TRIM27
tripartite motif containing 27, the group of Tripartite motif family|Ring finger proteins
Basic information
Region (hg38): 6:28903002-28923988
Previous symbols: [ "RFP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 TRIM27 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 | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 20 | 0 | 0 |
Variants in TRIM27
This is a list of pathogenic ClinVar variants found in the TRIM27 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-28904087-T-C | not specified | Uncertain significance (Dec 31, 2023) | ||
| 6-28904117-A-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 6-28904127-T-C | not specified | Uncertain significance (Sep 14, 2022) | ||
| 6-28904138-T-A | not specified | Uncertain significance (Jun 17, 2024) | ||
| 6-28904410-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 6-28904425-C-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 6-28904443-T-A | not specified | Uncertain significance (Aug 13, 2021) | ||
| 6-28904477-C-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 6-28909024-T-C | not specified | Uncertain significance (Oct 04, 2024) | ||
| 6-28920058-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 6-28920059-C-T | not specified | Uncertain significance (Sep 25, 2024) | ||
| 6-28920112-T-C | not specified | Uncertain significance (Nov 13, 2024) | ||
| 6-28920241-C-T | not specified | Uncertain significance (Aug 05, 2024) | ||
| 6-28921920-T-C | not specified | Uncertain significance (Jan 22, 2025) | ||
| 6-28921927-G-A | not specified | Uncertain significance (Feb 07, 2025) | ||
| 6-28921935-T-C | not specified | Uncertain significance (Mar 20, 2023) | ||
| 6-28923275-G-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 6-28923329-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
| 6-28923386-T-A | not specified | Uncertain significance (Dec 13, 2021) | ||
| 6-28923479-A-G | not specified | Uncertain significance (Apr 22, 2022) | ||
| 6-28923571-T-C | not specified | Uncertain significance (May 24, 2023) | ||
| 6-28923598-T-C | not specified | Uncertain significance (Oct 10, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TRIM27 | protein_coding | protein_coding | ENST00000377199 | 8 | 20988 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00315 | 124823 | 0 | 3 | 124826 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.70 | 116 | 295 | 0.393 | 0.0000154 | 3362 |
| Missense in Polyphen | 17 | 75.329 | 0.22568 | 799 | ||
| Synonymous | -0.173 | 122 | 120 | 1.02 | 0.00000614 | 984 |
| Loss of Function | 4.34 | 2 | 25.8 | 0.0776 | 0.00000120 | 291 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000551 | 0.0000546 |
| Finnish | 0.0000936 | 0.0000924 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000551 | 0.0000546 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination of PIK3C2B and inhibits its activity; mediates the formation of 'Lys-48'-linked polyubiquitin chains; the function inhibits CD4 T- cell activation. Acts as a regulator of retrograde transport: together with MAGEL2, mediates the formation of 'Lys-63'-linked polyubiquitin chains at 'Lys-220' of WASHC1, leading to promote endosomal F-actin assembly (PubMed:23452853). Has a transcriptional repressor activity by cooperating with EPC1. Induces apoptosis by activating Jun N-terminal kinase and p38 kinase and also increases caspase-3-like activity independently of mitochondrial events. May function in male germ cell development. Has DNA-binding activity and preferentially bound to double- stranded DNA. {ECO:0000269|PubMed:10976108, ECO:0000269|PubMed:12807881, ECO:0000269|PubMed:22128329, ECO:0000269|PubMed:23452853}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving TRIM27/RFP is found in papillary thyroid carcinomas (PTCs). Translocation t(6;10)(p21.3;q11.2) with RET. The translocation generates TRIM27/RET and delta TRIM27/RET oncogenes. {ECO:0000269|PubMed:12787916, ECO:0000269|PubMed:3037315}.;
- Pathway
- Signal Transduction;Regulation of PTEN stability and activity;PTEN Regulation;PIP3 activates AKT signaling;Intracellular signaling by second messengers
(Consensus)
Intolerance Scores
- loftool
- 0.112
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.37
Haploinsufficiency Scores
- pHI
- 0.396
- hipred
- Y
- hipred_score
- 0.785
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.975
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Trim27
- Phenotype
- neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;negative regulation of adaptive immune response;negative regulation of protein kinase activity;spermatogenesis;cell population proliferation;protein sumoylation;negative regulation of tumor necrosis factor production;negative regulation of viral transcription;Arp2/3 complex-mediated actin nucleation;retrograde transport, endosome to Golgi;innate immune response;negative regulation of gene expression, epigenetic;positive regulation of DNA-binding transcription factor activity;positive regulation of actin nucleation;protein trimerization;protein K63-linked ubiquitination;interferon-gamma secretion;negative regulation of calcium ion import;negative regulation of interleukin-2 secretion;negative regulation of viral release from host cell
- Cellular component
- fibrillar center;nucleus;nucleoplasm;nucleolus;cytoplasm;endosome;early endosome;cytosol;PML body;retromer complex;nuclear membrane
- Molecular function
- nucleic acid binding;DNA binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding;SUMO transferase activity;identical protein binding;metal ion binding;ubiquitin protein ligase activity