TRIM38

tripartite motif containing 38, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 6:25962801-25991231

Previous symbols: [ "RNF15" ]

Links

ENSG00000112343 ∙ NCBI:10475 ∙ ∙ HGNC:10059 ∙ Uniprot:O00635 ∙ 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 TRIM38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM38 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in TRIM38

This is a list of pathogenic ClinVar variants found in the TRIM38 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25966593-C-T		not specified	Uncertain significance (Aug 02, 2023)
6-25966633-C-G		not specified	Uncertain significance (Mar 21, 2023)
6-25966724-A-G		not specified	Uncertain significance (Sep 15, 2021)
6-25966838-G-A		not specified	Uncertain significance (Feb 22, 2023)
6-25966899-C-T		not specified	Uncertain significance (Dec 17, 2021)
6-25969374-G-C		not specified	Uncertain significance (Feb 17, 2024)
6-25969374-G-T		not specified	Uncertain significance (Oct 18, 2021)
6-25971899-C-T		not specified	Uncertain significance (Nov 01, 2022)
6-25971953-C-A		not specified	Uncertain significance (Nov 29, 2023)
6-25971963-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-25972033-T-A		not specified	Uncertain significance (Aug 21, 2023)
6-25972068-A-G		not specified	Uncertain significance (Jun 03, 2022)
6-25973175-G-A		not specified	Uncertain significance (Nov 30, 2021)
6-25983186-T-A		not specified	Uncertain significance (Sep 28, 2022)
6-25983199-G-A		not specified	Uncertain significance (Jul 13, 2022)
6-25983235-C-T		not specified	Uncertain significance (Dec 21, 2023)
6-25983344-A-G		not specified	Uncertain significance (Jun 26, 2023)
6-25983356-G-T		not specified	Uncertain significance (Dec 13, 2022)
6-25983376-G-A		not specified	Uncertain significance (Jun 17, 2022)
6-25983485-C-T		not specified	Uncertain significance (Dec 18, 2023)
6-25983539-A-G		not specified	Uncertain significance (Dec 19, 2023)
6-25983605-A-G		not specified	Uncertain significance (Jan 04, 2024)
6-25983629-G-A		not specified	Uncertain significance (Nov 30, 2021)
6-25983676-C-G		not specified	Uncertain significance (Mar 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM38	protein_coding	protein_coding	ENST00000357085	6	24355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.39e-8	0.597	125662	2	84	125748	0.000342

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.593	227	254	0.895	0.0000133	3063
Missense in Polyphen		56	66.467	0.84252		879
Synonymous	1.47	79	97.5	0.811	0.00000524	875
Loss of Function	1.16	15	20.7	0.724	9.60e-7	250

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00114	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00114	0.00114
South Asian	0.00138	0.00131
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase. Mediates 'Lys-48'-linked polyubiquitination and proteasomal degradation of the critical TLR adapter TICAM1, inhibiting TLR3-mediated type I interferon signaling. {ECO:0000269|PubMed:23056470}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0902

Intolerance Scores

• loftool: 0.922
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.0897
• hipred: N
• hipred_score: 0.148
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim38
• 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of interferon-beta production;positive regulation of I-kappaB kinase/NF-kappaB signaling;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of viral genome replication;positive regulation of viral entry into host cell;negative regulation of defense response to virus;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity;interferon-gamma-mediated signaling pathway;protein K48-linked ubiquitination
• Cellular component: cellular_component;cytosol
• Molecular function: protein binding;zinc ion binding;transferase activity