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TRAPPC9 trafficking protein particle complex subunit 9 [ Homo sapiens (human) ]

Gene ID: 83696, updated on 21-Mar-2023

Summary

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Official Symbol
TRAPPC9provided by HGNC
Official Full Name
trafficking protein particle complex subunit 9provided by HGNC
Primary source
HGNC:HGNC:30832
See related
Ensembl:ENSG00000167632 MIM:611966; AllianceGenome:HGNC:30832
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
T1; IBP; NIBP; MRT13; TRS120; IKBKBBP
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 2010]
Expression
Ubiquitous expression in brain (RPKM 3.1), thyroid (RPKM 2.8) and 25 other tissues See more
Orthologs
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Genomic context

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See TRAPPC9 in Genome Data Viewer
Location:
8q24.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (139727725..140458579, complement)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (140847842..141578742, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (140739968..141468678, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene potassium two pore domain channel subfamily K member 9 Neighboring gene Sharpr-MPRA regulatory region 3867 Neighboring gene Sharpr-MPRA regulatory region 15097 Neighboring gene Sharpr-MPRA regulatory region 11049 Neighboring gene uncharacterized LOC107986981 Neighboring gene uncharacterized LOC105375781 Neighboring gene chromosome 8 putative open reading frame 17 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene paternally expressed 13 Neighboring gene uncharacterized LOC124902029 Neighboring gene uncharacterized LOC105375779 Neighboring gene Sharpr-MPRA regulatory region 993 Neighboring gene Sharpr-MPRA regulatory region 8823 Neighboring gene uncharacterized LOC105375782 Neighboring gene chromatin accessibility complex subunit 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Neurodevelopmental Outcome and Epigenetic Changes at 2 Years Associated with the Oxygen Load Received upon Postnatal Stabilization: A Pilot Study. Lorente-Pozo S, et al. Neonatology, 2022. PMID 35760056
  2. Novel Compound Heterozygous Mutation in TRAPPC9 Gene: The Relevance of Whole Genome Sequencing. Alvarez-Mora MI, et al. Genes (Basel), 2021 Apr 12. PMID 33921338, Free PMC Article
  3. Identification of two novel homozygous nonsense mutations in TRAPPC9 in two unrelated consanguineous families with intellectual Disability from Iran. Yousefipour F, et al. Mol Genet Genomic Med, 2021 Dec. PMID 33513295, Free PMC Article
  4. NIK‑ and IKKβ‑binding protein contributes to gastric cancer chemoresistance by promoting epithelial‑mesenchymal transition through the NF‑κB signaling pathway. Fu ZH, et al. Oncol Rep, 2018 Jun. PMID 29620292
  5. The role of CNVs in the etiology of rare autosomal recessive disorders: the example of TRAPPC9-associated intellectual disability. Mortreux J, et al. Eur J Hum Genet, 2018 Jan. PMID 29187737, Free PMC Article

See all (79) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Neurodevelopmental Outcome and Epigenetic Changes at 2 Years Associated with the Oxygen Load Received upon Postnatal Stabilization: A Pilot Study.
    Title: Neurodevelopmental Outcome and Epigenetic Changes at 2 Years Associated with the Oxygen Load Received upon Postnatal Stabilization: A Pilot Study.
  2. Identification of two novel homozygous nonsense mutations in TRAPPC9 in two unrelated consanguineous families with intellectual Disability from Iran.
    Title: Identification of two novel homozygous nonsense mutations in TRAPPC9 in two unrelated consanguineous families with intellectual Disability from Iran.
  3. Further insights into the spectrum phenotype of TRAPPC9 and CDK5RAP2 genes, segregating independently in a large Tunisian family with intellectual disability and microcephaly.
    Title: Further insights into the spectrum phenotype of TRAPPC9 and CDK5RAP2 genes, segregating independently in a large Tunisian family with intellectual disability and microcephaly.
  4. Novel Compound Heterozygous Mutation in TRAPPC9 Gene: The Relevance of Whole Genome Sequencing.
    Title: Novel Compound Heterozygous Mutation in TRAPPC9 Gene: The Relevance of Whole Genome Sequencing.
  5. Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity.
    Title: Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity.
  6. TRAPPC9 is associated with ADHD risk.
    Title: Contribution of Intellectual Disability-Related Genes to ADHD Risk and to Locomotor Activity in Drosophila.
  7. CNVs significantly contribute to the mutational spectrum of TRAPPC9 gene associated with syndromic intellectual disability.
    Title: The role of CNVs in the etiology of rare autosomal recessive disorders: the example of TRAPPC9-associated intellectual disability.
  8. Data show that NIBP expression level is high in gastric cancer (GC) patients and indicate that the NIBPregulated NFkappaB signaling pathway plays a pivotal role in the chemoresistance of GC cells by promoting EMT.
    Title: NIK‑ and IKKβ‑binding protein contributes to gastric cancer chemoresistance by promoting epithelial‑mesenchymal transition through the NF‑κB signaling pathway.
  9. Homozygous TRAPPC9 gene nonsense mutation in OXTR gene is associated with intellectual disability, speech disorder, and secondary microcephaly.
    Title: Identification of a novel homozygous TRAPPC9 gene mutation causing non-syndromic intellectual disability, speech disorder, and secondary microcephaly.
  10. In this study, we report that WES analysis allowed identification of the causal molecular lesion in both patients. In the first family of Egyptian origin, a homozygous nonsense mutation (c.1423C>T; p.Arg377*) in TRAPPC9 was identified
    Title: Whole exome sequencing is necessary to clarify ID/DD cases with de novo copy number variants of uncertain significance: Two proof-of-concept examples.
Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual disability, autosomal recessive 13
MedGen: C2750791 OMIM: 613192 GeneReviews: Not available
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EBI GWAS Catalog

Description
Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
EBI GWAS Catalog
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4737, MGC4769, KIAA1882

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cerebral cortex development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of NF-kappaB transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
involved_in vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in vesicle tethering NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of TRAPP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of TRAPPII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

General protein information

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Preferred Names
trafficking protein particle complex subunit 9
Names
IKK2 binding protein
NIK and IKK-beta binding protein
NIK- and IKBKB-binding protein
TRAPP 120 kDa subunit
trafficking protein particle complex 9
tularik gene 1 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016478.3 RefSeqGene

    Range
    5001..735855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1041

mRNA and Protein(s)

  1. NM_001160372.4 → NP_001153844.1  trafficking protein particle complex subunit 9 isoform b

    See identical proteins and their annotated locations for NP_001153844.1

    Status: REVIEWED

    Source sequence(s)
    AB067469, AC007869, AC040978, AC091022, DA228705, DA778234, R49592
    Consensus CDS
    CCDS55278.1
    UniProtKB/Swiss-Prot
    Q96Q05, Q9BQA2
    Related
    ENSP00000405060.3, ENST00000438773.4
    Conserved Domains (1) summary
    pfam08626
    Location:14 → 1100
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  2. NM_001321646.2 → NP_001308575.1  trafficking protein particle complex subunit 9 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC007869, AC040978, BC006206, DA228705, DA778234, R49592
    UniProtKB/Swiss-Prot
    Q96Q05
    Related
    ENSP00000430116.1, ENST00000520857.5
    Conserved Domains (1) summary
    pfam08626
    Location:14 → 1091
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  3. NM_001374682.1 → NP_001361611.1  trafficking protein particle complex subunit 9 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC007869, AC021744, AC040978, AC091022, AC104244
    Conserved Domains (1) summary
    pfam08626
    Location:14 → 1107
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  4. NM_001374683.1 → NP_001361612.1  trafficking protein particle complex subunit 9 isoform e

    Status: REVIEWED

    Source sequence(s)
    AC007869, AC021744, AC040978, AC091022, AC104244
    Conserved Domains (1) summary
    pfam08626
    Location:14 → 1063
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  5. NM_001374684.1 → NP_001361613.1  trafficking protein particle complex subunit 9 isoform f

    Status: REVIEWED

    Source sequence(s)
    AC007869, AC021744, AC040978, AC091022, AC104244
    Conserved Domains (1) summary
    pfam08626
    Location:14 → 1052
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  6. NM_031466.8 → NP_113654.5  trafficking protein particle complex subunit 9 isoform b

    Status: REVIEWED

    Source sequence(s)
    AC007869, AC021744, AC040978, AC091022, AC104244
    Consensus CDS
    CCDS55278.1
    UniProtKB/Swiss-Prot
    Q9BQA2
    Related
    ENSP00000498020.1, ENST00000648948.2
    Conserved Domains (1) summary
    pfam08626
    Location:14 → 1100
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

RNA

  1. NR_164662.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC007869, AC021636, AC021744, AC040978, AC091022, AC104244

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    139727725..140458579 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011517326.3 → XP_011515628.1  trafficking protein particle complex subunit 9 isoform X1

    Conserved Domains (1) summary
    pfam08626
    Location:112 → 1189
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  2. XM_017013894.3 → XP_016869383.1  trafficking protein particle complex subunit 9 isoform X10

  3. XM_011517330.3 → XP_011515632.1  trafficking protein particle complex subunit 9 isoform X11

    Conserved Domains (1) summary
    pfam08626
    Location:16 → 583
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  4. XM_047422295.1 → XP_047278251.1  trafficking protein particle complex subunit 9 isoform X4

  5. XM_047422294.1 → XP_047278250.1  trafficking protein particle complex subunit 9 isoform X3

  6. XM_011517328.3 → XP_011515630.1  trafficking protein particle complex subunit 9 isoform X2

    Conserved Domains (1) summary
    pfam08626
    Location:112 → 1094
    TRAPPC9-Trs120; Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit

  7. XM_047422297.1 → XP_047278253.1  trafficking protein particle complex subunit 9 isoform X6

  8. XM_047422296.1 → XP_047278252.1  trafficking protein particle complex subunit 9 isoform X5

  9. XM_047422298.1 → XP_047278254.1  trafficking protein particle complex subunit 9 isoform X8

  10. XM_017013893.2 → XP_016869382.1  trafficking protein particle complex subunit 9 isoform X7

  11. XM_047422299.1 → XP_047278255.1  trafficking protein particle complex subunit 9 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    140847842..141578742 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361328.1 → XP_054217303.1  trafficking protein particle complex subunit 9 isoform X1

  2. XM_054361337.1 → XP_054217312.1  trafficking protein particle complex subunit 9 isoform X10

  3. XM_054361338.1 → XP_054217313.1  trafficking protein particle complex subunit 9 isoform X11

  4. XM_054361331.1 → XP_054217306.1  trafficking protein particle complex subunit 9 isoform X4

  5. XM_054361330.1 → XP_054217305.1  trafficking protein particle complex subunit 9 isoform X3

  6. XM_054361329.1 → XP_054217304.1  trafficking protein particle complex subunit 9 isoform X2

  7. XM_054361333.1 → XP_054217308.1  trafficking protein particle complex subunit 9 isoform X6

  8. XM_054361332.1 → XP_054217307.1  trafficking protein particle complex subunit 9 isoform X5

  9. XM_054361335.1 → XP_054217310.1  trafficking protein particle complex subunit 9 isoform X8

  10. XM_054361334.1 → XP_054217309.1  trafficking protein particle complex subunit 9 isoform X7

  11. XM_054361336.1 → XP_054217311.1  trafficking protein particle complex subunit 9 isoform X9

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96Q05.2 GenPept UniProtKB/Swiss-Prot:Q96Q05

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