TRIM25

tripartite motif containing 25, the group of Tripartite motif family|MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 17:56836386-56914080

Previous symbols: [ "ZNF147" ]

Links

ENSG00000121060 ∙ NCBI:7706 ∙ OMIM:600453 ∙ HGNC:12932 ∙ Uniprot:Q14258 ∙ 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 TRIM25 gene.

• not provided (92 variants)
• Inborn genetic diseases (33 variants)
• Immunoglobulin-mediated membranoproliferative glomerulonephritis (21 variants)
• Atypical hemolytic-uremic syndrome (5 variants)
• not specified (4 variants)
• Kidney disorder (2 variants)
• DGKE-related condition (2 variants)
• Hemolytic uremic syndrome, atypical, susceptibility to, 7 (1 variants)
• Nephrotic syndrome (1 variants)
• Hemolytic uremic syndrome, atypical, susceptibility to, 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM25 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	2	3
missense			16	2	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding	7	6	35	36	23	107
Total	7	6	51	39	26

Highest pathogenic variant AF is 0.000151

Variants in TRIM25

This is a list of pathogenic ClinVar variants found in the TRIM25 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-56843797-C-CA			Benign (May 12, 2021)
17-56843797-C-CAAAAA			Benign (Aug 20, 2019)
17-56843797-C-CAAAAAA			Benign (Dec 29, 2019)
17-56843961-G-A			Benign (Nov 11, 2018)
17-56844007-TC-T			Likely benign (Aug 19, 2022)
17-56844014-C-T			Likely benign (Sep 23, 2022)
17-56844016-C-T			Likely benign (Jan 28, 2024)
17-56844017-A-G		Immunoglobulin-mediated membranoproliferative glomerulonephritis	Likely pathogenic (Apr 04, 2024)
17-56844023-A-AT		Atypical hemolytic-uremic syndrome	Likely pathogenic (-)
17-56844034-G-A			Likely benign (Oct 29, 2023)
17-56844039-C-CA		Hemolytic uremic syndrome, atypical, susceptibility to, 7 • Atypical hemolytic-uremic syndrome	Likely pathogenic; risk factor (May 01, 2013)
17-56844058-G-A			Uncertain significance (Sep 06, 2022)
17-56844073-G-A			Likely benign (Dec 04, 2023)
17-56844085-T-G		Immunoglobulin-mediated membranoproliferative glomerulonephritis	Uncertain significance (-)
17-56844114-T-A			Uncertain significance (Apr 23, 2022)
17-56844115-TCCACCAAGTTATTTAACATCCA-T			Pathogenic (Apr 23, 2022)
17-56844116-C-A		Inborn genetic diseases	Uncertain significance (Apr 27, 2022)
17-56844122-A-G			Uncertain significance (Jun 16, 2017)
17-56844133-A-C		not specified • Immunoglobulin-mediated membranoproliferative glomerulonephritis	Benign (Jan 31, 2024)
17-56844133-A-T			Likely benign (Jul 20, 2022)
17-56844155-G-C		Inborn genetic diseases	Uncertain significance (Sep 06, 2022)
17-56844157-CA-C		Immunoglobulin-mediated membranoproliferative glomerulonephritis • Nephrotic syndrome	Pathogenic (Feb 26, 2022)
17-56844157-C-CA		Immunoglobulin-mediated membranoproliferative glomerulonephritis • Atypical hemolytic-uremic syndrome	Pathogenic (Feb 08, 2023)
17-56844182-A-T			Uncertain significance (Feb 04, 2022)
17-56844193-T-C			Likely benign (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM25	protein_coding	protein_coding	ENST00000316881	9	26130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00412	0.996	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.859	303	348	0.870	0.0000189	4099
Missense in Polyphen		84	111.81	0.75126		1428
Synonymous	0.603	144	154	0.938	0.00000901	1224
Loss of Function	3.16	9	26.6	0.339	0.00000122	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000623	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000777	0.0000653
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a ubiquitin E3 ligase and as an ISG15 E3 ligase. Involved in innate immune defense against viruses by mediating ubiquitination of DDX58. Mediates 'Lys-63'-linked polyubiquitination of the DDX58 N-terminal CARD-like region which is crucial for triggering the cytosolic signal transduction that leads to the production of interferons in response to viral infection. Promotes ISGylation of 14-3-3 sigma (SFN), an adapter protein implicated in the regulation of a large spectrum signaling pathway. Mediates estrogen action in various target organs. Mediates the ubiquitination and subsequent proteasomal degradation of ZFHX3 (PubMed:22452784). {ECO:0000269|PubMed:16352599, ECO:0000269|PubMed:17069755, ECO:0000269|PubMed:17392790, ECO:0000269|PubMed:22452784}.
• Pathway: Influenza A - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);RIG-I-like receptor signaling pathway - Homo sapiens (human);RIG-I-like Receptor Signaling;DNA Repair;estrogen responsive protein efp controls cell cycle and breast tumors growth;Cytokine Signaling in Immune system;NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10;Post-translational protein modification;TRAF6 mediated IRF7 activation;TRAF6 mediated NF-kB activation;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Metabolism of proteins;TCR;Innate Immune System;Immune System;TRAF3-dependent IRF activation pathway;Negative regulators of DDX58/IFIH1 signaling;Ovarian tumor domain proteases;Deubiquitination;Interferon gamma signaling;Termination of translesion DNA synthesis;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.170

Intolerance Scores

• loftool: 0.520
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.0876
• hipred: Y
• hipred_score: 0.686
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Trim25
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein monoubiquitination;viral process;translesion synthesis;ubiquitin-dependent ERAD pathway;negative regulation of type I interferon production;response to vitamin D;positive regulation of I-kappaB kinase/NF-kappaB signaling;response to estrogen;innate immune response;regulation of viral entry into host cell;negative regulation of viral entry into host cell;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity;defense response to virus;interferon-gamma-mediated signaling pathway;regulation of viral release from host cell;negative regulation of viral release from host cell;cellular response to leukemia inhibitory factor
• Cellular component: nucleoplasm;cytosol;nuclear body
• Molecular function: RNA binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;ligase activity;cadherin binding;ubiquitin protein ligase activity