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TRAPPC12 trafficking protein particle complex subunit 12 [ Homo sapiens (human) ]

Gene ID: 51112, updated on 3-Apr-2024

Summary

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Official Symbol
TRAPPC12provided by HGNC
Official Full Name
trafficking protein particle complex subunit 12provided by HGNC
Primary source
HGNC:HGNC:24284
See related
Ensembl:ENSG00000171853 MIM:614139; AllianceGenome:HGNC:24284
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PEBAS; TTC15; CGI-87; TTC-15
Summary
Involved in several processes, including endoplasmic reticulum to Golgi vesicle-mediated transport; positive regulation of protein localization to kinetochore; and regulation of kinetochore assembly. Located in Golgi apparatus; kinetochore; and nucleoplasm. Part of TRAPP complex. Colocalizes with endoplasmic reticulum-Golgi intermediate compartment and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 6.2), brain (RPKM 2.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
2p25.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (3379694..3479565)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (3401815..3501615)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (3383465..3483336)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3172751-3173696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3182069-3182826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3183585-3184342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3184343-3185098 Neighboring gene Sharpr-MPRA regulatory region 8446 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:3202367-3202905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3204190-3204746 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15224 Neighboring gene EARP complex and GARP complex interacting protein 1 Neighboring gene MPRA-validated peak3584 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:3237853-3239052 Neighboring gene Sharpr-MPRA regulatory region 3808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15226 Neighboring gene VISTA enhancer hs1385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3284251-3284751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3289510-3290088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3290089-3290666 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3310431-3310601 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3323251-3323862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3326607-3327134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3327135-3327662 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3358809-3358982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15227 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3381914-3382430 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3382431-3382947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3402817-3403742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3403743-3404668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3404669-3405592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3416341-3416841 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3415840-3416340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3434408-3434908 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:3437307-3437557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3463593-3464106 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3464459-3465326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475415-3475916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:3475917-3476416 Neighboring gene TRAPPC12 antisense RNA 1 Neighboring gene uncharacterized LOC112268321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11111 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:3522968-3523489 Neighboring gene acireductone dioxygenase 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. Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction. Milev MP, et al. Am J Hum Genet, 2017 Aug 3. PMID 28777934, Free PMC Article
  2. Mammalian TRAPPIII Complex positively modulates the recruitment of Sec13/31 onto COPII vesicles. Zhao S, et al. Sci Rep, 2017 Feb 27. PMID 28240221, Free PMC Article
  3. TRAMM/TrappC12 plays a role in chromosome congression, kinetochore stability, and CENP-E recruitment. Milev MP, et al. J Cell Biol, 2015 Apr 27. PMID 25918224, Free PMC Article
  4. TRAPP Complexes in Secretion and Autophagy. Kim JJ, et al. Front Cell Dev Biol, 2016. PMID 27066478, Free PMC Article
  5. C4orf41 and TTC-15 are mammalian TRAPP components with a role at an early stage in ER-to-Golgi trafficking. Scrivens PJ, et al. Mol Biol Cell, 2011 Jun 15. PMID 21525244, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRAPPC12, but not TRAPPC8, bound to Sec13/Sec31A tetramer but each Sec protein alone could not interact with TRAPPC12.
    Title: Mammalian TRAPPIII Complex positively modulates the recruitment of Sec13/31 onto COPII vesicles.
  2. The authors report that variants in TRAPPC12 result in progressive childhood encephalopathy. Fibroblasts derived from three affected individuals showed a fragmented Golgi that could be rescued by expression of wild-type TRAPPC12.
    Title: Mutations in TRAPPC12 Manifest in Progressive Childhood Encephalopathy and Golgi Dysfunction.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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
Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome
MedGen: C5567229 OMIM: 617669 GeneReviews: Not available
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EBI GWAS Catalog

Description
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of trafficking protein particle complex 12 (TRAPPC12) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

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

  • FLJ36862, FLJ44560

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 COPII vesicle coating NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in Golgi organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport 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 metaphase chromosome alignment IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein localization to kinetochore IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of kinetochore assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in vesicle tethering NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
part_of TRAPP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of TRAPP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of TRAPPIII 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
  
colocalizes_with endoplasmic reticulum-Golgi intermediate compartment IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in kinetochore IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with perinuclear region of cytoplasm IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
trafficking protein particle complex subunit 12
Names
TPR repeat protein 15
tetratricopeptide repeat domain 15
tetratricopeptide repeat protein 15
trafficking of membranes and mitosis
trafficking protein particle complex 12

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.

mRNA and Protein(s)

  1. NM_001321102.2 → NP_001308031.1  trafficking protein particle complex subunit 12

    Status: VALIDATED

    Source sequence(s)
    AC114810, AK098327
    Consensus CDS
    CCDS1652.1
    UniProtKB/Swiss-Prot
    B3KV01, D6W4Y2, Q8WVT3, Q8WVW1, Q9Y395
    UniProtKB/TrEMBL
    Q8N9N0
    Related
    ENSP00000371544.2, ENST00000382110.6
    Conserved Domains (4) summary
    sd00006
    Location:546 → 573
    TPR; TPR repeat [structural motif]
    pfam11035
    Location:61 → 134
    SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb
    pfam13414
    Location:622 → 685
    TPR_11; TPR repeat
    pfam13424
    Location:581 → 652
    TPR_12; Tetratricopeptide repeat

  2. NM_016030.6 → NP_057114.5  trafficking protein particle complex subunit 12

    See identical proteins and their annotated locations for NP_057114.5

    Status: VALIDATED

    Source sequence(s)
    AF151845, BC014164, BC017475, DA031172
    Consensus CDS
    CCDS1652.1
    UniProtKB/Swiss-Prot
    B3KV01, D6W4Y2, Q8WVT3, Q8WVW1, Q9Y395
    UniProtKB/TrEMBL
    Q8N9N0
    Related
    ENSP00000324318.5, ENST00000324266.10
    Conserved Domains (4) summary
    sd00006
    Location:546 → 573
    TPR; TPR repeat [structural motif]
    pfam11035
    Location:61 → 134
    SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb
    pfam13414
    Location:622 → 685
    TPR_11; TPR repeat
    pfam13424
    Location:581 → 652
    TPR_12; Tetratricopeptide repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    3379694..3479565
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510350.3 → XP_011508652.1  trafficking protein particle complex subunit 12 isoform X1

    UniProtKB/TrEMBL
    Q8N9N0
    Conserved Domains (4) summary
    sd00006
    Location:508 → 535
    TPR; TPR repeat [structural motif]
    pfam11035
    Location:61 → 134
    SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb
    pfam13414
    Location:584 → 647
    TPR_11; TPR repeat
    pfam13424
    Location:543 → 614
    TPR_12; Tetratricopeptide repeat

  2. XM_047444637.1 → XP_047300593.1  trafficking protein particle complex subunit 12 isoform X1

  3. XM_011510352.3 → XP_011508654.1  trafficking protein particle complex subunit 12 isoform X2

    Conserved Domains (1) summary
    pfam11035
    Location:61 → 134
    SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb

  4. XM_047444639.1 → XP_047300595.1  trafficking protein particle complex subunit 12 isoform X3

  5. XM_047444638.1 → XP_047300594.1  trafficking protein particle complex subunit 12 isoform X2

  6. XM_011510353.3 → XP_011508655.1  trafficking protein particle complex subunit 12 isoform X4

    Conserved Domains (1) summary
    pfam11035
    Location:61 → 134
    SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb

  7. XM_011510354.3 → XP_011508656.1  trafficking protein particle complex subunit 12 isoform X5

    Conserved Domains (1) summary
    pfam11035
    Location:61 → 134
    SnAPC_2_like; Small nuclear RNA activating complex subunit 2, SNAP190 Myb

  8. XM_011510355.3 → XP_011508657.1  trafficking protein particle complex subunit 12 isoform X6

    UniProtKB/TrEMBL
    Q53QD4
    Conserved Domains (4) summary
    TIGR02795
    Location:234 → 293
    tol_pal_ybgF; tol-pal system protein YbgF
    sd00006
    Location:231 → 258
    TPR; TPR repeat [structural motif]
    pfam13414
    Location:307 → 370
    TPR_11; TPR repeat
    pfam13424
    Location:266 → 337
    TPR_12; Tetratricopeptide repeat

  9. XM_011510356.2 → XP_011508658.1  trafficking protein particle complex subunit 12 isoform X7

    See identical proteins and their annotated locations for XP_011508658.1

    UniProtKB/TrEMBL
    A0A0J9YXQ9, Q53QD4
    Conserved Domains (3) summary
    sd00006
    Location:190 → 217
    TPR; TPR repeat [structural motif]
    cl26002
    Location:199 → 379
    TPR_11; TPR repeat
    cl26250
    Location:193 → 252
    TPR_6; Tetratricopeptide repeat

RNA

  1. XR_426956.4 RNA Sequence

  2. XR_007076381.1 RNA Sequence

  3. XR_001738761.2 RNA Sequence

  4. XR_007076382.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187522.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    9876..89035
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    3401815..3501615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342395.1 → XP_054198370.1  trafficking protein particle complex subunit 12 isoform X1

  2. XM_054342396.1 → XP_054198371.1  trafficking protein particle complex subunit 12 isoform X1

  3. XM_054342397.1 → XP_054198372.1  trafficking protein particle complex subunit 12 isoform X2

  4. XM_054342399.1 → XP_054198374.1  trafficking protein particle complex subunit 12 isoform X3

  5. XM_054342398.1 → XP_054198373.1  trafficking protein particle complex subunit 12 isoform X2

  6. XM_054342400.1 → XP_054198375.1  trafficking protein particle complex subunit 12 isoform X4

  7. XM_054342401.1 → XP_054198376.1  trafficking protein particle complex subunit 12 isoform X5

  8. XM_054342403.1 → XP_054198378.1  trafficking protein particle complex subunit 12 isoform X7

    UniProtKB/TrEMBL
    A0A0J9YXQ9

  9. XM_054342402.1 → XP_054198377.1  trafficking protein particle complex subunit 12 isoform X6

RNA

  1. XR_008486387.1 RNA Sequence

  2. XR_008486386.1 RNA Sequence

  3. XR_008486385.1 RNA Sequence

  4. XR_008486388.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8WVT3.3 GenPept UniProtKB/Swiss-Prot:Q8WVT3

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