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TRAPPC2L trafficking protein particle complex subunit 2L [ Homo sapiens (human) ]

Gene ID: 51693, updated on 5-Mar-2024

Summary

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Official Symbol
TRAPPC2Lprovided by HGNC
Official Full Name
trafficking protein particle complex subunit 2Lprovided by HGNC
Primary source
HGNC:HGNC:30887
See related
Ensembl:ENSG00000167515 MIM:610970; AllianceGenome:HGNC:30887
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
PERRB; HSPC176
Summary
This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in adrenal (RPKM 16.3), testis (RPKM 13.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q24.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (88856220..88862678)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (94926614..94933072)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (88922628..88929086)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88869451-88870026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88870745-88871628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88871629-88872511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88873249-88873762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88876670-88877205 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7879 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88878711-88879395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88879396-88880079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88882597-88883098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:88883099-88883598 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:88884193-88885392 Neighboring gene chromatin licensing and DNA replication factor 1 Neighboring gene adenine phosphoribosyltransferase Neighboring gene galactosamine (N-acetyl)-6-sulfatase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7882 Neighboring gene uncharacterized LOC107983950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7883 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:88930168-88930918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11373 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:88940900-88941052 Neighboring gene PABPN1 like, cytoplasmic Neighboring gene uncharacterized LOC101927793 Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 3

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. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function. Al-Deri N, et al. J Med Genet, 2021 Sep. PMID 32843486, Free PMC Article
  2. Slow overmethylation of housekeeping genes in the body mucosa is associated with the risk for gastric cancer. Oh JH, et al. Cancer Prev Res (Phila), 2014 Jun. PMID 24654229
  3. Transcriptional regulation of bidirectional gene pairs by 17-β-estradiol in MCF-7 breast cancer cells. Garcia SA, et al. Braz J Med Biol Res, 2011 Feb. PMID 21180879
  4. Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts. Milev MP, et al. J Med Genet, 2018 Nov. PMID 30120216
  5. A yeast two hybrid screen identifies SPATA4 as a TRAPP interactor. Duarte DT, et al. FEBS Lett, 2011 Sep 2. PMID 21827752

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype.
    Title: TRAPPC2L-related disorder: first homozygous protein-truncating variant and further delineation of the phenotype.
  2. A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function.
    Title: A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function.
  3. deleterious bi-allelic variants in TRAPPC2L are associated with encephalopathy and febrile illness-induced episodes of rhabdomyolysis and subsequent developmental arrest. While the exact pathophysiological route deserves further study, our results suggest a role for RAB11.
    Title: Bi-allelic mutations in TRAPPC2L result in a neurodevelopmental disorder and have an impact on RAB11 in fibroblasts.
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
Encephalopathy, progressive, early-onset, with episodic rhabdomyolysis
MedGen: C5193033 OMIM: 618331 GeneReviews: Not available
not available

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

  • FLJ44827, MGC111156

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 endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport NAS
Non-traceable Author Statement
more info
 PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
part_of TRAPPIII protein complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
trafficking protein particle complex subunit 2-like protein
Names
hematopoietic stem/progenitor cells 176
trafficking protein particle complex 2 like

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_001318524.2 → NP_001305453.1  trafficking protein particle complex subunit 2-like protein isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC011369, BC017440, BX419849, DA209193
    Consensus CDS
    CCDS82027.1
    UniProtKB/TrEMBL
    A0A0B4J294
    Related
    ENSP00000457728.1, ENST00000568583.5
    Conserved Domains (1) summary
    pfam04628
    Location:7 → 144
    Sedlin_N; Sedlin, N-terminal conserved region

  2. NM_001318525.2 → NP_001305454.1  trafficking protein particle complex subunit 2-like protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
    Source sequence(s)
    BC011369, BC017440, DA209193
    Consensus CDS
    CCDS92207.1
    UniProtKB/Swiss-Prot
    Q9UL33
    Related
    ENSP00000512526.1, ENST00000696289.1
    Conserved Domains (1) summary
    cd14854
    Location:3 → 135
    TRAPPC2L; Trafficking protein particle complex subunit 2-like

  3. NM_001318526.2 → NP_001305455.1  trafficking protein particle complex subunit 2-like protein isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, contains multiple coding region differences and uses an alternate start codon, compared to variant 1. It encodes isoform 4, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    BC011369, BC017440, BG283878, BI754306, DA209193, DA833474
    Consensus CDS
    CCDS82029.1
    UniProtKB/TrEMBL
    H3BQQ8
    Related
    ENSP00000455892.1, ENST00000561840.1
    Conserved Domains (1) summary
    cl21566
    Location:54 → 127
    Sedlin_N; Sedlin, N-terminal conserved region

  4. NM_001318527.2 → NP_001305456.1  trafficking protein particle complex subunit 2-like protein isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK307253, AK310805, BC011369, BC017440, BC105809, BX340702, BX419849
    UniProtKB/Swiss-Prot
    Q9UL33
    Conserved Domains (1) summary
    cl21566
    Location:33 → 111
    Sedlin_N; Sedlin, N-terminal conserved region

  5. NM_001318528.2 → NP_001305457.1  trafficking protein particle complex subunit 2-like protein isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 6, which is shorter than isoform 1.
    Source sequence(s)
    AK310805, BC011369, BC017440, DA295904
    UniProtKB/Swiss-Prot
    Q9UL33
    Conserved Domains (1) summary
    pfam04628
    Location:1 → 108
    Sedlin_N; Sedlin, N-terminal conserved region

  6. NM_001318529.2 → NP_001305458.1  trafficking protein particle complex subunit 2-like protein isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and 5' coding region, uses an alternate start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 7, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    BC011369, BC017440, BX384775, DA209193
    UniProtKB/Swiss-Prot
    Q9UL33
    Conserved Domains (1) summary
    cl21566
    Location:33 → 105
    Sedlin_N; Sedlin, N-terminal conserved region

  7. NM_001318530.2 → NP_001305459.1  trafficking protein particle complex subunit 2-like protein isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 8, which is shorter than isoform 1.
    Source sequence(s)
    BC011369, BC017440, DA833474
    Consensus CDS
    CCDS82028.1
    UniProtKB/TrEMBL
    H3BUK6
    Related
    ENSP00000457684.1, ENST00000567895.5
    Conserved Domains (1) summary
    cd14854
    Location:2 → 105
    TRAPPC2L; Trafficking protein particle complex subunit 2-like

  8. NM_001318532.2 → NP_001305461.1  trafficking protein particle complex subunit 2-like protein isoform 9

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs in the 5' UTR and 5' coding region, uses an alternate start codon and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 9, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK310805, BC011369, BC017440, DA209193
    UniProtKB/Swiss-Prot
    Q9UL33
    Conserved Domains (1) summary
    cl21566
    Location:33 → 104
    Sedlin_N; Sedlin, N-terminal conserved region

  9. NM_016209.5 → NP_057293.1  trafficking protein particle complex subunit 2-like protein isoform 2

    See identical proteins and their annotated locations for NP_057293.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    BC011369, BC017440, BC105809
    Consensus CDS
    CCDS10971.1
    UniProtKB/Swiss-Prot
    B2R4M9, Q6ZTA7, Q9NZZ4, Q9UL33
    Related
    ENSP00000301021.3, ENST00000301021.7
    Conserved Domains (1) summary
    cd14854
    Location:3 → 136
    TRAPPC2L; Trafficking protein particle complex subunit 2-like

RNA

  1. NR_134670.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC011369, BC017440, BC105809, BI754306

  2. NR_134671.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) contains multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK307253, AK310805, BC011369, BC017440

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    88856220..88862678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023270.1 → XP_016878759.1  trafficking protein particle complex subunit 2-like protein isoform X1

    UniProtKB/TrEMBL
    H3BQQ8
    Conserved Domains (1) summary
    cl21566
    Location:54 → 127
    Sedlin_N; Sedlin, N-terminal conserved region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    94926614..94933072
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380442.1 → XP_054236417.1  trafficking protein particle complex subunit 2-like protein isoform X1

    UniProtKB/TrEMBL
    H3BQQ8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UL33.1 GenPept UniProtKB/Swiss-Prot:Q9UL33

Gene LinkOut

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