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

ENSG00000122779 ∙ NCBI:8805 ∙ OMIM:603406 ∙ HGNC:11812 ∙ Uniprot:O15164 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM24 gene.

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.

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				1		1
missense		1	35		5	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	35	1	5

Variants in TRIM24

This is a list of pathogenic ClinVar variants found in the TRIM24 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-138460592-C-T		not specified	Uncertain significance (Aug 10, 2021)
7-138460603-G-C		not specified	Uncertain significance (Aug 10, 2021)
7-138460624-G-A		Ovarian cancer	Benign (Jan 01, 2022)
7-138460681-G-A		not specified	Uncertain significance (Apr 07, 2023)
7-138460741-A-T		not specified	Uncertain significance (Dec 06, 2021)
7-138460805-A-T		not specified	Uncertain significance (Nov 17, 2022)
7-138460807-C-T		Ovarian cancer	Benign (Jan 01, 2022)
7-138460838-G-C		not specified	Uncertain significance (Nov 07, 2022)
7-138460844-C-G		not specified	Uncertain significance (Apr 07, 2023)
7-138460889-G-T		not specified	Uncertain significance (Aug 02, 2021)
7-138460900-T-G		not specified	Uncertain significance (Oct 05, 2023)
7-138504301-C-T		not specified	Uncertain significance (Jun 07, 2023)
7-138504404-A-C		not specified	Uncertain significance (Jan 26, 2022)
7-138519305-G-A		not specified	Uncertain significance (Feb 09, 2023)
7-138525261-C-T		not specified	Uncertain significance (Apr 01, 2024)
7-138525263-T-C			Uncertain significance (Jan 01, 2024)
7-138538738-A-G		not specified	Uncertain significance (Jul 09, 2021)
7-138551078-C-T		not specified	Uncertain significance (Mar 28, 2023)
7-138551109-C-T		not specified	Uncertain significance (Jun 06, 2023)
7-138551121-A-G		not specified	Uncertain significance (Oct 10, 2023)
7-138551127-C-T		not specified	Uncertain significance (Nov 23, 2022)
7-138551173-C-T		TRIM24-related disorder	Likely benign (Aug 25, 2023)
7-138554757-G-A		not specified	Uncertain significance (Dec 18, 2023)
7-138554812-T-A		not specified	Uncertain significance (Dec 08, 2021)
7-138567494-G-A		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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