TRIM50

tripartite motif containing 50, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 7:73312535-73328082

Previous symbols: [ "TRIM50A" ]

Links

ENSG00000146755 ∙ NCBI:135892 ∙ OMIM:612548 ∙ HGNC:19017 ∙ Uniprot:Q86XT4 ∙ 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 TRIM50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM50 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				2	1	3
missense			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	3	1

Variants in TRIM50

This is a list of pathogenic ClinVar variants found in the TRIM50 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-73312941-C-T		not specified	Uncertain significance (Jun 12, 2023)
7-73312962-C-G		not specified	Uncertain significance (Aug 26, 2022)
7-73312966-G-T			Likely benign (Mar 01, 2023)
7-73312980-C-T		not specified	Uncertain significance (Nov 01, 2021)
7-73313007-C-G		not specified	Uncertain significance (Mar 12, 2024)
7-73313033-T-G		not specified	Uncertain significance (May 18, 2023)
7-73313147-C-T		not specified	Uncertain significance (Jan 23, 2023)
7-73313148-G-A		not specified	Uncertain significance (Sep 01, 2021)
7-73313161-G-A			Likely benign (Mar 01, 2023)
7-73313181-G-C		not specified	Uncertain significance (Jun 28, 2023)
7-73313208-G-A		not specified	Uncertain significance (Apr 08, 2023)
7-73313214-C-T		not specified	Uncertain significance (Jun 27, 2022)
7-73313223-C-T		not specified	Uncertain significance (Apr 29, 2024)
7-73313235-C-A		not specified	Uncertain significance (Dec 28, 2022)
7-73313249-G-A		not specified	Uncertain significance (Dec 26, 2023)
7-73313260-C-G		not specified	Uncertain significance (Jun 06, 2022)
7-73313300-C-T		not specified	Uncertain significance (Apr 29, 2024)
7-73313301-G-A		not specified	Uncertain significance (Dec 06, 2022)
7-73313343-G-A		not specified	Uncertain significance (Feb 28, 2024)
7-73313361-G-A		not specified	Uncertain significance (Sep 26, 2022)
7-73313394-G-A		not specified	Uncertain significance (May 30, 2024)
7-73313430-C-G		not specified	Uncertain significance (Jul 30, 2023)
7-73313438-A-C		not specified	Uncertain significance (Mar 28, 2022)
7-73313495-T-C		not specified	Uncertain significance (Jan 12, 2024)
7-73313496-T-C		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM50	protein_coding	protein_coding	ENST00000333149	6	15551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-10	0.206	124943	7	798	125748	0.00321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.127	299	305	0.980	0.0000204	3122
Missense in Polyphen		101	112.04	0.90145		1245
Synonymous	-1.51	156	134	1.17	0.00000901	995
Loss of Function	0.685	17	20.3	0.836	0.00000115	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00255	0.00251
Ashkenazi Jewish	0.0136	0.0130
East Asian	0.000558	0.000544
Finnish	0.0000518	0.0000462
European (Non-Finnish)	0.00262	0.00241
Middle Eastern	0.000558	0.000544
South Asian	0.0103	0.00988
Other	0.00262	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that ubiquitinates Beclin- 1/BECN1 in a 'Lys-63'-dependent manner enhancing its binding to ULK1. In turn, promotes starvation-induced autophagy activation. Interacts also with p62/SQSTM1 protein and thereby induces the formation and the autophagy clearance of aggresome-associated polyubiquitinated proteins through HDAC6 interaction. {ECO:0000269|PubMed:18398435, ECO:0000269|PubMed:22792322, ECO:0000269|PubMed:29604308}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Intolerance Scores

• loftool: 0.483
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.112
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.383

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim50
• Phenotype: digestive/alimentary phenotype

Gene ontology

• Biological process: regulation of establishment of protein localization
• Cellular component: cytosol;aggresome
• Molecular function: zinc ion binding;transferase activity;identical protein binding