
  HLERVYADIPFLLMTDLLSASPWALTIVSSELQLAPSMTTVDQLESQVDNVILQTGESAS
  ECFCLQCPSLGNIEGGVATGHYIISWKRTSAMENIPIITTVITLPHVIVENIPLHVNADL
  PSFGRVRESLPVKYHLQNKTDLVQDVEISVEPSDAFMFSGLKQIRLRILPGTEQEMLYNF
  YPLMAGYQQLPSLNINLLRFPNFTNQLLRRFIPTSIFVKPQGRLMDDTSIAAA

• Sequence length: 1133

Pathways

Reactome:

RAB GEFs exchange GTP for GDP on RABs

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Autosomal recessive limb-girdle muscular dystrophy	Pathogenic; Likely pathogenic	rs1414226750, rs1480951752, rs150331292	RCV005238115 RCV003226840 RCV003401410	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal recessive limb-girdle muscular dystrophy type R18	Likely pathogenic; Pathogenic	rs771717941, rs1180079162, rs1736442342, rs1216637259, rs759415592, rs2111348918, rs2111068286, rs1735877322, rs2111067026, rs1414226750, rs1735328958, rs2111348673, rs2111363477, rs1400419850, rs2111068100, rs1735567359, rs200561007, rs2477068133, rs2476948265, rs374498633, rs770361045, rs1377315723, rs2477083128, rs886041052, rs886041053, rs1234694300, rs1252513246, rs2477083166, rs1171897657, rs2476862111, rs1735351912, rs2476829947, rs2476847103, rs2476948907, rs150331292, rs769785004, rs1554009901, rs1186858080, rs140403642, rs1554007706, rs569565392, rs1483190866, rs750976634, rs397509417, rs397509418, rs1734714805, rs1735767573	RCV001336555 RCV001336033 RCV001336034 RCV001785081 RCV001783900 RCV001783901 RCV001783903 RCV002037649 RCV001999917 RCV001953797 RCV001927055 RCV001942047 RCV001967137 RCV001972821 RCV001956478 RCV003056872 RCV003112145 RCV002730698 RCV002851950 RCV002902895 RCV002933253 RCV003019843 RCV003059680 RCV000258796 RCV000258806 RCV003581927 RCV003581282 RCV003581447 RCV003582954 RCV003741707 RCV003742175 RCV003742284 RCV003740837 RCV003855591 RCV000416446 RCV003741194 RCV001055785 RCV000539818 RCV000554957 RCV000651606 RCV000754740 RCV002533849 RCV001784373 RCV003768286 RCV000054408 RCV000054409 RCV001223573 RCV001233161	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Colon adenocarcinoma	Likely pathogenic; Pathogenic	rs140403642	RCV005897022	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Limb-girdle muscular dystrophy	Likely pathogenic; Pathogenic	rs771717941, rs140403642	RCV004017819 RCV000825637	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Muscular dystrophy	Likely pathogenic; Pathogenic	rs397509417	RCV004798763	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Muscular dystrophy, limb-girdle, autosomal recessive 23	Likely pathogenic; Pathogenic	rs397509418	RCV001254697	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
TRAPPC11-related disorder	Likely pathogenic	rs1561063218	RCV003420743	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE LIMB GIRDLE MUSCULAR DYSTROPHY TYPE 2S	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Uncertain significance; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLUCOCORTICOID DEFICIENCY WITH ACHALASIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY, HYPERKINETIC MOVEMENT, TRUNCAL ATAXIA SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY-HYPERKINETIC MOVEMENT-TRUNCAL ATAXIA SYNDROME	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIMB-GIRDLE MUSCULAR DYSTROPHY AUTOSOMAL RECESSIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Myopathy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
OBESITY	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SARCOIDOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRAPPC11-RELATED LIMB-GIRDLE MUSCULAR DYSTROPHY R18	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRIPLE A SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRIPLE-A SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anterior hypopituitarism	Hypopituitarism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Apraxia of Phonation	Apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ataxia	Ataxia	Pubtator	23830518	Associate	★☆☆☆☆ Found in Text Mining only
Autosomal recessive limb girdle muscular dystrophy type 2S	Limb-Girdle Muscular Dystrophy	GENOMICS_ENGLAND_DG	23830518, 26912795, 27707803, 29855340		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive limb girdle muscular dystrophy type 2S	Limb-Girdle Muscular Dystrophy	ORPHANET_DG	23830518		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive limb girdle muscular dystrophy type 2S	Limb-Girdle Muscular Dystrophy	UNIPROT_DG	23830518		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autosomal recessive limb girdle muscular dystrophy type 2S	Limb-Girdle Muscular Dystrophy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Borderline intellectual disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral Infarction	Ischemic stroke	Pubtator	32912094	Associate	★☆☆☆☆ Found in Text Mining only
Cerebral Small Vessel Diseases	Cerebral microangiopathy	Pubtator	32912094	Associate	★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Disorders of Glycosylation	Congenital disorder of glycosylation	BEFREE	27862579		★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	BEFREE	29855340		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	29391579	Associate	★☆☆☆☆ Found in Text Mining only
Developmental regression	Developmental regression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	37974208	Associate	★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	29855340	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Achalasia	Achalasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Exophoria	Exophoria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty liver	Pubtator	37974208	Associate	★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glucocorticoid deficiency with achalasia	Glucocorticoid Deficiency With Achalasia	ORPHANET_DG	27707803		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hyperkinesis	Hyperkinesia	Pubtator	23830518	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	23830518		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	23830518, 29391579, 37197784	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual disability-hyperkinetic movement-truncal ataxia syndrome	Intellectual Disability-Hyperkinetic Movement-Truncal Ataxia Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Keratoderma, Palmoplantar	Palmoplantar keratoderma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	GWASCAT_DG	29494758		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	BEFREE	23830518		★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement disorder	Pubtator	23830518, 37197784	Associate	★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	BEFREE	23830518, 29855340		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	CLINVAR_DG	26322222, 27707803		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	BEFREE	29855340		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Myopathy	Myopathy	BEFREE	23830518, 29855340		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Myopathy	Myopathy	HPO_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Right ventricular dilatation	Right ventricular dilatation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Steatohepatitis	Fatty Liver	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Tonic - clonic seizures	Seizure	HPO_DG			★☆☆☆☆ Found in Text Mining only
TRAPPC11-related limb-girdle muscular dystrophy R18	Limb-Girdle Muscular Dystrophy	Orphanet			★☆☆☆☆ Found in Text Mining only
Triple A syndrome	Triple A Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations