TRIM54
protein-codingtripartite motif containing 54, the group of Tripartite motif family|Ring finger proteins
Gene summary
The protein encoded by this gene contains a RING finger motif and is highly similar to the ring finger proteins RNF28/MURF1 and RNF29/MURF2. In vitro studies demonstrated that this protein, RNF28, and RNF29 form heterodimers, which may be important for the regulation of titin kinase and microtubule-dependent signal pathways in striated muscles. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
- RNF30
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TRIM54 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_187841.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 3 | 2 | 6 | ||
| missense | 62 | 1 | 63 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 67 | 4 | 2 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_912730.2 | 8 | MANE Select | |
| Ensembl | ENSP00000369415.3 | 8 | MANE Select | |
| RefSeq | NP_115935.3 | 9 | Standard | |
| Ensembl | ENSP00000296098.4 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- microtubule-based process
- negative regulation of microtubule depolymerization
- signal transduction
- multicellular organism development
- muscle cell development
Molecular Function
- protein binding
- microtubule binding
- zinc ion binding
Cellular Component
- microtubule
- microtubule associated complex
- Z disc
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296098
- Coding exons
- 9
- Length
- 25048
- Individuals with no LoFs
- 125495
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 253
- Defined
- 125748
- p
- 0.00101
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.487 | 226 | 248 | 0.913 | 0.0000157 | 2603 |
| Missense (PolyPhen) | 55 | 58.855 | 0.9345 | 626 | ||
| Synonymous | 0.307 | 100 | 104 | 0.962 | 0.00000680 | 776 |
| Loss of Function | -0.865 | 24 | 19.8 | 1.21 | 9.27e-7 | 236 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00049 | 0.00049 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0058 | 0.0057 | notable |
| Finnish | 0.00066 | 0.00065 | rare |
| European (Non-Finnish) | 0.00085 | 0.00084 | rare |
| South Asian | 0.00051 | 0.00049 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May bind and stabilize microtubules during myotubes formation. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.841
- RVIS EVS
- -0.76
- RVIS percentile EVS
- 13.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.844
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |