TRIM46
Basic information
Region (hg38): 1:155173787-155184971
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 29 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 29 | 1 | 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) | ||
1-155175590-C-A | not specified | Uncertain significance (Apr 17, 2024) | ||
1-155175622-C-A | not specified | Uncertain significance (Feb 05, 2024) | ||
1-155175903-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
1-155175930-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
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) | ||
1-155178045-G-A | not specified | Uncertain significance (Apr 12, 2024) | ||
1-155178125-C-T | not specified | Uncertain significance (Jan 26, 2023) | ||
1-155178134-G-A | not specified | Uncertain significance (Apr 05, 2023) | ||
1-155178499-C-G | not specified | Uncertain significance (Apr 12, 2024) | ||
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) | |||
1-155179749-G-A | not specified | Uncertain significance (May 21, 2024) | ||
1-155179763-G-A | not specified | Uncertain significance (Jun 12, 2023) |
GnomAD
Source:
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:
- 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
- Phenotype
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