Menu
GeneBe

TRAPPC2B

trafficking protein particle complex subunit 2B

Basic information

Region (hg38): 19:57363550-57365405

Previous symbols: [ "SEDLP", "TRAPPC2P1" ]

Links

ENSG00000256060NCBI:10597HGNC:10710Uniprot:P0DI82AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC2B gene.

  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC2B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
1
missense
0
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 0 1 0

Variants in TRAPPC2B

This is a list of pathogenic ClinVar variants found in the TRAPPC2B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
19-57365022-T-C Likely benign (Jul 01, 2022)2650570

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRAPPC2Bprotein_codingprotein_codingENST00000543226 11843
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.02950.6071245351541245900.000221
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.01187877.71.000.00000414950
Missense in Polyphen2219.5161.1273286
Synonymous0.6382327.20.8450.00000169236
Loss of Function0.17522.290.8759.75e-829

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.002210.00219
East Asian0.00005600.0000556
Finnish0.00004670.0000464
European (Non-Finnish)0.0001790.000168
Middle Eastern0.00005600.0000556
South Asian0.0002300.000229
Other0.0006670.000661

dbNSFP

Source: dbNSFP

Function
FUNCTION: Prevents transcriptional repression and induction of cell death by ENO1. May play a role in vesicular transport from endoplasmic reticulum to Golgi. {ECO:0000269|PubMed:11134351}.;
Pathway
Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

pRec
0.355

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.215
ghis
0.523

Gene ontology

Biological process
endoplasmic reticulum to Golgi vesicle-mediated transport
Cellular component
nucleus;nucleoplasm;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
Molecular function