TRIM46

tripartite motif containing 46, the group of Tripartite motif family|Ring finger proteins

Basic information

Region (hg38): 1:155173786-155184971

Links

ENSG00000163462 ∙ NCBI:80128 ∙ OMIM:600986 ∙ HGNC:19019 ∙ Uniprot:Q7Z4K8 ∙ 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 TRIM46 gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRIM46 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	1

Variants in TRIM46

This is a list of pathogenic ClinVar variants found in the TRIM46 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155173998-C-A		not specified	Uncertain significance (Aug 20, 2023)
1-155175400-C-A		not specified	Uncertain significance (Feb 01, 2023)
1-155175524-G-C		not specified	Uncertain significance (Jan 23, 2023)
1-155175576-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-155175582-G-A		not specified	Uncertain significance (Jun 22, 2023)
1-155175622-C-A		not specified	Uncertain significance (Feb 05, 2024)
1-155175903-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-155175986-C-T		not specified	Uncertain significance (Dec 07, 2023)
1-155176026-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-155177241-C-A		not specified	Uncertain significance (Jan 04, 2024)
1-155177241-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-155178015-A-C		not specified	Uncertain significance (Feb 10, 2023)
1-155178125-C-T		not specified	Uncertain significance (Jan 26, 2023)
1-155178134-G-A		not specified	Uncertain significance (Apr 05, 2023)
1-155178500-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-155178511-G-A		not specified	Uncertain significance (May 17, 2023)
1-155178526-C-T		not specified	Uncertain significance (Feb 06, 2024)
1-155179709-C-G		not specified	Uncertain significance (Aug 02, 2023)
1-155179729-C-T			Benign (Dec 31, 2019)
1-155179763-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-155179791-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-155181855-T-G		not specified	Uncertain significance (Jan 03, 2024)
1-155181869-G-A		not specified	Uncertain significance (Feb 27, 2024)
1-155181876-G-A		not specified	Uncertain significance (Mar 13, 2023)
1-155181884-G-A		not specified	Likely benign (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRIM46	protein_coding	protein_coding	ENST00000334634	10	11575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000750	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.25	296	500	0.592	0.0000330	4840
Missense in Polyphen		88	188.42	0.46705		1733
Synonymous	1.21	187	209	0.894	0.0000129	1650
Loss of Function	4.93	3	34.0	0.0882	0.00000205	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000186	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-associated protein that is involved in the formation of parallel microtubule bundles linked by cross-bridges in the proximal axon. Required for the uniform orientation and maintenance of the parallel microtubule fascicles, which are important for efficient cargo delivery and trafficking in axons. Thereby also required for proper axon specification, the establishment of neuronal polarity and proper neuronal migration. {ECO:0000250|UniProtKB:Q7TNM2}.
• Pathway: Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.0222
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.599
• hipred: Y
• hipred_score: 0.662
• ghis: 0.644

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.856

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trim46

Gene ontology

• Biological process: microtubule bundle formation;neuron migration;axonogenesis;negative regulation of axon extension;anterograde synaptic vesicle transport;protein localization to axon;positive regulation of anterograde dense core granule transport;regulation of cellular protein localization
• Cellular component: cytoskeleton;axon initial segment;main axon;axon cytoplasm;proximal neuron projection
• Molecular function: zinc ion binding