GeneBe

TRAPPC11

trafficking protein particle complex subunit 11, the group of Trafficking protein particle complex subunits

Basic information

Region (hg38): 4:183659267-183713594

Previous symbols: [ "C4orf41" ]

Links

ENSG00000168538 ∙ NCBI:60684 ∙ OMIM:614138 ∙ HGNC:25751 ∙ Uniprot:Q7Z392 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • autosomal recessive limb-girdle muscular dystrophy type R18 (Definitive), mode of inheritance: AR
  • autosomal recessive limb-girdle muscular dystrophy type R18 (Definitive), mode of inheritance: AR
  • autosomal recessive limb-girdle muscular dystrophy type R18 (Strong), mode of inheritance: AR
  • autosomal recessive limb-girdle muscular dystrophy type R18 (Strong), mode of inheritance: AR
  • triple-A syndrome (Supportive), mode of inheritance: AR
  • autosomal recessive limb-girdle muscular dystrophy type R18 (Supportive), mode of inheritance: AR
  • intellectual disability-hyperkinetic movement-truncal ataxia syndrome (Supportive), mode of inheritance: AR
  • autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Muscular dystrophy, limb-girdle, autosomal recessive, 18ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal; Neurologic23830518; 27707803; 28827486

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAPPC11 gene.

  • Autosomal_recessive_limb-girdle_muscular_dystrophy_type_R18 (804 variants)
  • not_provided (198 variants)
  • Inborn_genetic_diseases (117 variants)
  • not_specified (36 variants)
  • TRAPPC11-related_disorder (15 variants)
  • Autosomal_recessive_limb-girdle_muscular_dystrophy (4 variants)
  • Limb-girdle_muscular_dystrophy (2 variants)
  • Muscular_dystrophy,_limb-girdle,_autosomal_recessive_23 (2 variants)
  • Muscular_dystrophy (1 variants)
  • Myopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAPPC11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021942.6. 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
10
clinvar
207
clinvar
1
clinvar
 218
missense
5
clinvar
414
clinvar
18
clinvar
2
clinvar
 439
nonsense
12
clinvar
8
clinvar
2
clinvar
 22
start loss
1
 1
frameshift
15
clinvar
13
clinvar
 28
splice donor/acceptor (+/-2bp)
2
clinvar
13
clinvar
 15
Total 29 39 427 225 3

Highest pathogenic variant AF is 0.0000648521

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRAPPC11protein_codingprotein_codingENST00000334690 2954326
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
4.56e-101.001256700781257480.000310
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9325345980.8930.00003007426
Missense in Polyphen6892.0140.739021085
Synonymous0.5332092190.9540.00001192132
Loss of Function4.462867.50.4150.00000349814

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006140.000610
Ashkenazi Jewish0.00009930.0000992
East Asian0.0003360.000326
Finnish0.00009250.0000924
European (Non-Finnish)0.0003910.000387
Middle Eastern0.0003360.000326
South Asian0.0003060.000294
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in endoplasmic reticulum to Golgi apparatus trafficking at a very early stage. {ECO:0000269|PubMed:21525244, ECO:0000269|PubMed:27862579}.;
Disease
DISEASE: Limb-girdle muscular dystrophy 2S (LGMD2S) [MIM:615356]: A form of limb-girdle muscular dystrophy characterized by proximal muscle weakness with childhood onset, resulting in gait abnormalities and scapular winging. Serum creatine kinase is increased. A subset of patients may show a hyperkinetic movement disorder with chorea, ataxia, or dystonia and global developmental delay. {ECO:0000269|PubMed:23830518}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

pRec
0.106

Intolerance Scores

loftool
rvis_EVS
-0.97
rvis_percentile_EVS
8.99

Haploinsufficiency Scores

pHI
0.0922
hipred
Y
hipred_score
0.544
ghis
0.664

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Trappc11
Phenotype

Zebrafish Information Network

Gene name
trappc11
Affected structure
hepatocyte
Phenotype tag
abnormal
Phenotype quality
increased size

Gene ontology

Biological process
endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;protein complex oligomerization;regulation of protein complex stability
Cellular component
Golgi apparatus;cytosol;TRAPP complex
Molecular function
protein binding;Rab guanyl-nucleotide exchange factor activity