TRIM39

tripartite motif containing 39, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 6:30326479-30343729

Previous symbols: [ "RNF23" ]

Links

ENSG00000204599 ∙ NCBI:56658 ∙ OMIM:605700 ∙ HGNC:10065 ∙ Uniprot:Q9HCM9 ∙ 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 TRIM39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM39 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			5	4		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	4	0

Variants in TRIM39

This is a list of pathogenic ClinVar variants found in the TRIM39 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30340273-A-C		not specified	Likely benign (Aug 10, 2023)
6-30340279-C-T		not specified	Likely benign (Dec 21, 2022)
6-30340318-C-T		not specified	Uncertain significance (Dec 09, 2023)
6-30340333-C-T		not specified	Likely benign (Dec 18, 2023)
6-30341823-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-30341942-G-A		not specified	Uncertain significance (Apr 11, 2023)
6-30342080-A-G		not specified	Likely benign (Jan 30, 2024)
6-30342132-G-A		not specified	Uncertain significance (Oct 06, 2022)
6-30342233-A-G		not specified	Uncertain significance (May 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM39	protein_coding	protein_coding	ENST00000376656	7	17251

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00526	123226	0	1	123227	0.00000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.79	124	313	0.397	0.0000193	3338
Missense in Polyphen		18	118.29	0.15217		1305
Synonymous	1.79	93	118	0.790	0.00000633	1058
Loss of Function	4.45	3	28.8	0.104	0.00000197	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000100	0.000100
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase. May facilitate apoptosis by inhibiting APC/C-Cdh1-mediated poly-ubiquitination and subsequent proteasome-mediated degradation of the pro-apoptotic protein MOAP1. {ECO:0000269|PubMed:19100260, ECO:0000269|PubMed:22529100}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Intolerance Scores

• loftool: 0.0920
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.576
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.166

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim39

Gene ontology

• Biological process: apoptotic process;protein ubiquitination;negative regulation of ubiquitin-dependent protein catabolic process;positive regulation of apoptotic signaling pathway
• Cellular component: mitochondrion;cytosol
• Molecular function: protein binding;zinc ion binding;transferase activity;identical protein binding