GeneBe

TBC1D20

TBC1 domain family member 20

Basic information

Region (hg38): 20:423596-462566

Previous symbols: [ "C20orf140" ]

Links

ENSG00000125875 ∙ NCBI:128637 ∙ OMIM:611663 ∙ HGNC:16133 ∙ Uniprot:Q96BZ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • Warburg micro syndrome 4 (Definitive), 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Warburg micro syndrome 4ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic24239381

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TBC1D20 gene.

  • not_provided (95 variants)
  • Inborn_genetic_diseases (55 variants)
  • not_specified (9 variants)
  • TBC1D20-related_disorder (8 variants)
  • Warburg_micro_syndrome_4 (8 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. These statistics are base on transcript: NM_000144628.4. 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
1
clinvar
31
clinvar
2
clinvar
 34
missense
70
clinvar
1
clinvar
1
clinvar
 72
nonsense
3
clinvar
 3
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 5 1 70 32 3

Highest pathogenic variant AF is 0.0000027362

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TBC1D20protein_codingprotein_codingENST00000354200 827074
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9310.0692125742051257470.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.211762280.7730.00001322629
Missense in Polyphen3879.3570.47885906
Synonymous0.7428190.00.9000.00000488811
Loss of Function3.41217.30.1159.00e-7200

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009040.0000904
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002660.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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