TOB2
Basic information
Region (hg38): 22:41433492-41446801
Previous symbols: [ "TROB2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TOB2 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 | 2 | |||||
missense | 13 | 14 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 13 | 2 | 1 |
Variants in TOB2
This is a list of pathogenic ClinVar variants found in the TOB2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-41436315-T-C | not specified | Uncertain significance (Aug 23, 2021) | ||
22-41436421-C-T | not specified | Likely benign (Jan 26, 2022) | ||
22-41436465-C-G | not specified | Uncertain significance (Apr 08, 2024) | ||
22-41436501-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
22-41436506-G-A | Likely benign (Feb 01, 2023) | |||
22-41436549-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
22-41436557-G-A | Benign (Jan 19, 2018) | |||
22-41436684-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
22-41436685-G-A | not specified | Uncertain significance (Jul 20, 2021) | ||
22-41436694-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
22-41436696-G-A | not specified | Uncertain significance (Jan 23, 2023) | ||
22-41436697-G-T | not specified | Uncertain significance (Aug 12, 2021) | ||
22-41436925-C-G | not specified | Uncertain significance (Oct 02, 2023) | ||
22-41436985-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
22-41437005-A-C | not specified | Uncertain significance (Apr 15, 2024) | ||
22-41437098-C-T | not specified | Uncertain significance (Jun 12, 2023) | ||
22-41437125-C-T | not specified | Uncertain significance (Jan 19, 2024) | ||
22-41437147-C-G | not specified | Uncertain significance (Aug 15, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TOB2 | protein_coding | protein_coding | ENST00000327492 | 1 | 13532 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.887 | 0.112 | 125684 | 0 | 1 | 125685 | 0.00000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.791 | 174 | 206 | 0.845 | 0.0000120 | 2246 |
Missense in Polyphen | 41 | 73.285 | 0.55946 | 782 | ||
Synonymous | 0.915 | 78 | 89.0 | 0.877 | 0.00000540 | 720 |
Loss of Function | 2.46 | 0 | 7.08 | 0.00 | 3.00e-7 | 93 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.0000993 | 0.0000993 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Anti-proliferative protein inhibits cell cycle progression from the G0/G1 to S phases.;
- Pathway
- RNA degradation - Homo sapiens (human);Bone Morphogenic Protein (BMP) Signalling and Regulation
(Consensus)
Recessive Scores
- pRec
- 0.160
Intolerance Scores
- loftool
- rvis_EVS
- -0.58
- rvis_percentile_EVS
- 18.59
Haploinsufficiency Scores
- pHI
- 0.382
- hipred
- N
- hipred_score
- 0.437
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.959
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tob2
- Phenotype
- skeleton phenotype; immune system phenotype; hematopoietic system phenotype; cellular phenotype;
Gene ontology
- Biological process
- female gamete generation;negative regulation of cell population proliferation;regulation of gene expression;negative regulation of osteoclast differentiation;positive regulation of ossification;negative regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- transcription corepressor activity;protein binding;vitamin D receptor binding