TRIM52
Basic information
Region (hg38): 5:181254077-181261150
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 TRIM52 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 | 14 | 16 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 14 | 2 | 0 |
Variants in TRIM52
This is a list of pathogenic ClinVar variants found in the TRIM52 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
5-181257472-A-G | not specified | Likely benign (Jul 11, 2023) | ||
5-181257488-T-C | not specified | Uncertain significance (Jun 10, 2024) | ||
5-181260006-A-G | not specified | Uncertain significance (May 03, 2023) | ||
5-181260011-T-C | not specified | Uncertain significance (Jan 03, 2022) | ||
5-181260021-C-T | not specified | Uncertain significance (Jun 16, 2024) | ||
5-181260176-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
5-181260254-C-T | not specified | Uncertain significance (May 26, 2022) | ||
5-181260259-C-A | not specified | Uncertain significance (Dec 12, 2023) | ||
5-181260334-G-T | not specified | Uncertain significance (Jun 02, 2023) | ||
5-181260347-G-T | not specified | Likely benign (Dec 27, 2022) | ||
5-181260349-T-A | not specified | Uncertain significance (Aug 10, 2021) | ||
5-181260398-A-C | not specified | Uncertain significance (Nov 21, 2022) | ||
5-181260407-A-G | not specified | Uncertain significance (Mar 15, 2024) | ||
5-181260476-T-C | not specified | Uncertain significance (Aug 28, 2023) | ||
5-181260516-C-T | not specified | Uncertain significance (Apr 20, 2024) | ||
5-181260526-G-C | not specified | Uncertain significance (Feb 28, 2024) | ||
5-181260560-A-G | not specified | Uncertain significance (Apr 09, 2024) | ||
5-181260578-T-A | not specified | Uncertain significance (Jan 26, 2022) | ||
5-181260602-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
5-181260670-C-A | not specified | Uncertain significance (May 16, 2024) | ||
5-181260737-T-G | not specified | Uncertain significance (Apr 07, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TRIM52 | protein_coding | protein_coding | ENST00000327767 | 2 | 6703 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.14e-9 | 0.0522 | 125643 | 1 | 104 | 125748 | 0.000418 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.113 | 151 | 155 | 0.975 | 0.00000721 | 1998 |
Missense in Polyphen | 36 | 34.058 | 1.057 | 426 | ||
Synonymous | 0.250 | 55 | 57.4 | 0.958 | 0.00000274 | 518 |
Loss of Function | -0.349 | 13 | 11.7 | 1.11 | 5.55e-7 | 131 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00123 | 0.00123 |
Ashkenazi Jewish | 0.000201 | 0.000198 |
East Asian | 0.00201 | 0.00201 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000238 | 0.000229 |
Middle Eastern | 0.00201 | 0.00201 |
South Asian | 0.000131 | 0.000131 |
Other | 0.000978 | 0.000978 |
dbNSFP
Source:
Intolerance Scores
- loftool
- 0.736
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.09
Haploinsufficiency Scores
- pHI
- 0.0744
- hipred
- N
- hipred_score
- 0.180
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Gene ontology
- Biological process
- positive regulation of NF-kappaB transcription factor activity
- Cellular component
- nuclear body
- Molecular function
- zinc ion binding