TRIM13

tripartite motif containing 13, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 13:49995888-50020481

Previous symbols: [ "RFP2" ]

Links

ENSG00000204977 ∙ NCBI:10206 ∙ OMIM:605661 ∙ HGNC:9976 ∙ Uniprot:O60858 ∙ 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 TRIM13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM13 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			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11			11
Total	0	0	21	2	0

Variants in TRIM13

This is a list of pathogenic ClinVar variants found in the TRIM13 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-50012085-C-G		not specified	Uncertain significance (Jan 29, 2024)
13-50012194-T-C		not specified	Uncertain significance (Jan 23, 2023)
13-50012244-C-T		not specified	Uncertain significance (Mar 02, 2023)
13-50012269-T-C		not specified	Uncertain significance (Jun 09, 2022)
13-50012273-G-T		not specified	Uncertain significance (Jun 17, 2024)
13-50012289-T-G		not specified	Uncertain significance (Dec 21, 2023)
13-50012419-G-A		not specified	Uncertain significance (Dec 22, 2023)
13-50012478-G-C		not specified	Uncertain significance (Aug 08, 2023)
13-50012501-G-T		not specified	Uncertain significance (May 04, 2023)
13-50012581-C-T		not specified	Uncertain significance (May 18, 2022)
13-50012760-G-A		not specified	Likely benign (Nov 21, 2022)
13-50012824-A-G		not specified	Uncertain significance (Jan 08, 2024)
13-50012858-C-G		not specified	Uncertain significance (Mar 25, 2024)
13-50012950-A-G		not specified	Uncertain significance (Jun 07, 2024)
13-50013004-G-C		not specified	Likely benign (Dec 21, 2022)
13-50015518-T-G		not specified	Uncertain significance (Jan 03, 2024)
13-50015537-T-C		not specified	Uncertain significance (Aug 17, 2022)
13-50015581-C-T		not specified	Uncertain significance (Feb 27, 2024)
13-50015606-G-A		not specified	Uncertain significance (Nov 02, 2021)
13-50015624-T-C		not specified	Uncertain significance (Sep 28, 2022)
13-50015701-C-G		not specified	Uncertain significance (Jul 14, 2022)
13-50015726-A-G		not specified	Uncertain significance (Jun 29, 2022)
13-50015767-C-T		not specified	Uncertain significance (Nov 02, 2023)
13-50015822-T-G		not specified	Uncertain significance (Mar 18, 2024)
13-50015843-G-A		not specified	Uncertain significance (May 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM13	protein_coding	protein_coding	ENST00000356017	2	24594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.637	0.362	125702	0	31	125733	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.939	176	215	0.820	0.0000106	2735
Missense in Polyphen		46	86.424	0.53226		1150
Synonymous	-1.29	92	77.6	1.19	0.00000351	764
Loss of Function	2.66	2	11.9	0.168	4.99e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000348	0.000348
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000986	0.0000967
Middle Eastern	0.000218	0.000217
South Asian	0.000105	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endoplasmic reticulum (ER) membrane anchored E3 ligase involved in the retrotranslocation and turnover of membrane and secretory proteins from the ER through a set of processes named ER-associated degradation (ERAD). This process acts on misfolded proteins as well as in the regulated degradation of correctly folded proteins. Enhances ionizing radiation-induced p53/TP53 stability and apoptosis via ubiquitinating MDM2 and AKT1 and decreasing AKT1 kinase activity through MDM2 and AKT1 proteasomal degradation. Regulates ER stress-induced autophagy, and may act as a tumor suppressor (PubMed:22178386). Plays also a role in innate immune response by stimulating NF-kappa-B activity in the TLR2 signaling pathway. Ubiquitinates TRAF6 via the 'Lys-29'-linked polyubiquitination chain resulting in NF-kappa-B activation (PubMed:28087809). Participates as well in T-cell receptor- mediated NF-kappa-B activation (PubMed:25088585). In the presence of TNF, modulates the IKK complex by regulating IKBKG/NEMO ubiquitination leading to the repression of NF-kappa-B (PubMed:25152375). {ECO:0000269|PubMed:17314412, ECO:0000269|PubMed:21333377, ECO:0000269|PubMed:22178386, ECO:0000269|PubMed:25088585, ECO:0000269|PubMed:25152375, ECO:0000269|PubMed:28087809}.
• Pathway: ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.628
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.444
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.318

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim13

Gene ontology

• Biological process: anatomical structure morphogenesis;response to gamma radiation;positive regulation of cell death;positive regulation of macroautophagy;ubiquitin-dependent ERAD pathway;negative regulation of viral transcription;positive regulation of I-kappaB kinase/NF-kappaB signaling;proteasome-mediated ubiquitin-dependent protein catabolic process;innate immune response;positive regulation of NF-kappaB transcription factor activity;protein autoubiquitination;negative regulation of viral release from host cell;endoplasmic reticulum mannose trimming
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;endoplasmic reticulum quality control compartment;perinuclear endoplasmic reticulum
• Molecular function: ubiquitin-protein transferase activity;protein binding;zinc ion binding;ubiquitin protein ligase activity