TRIM23

tripartite motif containing 23, the group of ARF GTPase family|Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 5:65589690-65625975

Previous symbols: [ "ARFD1" ]

Links

ENSG00000113595 ∙ NCBI:373 ∙ OMIM:601747 ∙ HGNC:660 ∙ Uniprot:P36406 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRIM23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM23 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					1	1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	1

Variants in TRIM23

This is a list of pathogenic ClinVar variants found in the TRIM23 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-65591806-C-T		not specified	Uncertain significance (Sep 14, 2023)
5-65591878-C-T		not specified	Uncertain significance (Feb 27, 2023)
5-65591906-G-A		not specified	Uncertain significance (Feb 27, 2024)
5-65594570-G-A		not specified	Uncertain significance (Apr 01, 2024)
5-65609274-G-A		not specified	Uncertain significance (Sep 26, 2023)
5-65609344-G-A		not specified	Uncertain significance (Jul 26, 2022)
5-65609429-T-C		TRIM23-related disorder	Benign (Apr 29, 2020)
5-65610880-C-T		not specified	Uncertain significance (Jan 25, 2023)
5-65610896-C-T		not specified	Uncertain significance (Nov 05, 2021)
5-65610934-A-G		not specified	Uncertain significance (May 05, 2023)
5-65610977-G-A		not specified	Uncertain significance (Jun 09, 2022)
5-65610980-T-C		not specified	Uncertain significance (Oct 10, 2023)
5-65611001-T-C		not specified	Uncertain significance (Feb 22, 2024)
5-65611625-T-C		not specified	Uncertain significance (Jul 16, 2024)
5-65611701-C-T		not specified	Uncertain significance (Feb 02, 2022)
5-65611787-G-A		TRIM23-related disorder	Uncertain significance (Aug 27, 2024)
5-65611875-T-A		not specified	Uncertain significance (Sep 06, 2022)
5-65614136-A-G		not specified	Uncertain significance (Nov 19, 2022)
5-65614144-A-G		not specified	Uncertain significance (Sep 12, 2023)
5-65614192-T-G		not specified	Uncertain significance (Jun 07, 2024)
5-65618146-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-65618176-G-C		not specified	Uncertain significance (Nov 25, 2024)
5-65618197-C-T		not specified	Uncertain significance (May 03, 2024)
5-65618209-T-C		not specified	Uncertain significance (Jan 24, 2023)
5-65624213-C-T		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM23	protein_coding	protein_coding	ENST00000231524	11	36296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000394	1.00	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	191	316	0.605	0.0000166	3736
Missense in Polyphen		45	113.29	0.39721		1375
Synonymous	0.724	99	109	0.912	0.00000528	1109
Loss of Function	3.44	12	33.5	0.358	0.00000203	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000234	0.000234
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an E3 ubiquitin-protein ligase. Plays an essential role in autophagy activation during viral infection. Mechanistically, activates TANK-binding kinase 1/TBK1 by facilitating its dimerization and ability to phosphorylate the selective autophagy receptor SQSTM1. In order to achieve this function, TRIM23 mediates 'Lys-27'-linked auto-ubiquitination of its ADP-ribosylation factor (ARF) domain to induce its GTPase activity and its recruitment to autophagosomes (PubMed:28871090). {ECO:0000269|PubMed:15684077, ECO:0000269|PubMed:28871090}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.518
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.661
• hipred: Y
• hipred_score: 0.793
• ghis: 0.663

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim23

Gene ontology

• Biological process: intracellular protein transport;Golgi to plasma membrane transport;viral process;vesicle-mediated transport;protein ubiquitination;positive regulation of catalytic activity;innate immune response
• Cellular component: Golgi membrane;nucleus;cytoplasm;lysosomal membrane;Golgi apparatus;plasma membrane
• Molecular function: nucleic acid binding;GTPase activity;ubiquitin-protein transferase activity;protein binding;GTP binding;enzyme activator activity;zinc ion binding;GDP binding;identical protein binding