TRIM40

tripartite motif containing 40, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 6:30136124-30148735

Links

ENSG00000204614 ∙ NCBI:135644 ∙ OMIM:616976 ∙ HGNC:18736 ∙ Uniprot:Q6P9F5 ∙ 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 TRIM40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM40 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	3		13
nonsense						0
start loss				1		1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	10	4	1

Variants in TRIM40

This is a list of pathogenic ClinVar variants found in the TRIM40 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30137039-G-A			Likely benign (Dec 13, 2017)
6-30137068-A-C		not specified	Uncertain significance (Sep 20, 2023)
6-30137073-G-A		not specified	Likely benign (Feb 21, 2024)
6-30137140-G-A		not specified	Uncertain significance (Nov 17, 2023)
6-30137226-G-C		not specified	Uncertain significance (Oct 12, 2021)
6-30137283-G-A		not specified	Uncertain significance (Jun 10, 2022)
6-30137310-G-A		not specified	Uncertain significance (Feb 27, 2024)
6-30137326-C-T		not specified	Uncertain significance (Jul 07, 2022)
6-30146007-G-A		not specified	Uncertain significance (Mar 20, 2024)
6-30146009-C-T		not specified	Uncertain significance (May 23, 2024)
6-30146046-A-G		not specified	Uncertain significance (Jan 03, 2022)
6-30146070-A-C		not specified	Uncertain significance (Dec 09, 2023)
6-30147082-G-A		not specified	Likely benign (Apr 07, 2022)
6-30147160-T-A		not specified	Uncertain significance (Mar 18, 2024)
6-30147183-A-G		not specified	Uncertain significance (Oct 29, 2021)
6-30147199-A-G		not specified	Likely benign (Nov 09, 2022)
6-30147543-G-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM40	protein_coding	protein_coding	ENST00000307859	5	12628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.17e-11	0.0183	123348	31	2369	125748	0.00959

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.147	117	122	0.963	0.00000613	1487
Missense in Polyphen		32	29.308	1.0919		358
Synonymous	0.315	46	48.8	0.943	0.00000247	443
Loss of Function	-0.799	14	11.1	1.26	6.12e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0289	0.0286
Ashkenazi Jewish	0.0465	0.0459
East Asian	0.00292	0.00289
Finnish	0.000878	0.000832
European (Non-Finnish)	0.00835	0.00821
Middle Eastern	0.00292	0.00289
South Asian	0.00243	0.00239
Other	0.0144	0.0141

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway. Promotes neddylation of IKBKG/NEMO, stabilizing NFKBIA, and inhibiting of NF-kappaB nuclear translocation and activity. {ECO:0000269|PubMed:21474709}.

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.06

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim40

Gene ontology

• Biological process: negative regulation of cell growth;negative regulation of NF-kappaB transcription factor activity;negative regulation of protein catabolic process;protein neddylation;negative regulation of protein localization to nucleus;negative regulation of NIK/NF-kappaB signaling
• Cellular component: IkappaB kinase complex
• Molecular function: protein binding;zinc ion binding