TRIM24
tripartite motif containing 24, the group of Tripartite motif family|Ring finger proteins|Bromodomain containing|PHD finger proteins
Basic information
Region (hg38): 7:138460259-138589996
Previous symbols: [ "TIF1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (73 variants)
- Ovarian_cancer (5 variants)
- not_provided (2 variants)
- TRIM24-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM24 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015905.3. 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 | 1 | |||||
| missense | 74 | 80 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 74 | 1 | 5 |
Highest pathogenic variant AF is 0.00000867551
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRIM24 | protein_coding | protein_coding | ENST00000343526 | 19 | 129660 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 6.49e-8 | 125697 | 0 | 6 | 125703 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.43 | 321 | 547 | 0.587 | 0.0000271 | 6880 |
| Missense in Polyphen | 51 | 163.59 | 0.31175 | 2018 | ||
| Synonymous | 1.62 | 164 | 193 | 0.852 | 0.00000942 | 1966 |
| Loss of Function | 6.60 | 2 | 54.6 | 0.0366 | 0.00000291 | 635 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000447 | 0.0000440 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coactivator that interacts with numerous nuclear receptors and coactivators and modulates the transcription of target genes. Interacts with chromatin depending on histone H3 modifications, having the highest affinity for histone H3 that is both unmodified at 'Lys-4' (H3K4me0) and acetylated at 'Lys-23' (H3K23ac). Has E3 protein-ubiquitin ligase activity. Promotes ubiquitination and proteasomal degradation of p53/TP53. Plays a role in the regulation of cell proliferation and apoptosis, at least in part via its effects on p53/TP53 levels. Up-regulates ligand-dependent transcription activation by AR, GCR/NR3C1, thyroid hormone receptor (TR) and ESR1. Modulates transcription activation by retinoic acid (RA) receptors, including RARA. Plays a role in regulating retinoic acid-dependent proliferation of hepatocytes (By similarity). {ECO:0000250, ECO:0000269|PubMed:16322096, ECO:0000269|PubMed:19556538, ECO:0000269|PubMed:21164480}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving TRIM24/TIF1 is found in papillary thyroid carcinomas (PTCs). Translocation t(7;10)(q32;q11) with RET. The translocation generates the TRIM24/RET (PTC6) oncogene. {ECO:0000269|PubMed:10439047}.;
- Pathway
- Neutrophil degranulation;Disease;HSF1 activation;west nile virus;Translation;Cellular responses to stress;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Cellular responses to external stimuli;EGFR1;Cellular response to heat stress;Signaling by FGFR in disease;Protein methylation;Peptide chain elongation;Eukaryotic Translation Elongation;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction;Regulation of Androgen receptor activity
(Consensus)
Recessive Scores
- pRec
- 0.285
Intolerance Scores
- loftool
- 0.240
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.69
Haploinsufficiency Scores
- pHI
- 0.903
- hipred
- Y
- hipred_score
- 0.715
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trim24
- Phenotype
- liver/biliary system phenotype; neoplasm; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- transcription by RNA polymerase II;negative regulation of cell population proliferation;protein ubiquitination;peptidyl-tyrosine phosphorylation;protein catabolic process;regulation of protein stability;regulation of apoptotic process;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;protein autophosphorylation;calcium ion homeostasis;regulation of vitamin D receptor signaling pathway;cellular response to estrogen stimulus;regulation of signal transduction by p53 class mediator
- Cellular component
- nucleus;nucleoplasm;nuclear euchromatin;perichromatin fibrils;cytosol
- Molecular function
- p53 binding;chromatin binding;transcription coactivator activity;protein tyrosine kinase activity;ubiquitin-protein transferase activity;signaling receptor binding;protein binding;zinc ion binding;nuclear receptor binding;estrogen response element binding;methylated histone binding;ubiquitin protein ligase activity;lysine-acetylated histone binding