TBC1D20
Basic information
Region (hg38): 20:423596-462566
Previous symbols: [ "C20orf140" ]
Links
Phenotypes
GenCC
Source:
- Warburg micro syndrome 4 (Strong), mode of inheritance: AR
- Warburg micro syndrome (Supportive), mode of inheritance: AR
- Warburg micro syndrome 4 (Moderate), mode of inheritance: AR
- Warburg micro syndrome 4 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Warburg micro syndrome 4 | 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 | Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic | 24239381 |
ClinVar
This is a list of variants' phenotypes submitted to
- Polyglucosan body myopathy type 1 (4 variants)
- Glycogen storage disease, type IV;Polyglucosan body myopathy type 1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBC1D20 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 | 24 | 26 | ||||
missense | 47 | 50 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 2 | 3 | 5 | |||
non coding | 49 | 86 | 27 | 171 | ||
Total | 5 | 5 | 96 | 111 | 31 |
Highest pathogenic variant AF is 0.0000131
Variants in TBC1D20
This is a list of pathogenic ClinVar variants found in the TBC1D20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-427295-G-A | Polyglucosan body myopathy type 1 | Benign (Dec 27, 2023) | ||
20-427297-C-T | Polyglucosan body myopathy type 1 | Likely benign (Dec 06, 2023) | ||
20-427301-G-A | Polyglucosan body myopathy type 1 | Likely benign (Sep 10, 2022) | ||
20-427302-T-C | Polyglucosan body myopathy type 1 | Likely benign (Jun 20, 2023) | ||
20-427309-G-A | Polyglucosan body myopathy type 1 • RBCK1-related disorder | Likely benign (Nov 25, 2023) | ||
20-427323-C-G | Polyglucosan body myopathy type 1 • Inborn genetic diseases | Uncertain significance (Jul 05, 2023) | ||
20-427327-G-A | Polyglucosan body myopathy type 1 | Likely benign (Nov 21, 2021) | ||
20-427332-A-G | Polyglucosan body myopathy type 1 | Uncertain significance (Apr 04, 2022) | ||
20-427337-C-T | Polyglucosan body myopathy type 1 | Pathogenic (Jul 14, 2023) | ||
20-427338-G-A | Polyglucosan body myopathy type 1 | Uncertain significance (Dec 02, 2021) | ||
20-427348-C-T | Polyglucosan body myopathy type 1 | Likely benign (Oct 14, 2023) | ||
20-427351-G-C | Polyglucosan body myopathy type 1 | Likely benign (Apr 04, 2022) | ||
20-427351-G-T | Polyglucosan body myopathy type 1 | Likely benign (Jul 30, 2021) | ||
20-427352-G-A | Polyglucosan body myopathy type 1 | Uncertain significance (Dec 07, 2023) | ||
20-427373-C-T | Polyglucosan body myopathy type 1 | Uncertain significance (Aug 10, 2022) | ||
20-427374-G-A | Polyglucosan body myopathy type 1 | Uncertain significance (Sep 26, 2021) | ||
20-427377-G-T | Polyglucosan body myopathy type 1 | Uncertain significance (Jun 09, 2022) | ||
20-427391-C-CT | Polyglucosan body myopathy type 1 | Likely pathogenic (-) | ||
20-427392-A-AT | Polyglucosan body myopathy type 1 | Pathogenic (Sep 10, 2022) | ||
20-427395-G-T | Polyglucosan body myopathy type 1;Glycogen storage disease, type IV | Pathogenic (Mar 03, 2016) | ||
20-427400-A-T | Polyglucosan body myopathy type 1 | Uncertain significance (Nov 28, 2018) | ||
20-427402-C-A | Polyglucosan body myopathy type 1 | Likely benign (Jun 29, 2022) | ||
20-427412-AA-CT | Polyglucosan body myopathy type 1 | Uncertain significance (Jun 19, 2022) | ||
20-427419-G-A | Polyglucosan body myopathy type 1 | Pathogenic (Jul 08, 2023) | ||
20-427432-G-A | Polyglucosan body myopathy type 1 | Likely benign (Jan 23, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TBC1D20 | protein_coding | protein_coding | ENST00000354200 | 8 | 27074 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.931 | 0.0692 | 125742 | 0 | 5 | 125747 | 0.0000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.21 | 176 | 228 | 0.773 | 0.0000132 | 2629 |
Missense in Polyphen | 38 | 79.357 | 0.47885 | 906 | ||
Synonymous | 0.742 | 81 | 90.0 | 0.900 | 0.00000488 | 811 |
Loss of Function | 3.41 | 2 | 17.3 | 0.115 | 9.00e-7 | 200 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000904 | 0.0000904 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000266 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: GTPase-activating protein specific for Rab1 and Rab2 small GTPase families for which it can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude.;
- Disease
- DISEASE: Warburg micro syndrome 4 (WARBM4) [MIM:615663]: A form of Warburg micro syndrome, a rare syndrome characterized by microcephaly, microphthalmia, microcornia, congenital cataracts, optic atrophy, cortical dysplasia, in particular corpus callosum hypoplasia, severe mental retardation, spastic diplegia, and hypogonadism. {ECO:0000269|PubMed:24239381}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Rab regulation of trafficking;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.224
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 39.95
Haploinsufficiency Scores
- pHI
- 0.223
- hipred
- Y
- hipred_score
- 0.654
- ghis
- 0.591
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.359
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tbc1d20
- Phenotype
- vision/eye phenotype; reproductive system phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- acrosome assembly;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;virion assembly;lipid droplet organization;positive regulation of GTPase activity;positive regulation by host of viral genome replication;positive regulation by virus of viral protein levels in host cell;COPII vesicle coating;lens fiber cell morphogenesis;seminiferous tubule development;COPII-coated vesicle cargo loading;regulation of cilium assembly;positive regulation of ER to Golgi vesicle-mediated transport
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of Golgi membrane;nuclear membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
- Molecular function
- GTPase activator activity;protein binding;Rab GTPase binding