TRAPPC11
Basic information
Region (hg38): 4:183659267-183713594
Previous symbols: [ "C4orf41" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Muscular dystrophy, limb-girdle, autosomal recessive, 18 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic | 23830518; 27707803; 28827486 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 10 | 207 | 218 | |||
missense | 414 | 18 | 439 | |||
nonsense | 12 | 22 | ||||
start loss | 1 | 1 | ||||
frameshift | 15 | 13 | 28 | |||
splice donor/acceptor (+/-2bp) | 13 | 15 | ||||
Total | 29 | 39 | 427 | 225 | 3 |
Highest pathogenic variant AF is 0.0000648521
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TRAPPC11 | protein_coding | protein_coding | ENST00000334690 | 29 | 54326 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.56e-10 | 1.00 | 125670 | 0 | 78 | 125748 | 0.000310 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.932 | 534 | 598 | 0.893 | 0.0000300 | 7426 |
Missense in Polyphen | 68 | 92.014 | 0.73902 | 1085 | ||
Synonymous | 0.533 | 209 | 219 | 0.954 | 0.0000119 | 2132 |
Loss of Function | 4.46 | 28 | 67.5 | 0.415 | 0.00000349 | 814 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000614 | 0.000610 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000336 | 0.000326 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.000391 | 0.000387 |
Middle Eastern | 0.000336 | 0.000326 |
South Asian | 0.000306 | 0.000294 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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