TRIM63
protein-codingtripartite motif containing 63, the group of Tripartite motif family|Ring finger proteins
Gene summary
This gene encodes a member of the RING zinc finger protein family found in striated muscle and iris. The product of this gene is an E3 ubiquitin ligase that localizes to the Z-line and M-line lattices of myofibrils. This protein plays an important role in the atrophy of skeletal and cardiac muscle and is required for the degradation of myosin heavy chain proteins, myosin light chain, myosin binding protein, and for muscle-type creatine kinase. [provided by RefSeq, Feb 2012]
- RNF28
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0005045
Submitter: ClinGen
*TRIM63* was first reported in relation to autosomal recessive hypertrophic cardiomyopathy (HCM) in humans in 2015, where a homozygous truncating variant (p.Q247X) was identified in a single proband whose phenotype included HCM and skeletal myopathy (Olivé et al, PMID 25801283). The *TRIM63* gene encodes an E3 ubiquitin ligase and is part of the ubiquitin-proteasome system, which targets cellular proteins, including sarcomeric proteins, for degradation. *TRIM63* has been associated with autosomal recessive (AR) HCM in 32 probands across 5 publications; the Q247X variant is a recurrent variant reported in 11 of these 32 probands in either a homozygous or compound heterozygous state (Olivé et al, 2015, PMID 25801283; Jokela et al, 2019, PMID 30372688; Salazar-Mendiguchía J et al, 2020, PMID 32451364; Andreeva et al, 2022, PMID 35273634; Allouba M, et al., 2023, PMID: 37431535); however, the Q247X variant has limited functional evidence for disease causation. Case-control evidence showed enrichment of biallelic TRIM63 variants in cases compared to controls, but this study did not calculate or report statistical significance (Salazar-Mendiguchía J et al, 2020, PMID 32451364). Importantly, there have been at least 2 reports of co-occurring HCM and skeletal myopathy in the presence of biallelic *TRIM63* variants (Olivé et al, 2015, PMID 25801283; Jokela et al, 2019, PMID 30372688). One of the described probands was also found to have a heterozygous TRIM54 variant. This raises the possibility of a broader phenotype including skeletal myopathy, but more evidence is needed. This gene-disease relationship is also supported by expression studies (Bodine et al, 2001, PMID 11679633; Fagerberg et al, 2014, PMID 24309898), protein interaction with TNNI3, MYBPC3, TNNT2, and MYH7 (Kedar et al, 2004, PMID 15601779, Mearini et al, 2010, PMID 19850579, Witt et al, 2005, PMID 15967462, Fielitz et al, 2007, PMID 17786241), biochemical function (Kedar et al, 2004, PMID 15601779, Mearini et al, 2010, PMID 19850579, Arya et al, 2004, PMID 15596539), and a model system (Willis et al, 2007, PMID 17272810). In summary, the evidence supporting the relationship between TRIM63 and autosomal recessive HCM is moderate. This classification was approved by the ClinGen Hereditary Cardiovascular Diseases GCEP on June 6, 2024.
Inheritance Pattern: AD
Disease ID:MONDO:0024573
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0005045
Submitter: ClinGen
The TRIM63 gene encodes an E3 ubiquitin ligase and is part of the ubiquitin-proteasome system, which targets cellular proteins, including sarcomeric proteins, for degradation. TRIM63 was first reported in relation to autosomal dominant hypertrophic cardiomyopathy in 2012 (Chen et al, 2012, PMID 22821932) and has been reported in no subsequent clinical reports, though evidence for autosomal recessive disease is emerging. The split curation for autosomal recessive inheritance has been curated separately. Chen et al. reported 3 variants in 5 probands, including 2 missense variants in 3 probands, and one truncating variant (p.Q247X) in 2 probands without segregation. The p.Q247X variant has an allele frequency of 0.0007 (0.008 in the Ashkenazi Jewish population), considered too high for AD inheritance. All 3 variants have limited functional evidence for disease causation. A case control study utilizing aggregate variant analysis reported rare variants in TRIM63 at a higher frequency in cases compared to controls (Su et al, 2014, PMID 24865491). A second case control study (Walsh et al, 2017, PMID 27532257) found no enrichment of rare variants in cases vs. controls. Notably, multiple reports of AR inheritance have demonstrated no disease in heterozygote relatives (Olive et al, 2015, PMID 25801283, Andreeva et al, 2022, PMID 35273634, Salazar-Mendiguchia et al, 2020, PMID 32451364). This gene-disease association is supported by expression studies (Bodine et al, 2001, PMID 11679633; Fagerberg et al, 2014, PMID 24309898), protein interaction with TNNI3, MYBPC3, TNNT2, and MYH7 (Kedar et al, 2004, PMID 15601779, Mearini et al, 2010, PMID 19850579, Witt et al, 2005, PMID 15967462, Fielitz et al, 2007, PMID 17786241), and biochemical function (Kedar et al, 2004, PMID 15601779, Mearini et al, 2010, PMID 19850579, Arya et al, 2004, PMID 15596539). The original curation was published on December 20th, 2016 with a classification of Limited. At the time of this re-curation, no new genetic level evidence has emerged to support the disease mode of inheritance. In summary, the evidence supporting the relationship between TRIM63 and autosomal dominant HCM has been disputed, and no valid evidence remains to support the claim. More evidence is needed to either support or entirely refute the role TRIM63 plays in this disease. This classification was approved by the ClinGen Hypertrophic Cardiomyopathy Gene Curation Expert Panel on October 27th, 2022.
Inheritance Pattern: AR
Disease ID:MONDO:0005045
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0005045
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TRIM63 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032588.4. 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 | 24 | 2 | 27 | ||
| missense | 1 | 3 | 85 | 7 | 96 | |
| nonsense | 2 | 1 | 3 | |||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 1 | 2 | 4 | ||
| splice donor/acceptor (+/-2bp) | 2 | 2 | 4 | |||
| Total | 4 | 6 | 92 | 31 | 2 | 135 |
Highest pathogenic variant AF is 0.00050674943
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115977.2 | 9 | MANE Select | |
| Ensembl | ENSP00000363390.3 | 9 | MANE Select |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway
- Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling
- Immune System
- Adaptive Immune System
- Antigen processing: Ubiquitination & Proteasome degradation
Biological Process
- muscle contraction
- signal transduction
- negative regulation of cardiac muscle hypertrophy
- skeletal muscle atrophy
- response to electrical stimulus involved in regulation of muscle adaptation
Molecular Function
- ubiquitin-protein transferase activity
- protein binding
- zinc ion binding
- titin binding
Cellular Component
- nucleus
- cytoplasm
- microtubule
- Z disc
- M band
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000374272
- Coding exons
- 9
- Length
- 17133
- Individuals with no LoFs
- 125511
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 237
- Defined
- 125748
- p
- 0.000943
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.177 | 212 | 205 | 1.03 | 0.0000117 | 2354 |
| Missense (PolyPhen) | 94 | 85.516 | 1.0992 | 889 | ||
| Synonymous | -0.414 | 85 | 80.3 | 1.06 | 0.00000480 | 618 |
| Loss of Function | -0.00863 | 19 | 19.0 | 1.00 | 8.73e-7 | 225 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0.0080 | 0.0081 | notable |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.00079 | 0.00079 | rare |
| European (Non-Finnish) | 0.00083 | 0.00083 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: E3 ubiquitin ligase. Mediates the ubiquitination and subsequent proteasomal degradation of CKM, GMEB1 and HIBADH. Regulates the proteasomal degradation of muscle proteins under amino acid starvation, where muscle protein is catabolized to provide other organs with amino acids. Inhibits de novo skeletal muscle protein synthesis under amino acid starvation. Regulates proteasomal degradation of cardiac troponin I/TNNI3 and probably of other sarcomeric-associated proteins. May play a role in striated muscle atrophy and hypertrophy by regulating an anti- hypertrophic PKC-mediated signaling pathway. May regulate the organization of myofibrils through TTN in muscle cells. {ECO:0000269|PubMed:11927605, ECO:0000269|PubMed:18222470}.;
Recessive Scores
- pRec
- 0.388
Intolerance Scores
- LoFtool
- 0.628
- RVIS EVS
- -0.4
- RVIS percentile EVS
- 26.85
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.905
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |