TRAPPC13

trafficking protein particle complex subunit 13, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 5:65624789-65666233

Previous symbols: [ "C5orf44" ]

Links

ENSG00000113597NCBI:80006HGNC:25828Uniprot:A5PLN9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC13 gene.

  • not_specified (32 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024941.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
32
clinvar
32
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 32 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRAPPC13protein_codingprotein_codingENST00000438419 1341518
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002410.9951246220151246370.0000602
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.801281990.6420.000009572717
Missense in Polyphen2054.6980.36564795
Synonymous0.2816871.00.9580.00000353765
Loss of Function2.59820.70.3868.71e-7316

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002780.000277
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004670.0000464
European (Non-Finnish)0.00006280.0000531
Middle Eastern0.000.00
South Asian0.000.00
Other0.0001670.000165

dbNSFP

Source: dbNSFP

Pathway
Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

pRec
0.108

Intolerance Scores

loftool
rvis_EVS
0.13
rvis_percentile_EVS
63

Haploinsufficiency Scores

pHI
hipred
Y
hipred_score
0.591
ghis
0.605

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Trappc13
Phenotype

Gene ontology

Biological process
Cellular component
cytosol
Molecular function
protein binding;Rab guanyl-nucleotide exchange factor activity