TUB
Basic information
Region (hg38): 11:8019244-8106243
Links
Phenotypes
GenCC
Source:
- retinal dystrophy and obesity (Moderate), mode of inheritance: AR
- retinitis pigmentosa (Supportive), mode of inheritance: AD
- retinal dystrophy and obesity (Limited), mode of inheritance: AR
- essential tremor (Limited), mode of inheritance: AD
- retinal dystrophy and obesity (Limited), mode of inheritance: AR
- retinal dystrophy and obesity (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Retinal dystrophy and obesity | 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 | Endocrine; Ophthalmologic | 24375934 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (418 variants)
- TUB-related_disorder (175 variants)
- not_specified (73 variants)
- Retinal_dystrophy_and_obesity (20 variants)
- Retinal_dystrophy (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUB gene is commonly pathogenic or not. These statistics are base on transcript: NM_000177972.3. 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 | 129 | 142 | ||||
missense | 229 | 237 | ||||
nonsense | 3 | |||||
start loss | 1 | 1 | ||||
frameshift | 7 | |||||
splice donor/acceptor (+/-2bp) | 6 | |||||
Total | 9 | 5 | 238 | 138 | 6 |
Highest pathogenic variant AF is 0.00003903573
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TUB | protein_coding | protein_coding | ENST00000305253 | 13 | 86869 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00315 | 0.997 | 125714 | 0 | 33 | 125747 | 0.000131 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.470 | 331 | 356 | 0.930 | 0.0000227 | 3655 |
Missense in Polyphen | 135 | 165.29 | 0.81676 | 1697 | ||
Synonymous | -1.48 | 157 | 135 | 1.16 | 0.00000841 | 1109 |
Loss of Function | 3.41 | 10 | 30.2 | 0.331 | 0.00000175 | 326 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000416 | 0.000416 |
Ashkenazi Jewish | 0.0000997 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000139 | 0.0000924 |
European (Non-Finnish) | 0.000115 | 0.000114 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000165 | 0.000163 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in signal transduction from heterotrimeric G protein-coupled receptors. Binds to membranes containing phosphatidylinositol 4,5-bisphosphate. Can bind DNA (in vitro). May contribute to the regulation of transcription in the nucleus. Could be involved in the hypothalamic regulation of body weight (By similarity). Contribute to stimulation of phagocytosis of apoptotic retinal pigment epithelium (RPE) cells and macrophages. {ECO:0000250, ECO:0000269|PubMed:19837063}.;
- Disease
- DISEASE: Retinal dystrophy and obesity (RDOB) [MIM:616188]: A disease characterized by obesity, night blindness, decreased visual acuity, and electrophysiological features of a rod cone dystrophy. {ECO:0000269|PubMed:24375934}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- g-protein signaling through tubby proteins
(Consensus)
Recessive Scores
- pRec
- 0.253
Intolerance Scores
- loftool
- 0.0654
- rvis_EVS
- -0.91
- rvis_percentile_EVS
- 10.12
Haploinsufficiency Scores
- pHI
- 0.282
- hipred
- Y
- hipred_score
- 0.544
- ghis
- 0.631
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.726
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tub
- Phenotype
- vision/eye phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; pigmentation phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- phagocytosis, recognition;sensory perception of sound;response to hormone;photoreceptor cell maintenance;positive regulation of phagocytosis;retina development in camera-type eye;protein localization to cilium;receptor localization to non-motile cilium;protein localization to photoreceptor outer segment
- Cellular component
- extracellular region;nucleus;cytoplasm;cytosol;plasma membrane;cilium
- Molecular function
- phosphatidylinositol binding;protein-containing complex binding