TOB1
transducer of ERBB2, 1, the group of BTG/Tob family
Basic information
Region (hg38): 17:50862223-50867978
Previous symbols: [ "TROB1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 TOB1 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 | 0 | |||||
| missense | 18 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 18 | 0 | 0 |
Variants in TOB1
This is a list of pathogenic ClinVar variants found in the TOB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-50863056-A-G | not specified | Uncertain significance (Mar 11, 2024) | ||
| 17-50863068-T-C | not specified | Uncertain significance (Mar 23, 2023) | ||
| 17-50863117-G-A | not specified | Uncertain significance (May 03, 2023) | ||
| 17-50863137-C-A | not specified | Uncertain significance (Mar 07, 2024) | ||
| 17-50863146-G-A | not specified | Uncertain significance (Mar 22, 2023) | ||
| 17-50863189-G-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-50863203-T-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 17-50863232-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 17-50863342-T-C | not specified | Uncertain significance (Jun 24, 2022) | ||
| 17-50863350-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 17-50863399-T-C | not specified | Uncertain significance (Jul 13, 2021) | ||
| 17-50863414-C-T | not specified | Uncertain significance (May 08, 2024) | ||
| 17-50863450-T-A | not specified | Uncertain significance (May 18, 2023) | ||
| 17-50863557-G-A | not specified | Uncertain significance (Jan 07, 2022) | ||
| 17-50863594-T-C | not specified | Uncertain significance (Apr 11, 2023) | ||
| 17-50863649-C-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 17-50863669-T-C | not specified | Uncertain significance (Feb 12, 2024) | ||
| 17-50863894-C-G | not specified | Uncertain significance (Feb 17, 2024) | ||
| 17-50863941-T-C | not specified | Uncertain significance (Apr 18, 2023) | ||
| 17-50864001-T-C | not specified | Uncertain significance (Jun 24, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TOB1 | protein_coding | protein_coding | ENST00000499247 | 1 | 5756 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.954 | 0.0462 | 125745 | 0 | 2 | 125747 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.45 | 134 | 190 | 0.704 | 0.00000963 | 2307 |
| Missense in Polyphen | 39 | 72.275 | 0.5396 | 845 | ||
| Synonymous | -0.669 | 78 | 70.8 | 1.10 | 0.00000374 | 660 |
| Loss of Function | 2.88 | 0 | 9.64 | 0.00 | 4.09e-7 | 121 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| 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 | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Anti-proliferative protein; the function is mediated by association with deadenylase subunits of the CCR4-NOT complex (PubMed:8632892, PubMed:23236473). Mediates CPEB3-accelerated mRNA deadenylation by binding to CPEB3 and recruiting CNOT7 which leads to target mRNA deadenylation and decay (PubMed:21336257). {ECO:0000269|PubMed:21336257, ECO:0000269|PubMed:23236473, ECO:0000269|PubMed:8632892}.;
- Pathway
- RNA degradation - Homo sapiens (human);Bone Morphogenic Protein (BMP) Signalling and Regulation;Exercise-induced Circadian Regulation
(Consensus)
Recessive Scores
- pRec
- 0.221
Intolerance Scores
- loftool
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 34.32
Haploinsufficiency Scores
- pHI
- 0.787
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.843
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tob1
- Phenotype
- cellular phenotype; skeleton phenotype;
Zebrafish Information Network
- Gene name
- tob1a
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- kinked
Gene ontology
- Biological process
- negative regulation of cell population proliferation;positive regulation of signal transduction;regulation of gene expression;negative regulation of translation;negative regulation of BMP signaling pathway;negative regulation of osteoblast differentiation;negative regulation of nuclear-transcribed mRNA poly(A) tail shortening;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;regulation of SMAD protein signal transduction;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay;negative regulation of nucleic acid-templated transcription
- Cellular component
- nucleus;cytoplasm;CCR4-NOT complex
- Molecular function
- transcription corepressor activity;SH3/SH2 adaptor activity;protein binding;receptor tyrosine kinase binding;SMAD binding