BTG2
BTG anti-proliferation factor 2, the group of BTG/Tob family
Basic information
Region (hg38): 1:203305491-203309602
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 BTG2 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in BTG2
This is a list of pathogenic ClinVar variants found in the BTG2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-203305628-G-A | not specified | Uncertain significance (Mar 18, 2024) | ||
| 1-203305700-G-C | not specified | Uncertain significance (Dec 28, 2022) | ||
| 1-203305734-A-C | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 1-203305738-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 1-203305751-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 1-203307227-A-G | not specified | Uncertain significance (Jul 13, 2022) | ||
| 1-203307361-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 1-203307382-G-A | Uncertain significance (Sep 16, 2020) | |||
| 1-203307394-C-G | not specified | Uncertain significance (Nov 09, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BTG2 | protein_coding | protein_coding | ENST00000290551 | 2 | 4112 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0190 | 0.750 | 125726 | 0 | 8 | 125734 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.718 | 71 | 90.2 | 0.787 | 0.00000467 | 1005 |
| Missense in Polyphen | 15 | 34.988 | 0.42872 | 373 | ||
| Synonymous | -0.896 | 46 | 38.9 | 1.18 | 0.00000218 | 311 |
| Loss of Function | 0.815 | 3 | 4.96 | 0.605 | 2.12e-7 | 55 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000440 | 0.0000440 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| 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. Activates mRNA deadenylation in a CNOT6 and CNOT7-dependent manner. In vitro can inhibit deadenylase activity of CNOT7 and CNOT8. Involved in cell cycle regulation. Could be involved in the growth arrest and differentiation of the neuronal precursors (By similarity). Modulates transcription regulation mediated by ESR1. Involved in mitochondrial depolarization and neurite outgrowth. {ECO:0000250, ECO:0000269|PubMed:12771185, ECO:0000269|PubMed:15788397, ECO:0000269|PubMed:18337750, ECO:0000269|PubMed:18773938, ECO:0000269|PubMed:23236473}.;
- Pathway
- RNA degradation - Homo sapiens (human);Spinal Cord Injury;TP53 Regulates Transcription of Cell Cycle Genes;Gene expression (Transcription);btg family proteins and cell cycle regulation;Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Direct p53 effectors
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.318
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.590
- hipred
- N
- hipred_score
- 0.495
- ghis
- 0.493
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Btg2
- Phenotype
- skeleton phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;DNA repair;protein methylation;cellular response to DNA damage stimulus;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;negative regulation of cell population proliferation;associative learning;response to mechanical stimulus;anterior/posterior pattern specification;response to organic cyclic compound;negative regulation of translation;dentate gyrus development;central nervous system neuron development;neuron projection development;skeletal muscle cell differentiation;response to peptide hormone;negative regulation of neuron apoptotic process;negative regulation of mitotic cell cycle;response to electrical stimulus;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;negative regulation of neural precursor cell proliferation
- Cellular component
- nucleus;cytoplasm;cytosol;extracellular exosome
- Molecular function
- DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding