TRIM37
protein-codingtripartite motif containing 37, the group of Tripartite motif family|Ring finger proteins
Gene summary
This gene encodes a member of the tripartite motif (TRIM) family, whose members are involved in diverse cellular functions such as developmental patterning and oncogenesis. The TRIM motif includes zinc-binding domains, a RING finger region, a B-box motif and a coiled-coil domain. The RING finger and B-box domains chelate zinc and might be involved in protein-protein and/or protein-nucleic acid interactions. Mutations in this gene are associated with mulibrey (muscle-liver-brain-eye) nanism, an autosomal recessive disorder that involves several tissues of mesodermal origin. TRIM37 localizes in peroxisomal membranes, and has been implicated in human peroxisomal biogenesis disorders. [provided by RefSeq, Jul 2020]
- MUL
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~124.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009664
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009664
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009664
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0009664
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009664
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009664
Submitter: ClinGen
The relationship between TRIM37 and Mulibrey Nanism, an autosomal recessive disorder, was evaluated using the ClinGen Clinical Validity Framework as of February, 2020. TRIM37 encodes a member of the tripartite motif family. Mulibrey nanism is a multi-organ defect affecting the muscles, liver, brain, eye (Braverman et al, 2012, Gene Reviews) and characterized by severe growth failure of prenatal onset, characteristic dysmorphic features, perimyocardial heart disease, metabolic syndrome and hepatomegaly (Kallijarvi et al, 2006; PMID: 16514549). TRIM37 was first reported in relation to autosomal recessive mulibrey nanism in 2000. (Avela et al, PMID: 10888877). At least 20 nonsense, splice site, frameshift, deletion/duplication and missense variants have been reported in humans in the ClinVar database. Evidence supporting this gene-disease relationship includes case-level data and experimental data. Summary of Case Level Data (12 points): Variants in this gene have been reported in at least 8 probands in 4 publications (PMID: 27256967, 17100991, 15108285, 10888877). More evidence is available in the literature, but the maximum score (12 points) for genetic evidence is reached. Two founder mutations in the Finnish population have been described: c.493-2A>G, referred to as the Finnish major mutation is most frequently seen, and Glu738fs, referred to as the Finnish minor mutation. The mechanism for disease is expected to be biallelic loss of function. Summary of experimental data (2 points): This gene-disease association is supported by in vitro functional assays and animal models. TRIM37 is shown to partially localize with the proxisome and interact with PEX5 to ubiquitylate it. Depletion of TRIM37 is shown to result in peroxisomal matrix protein import defect (PMID: 28724525). Mouse models of TRIM37 recapitulate the human disease; however no overt peroxisome pathology is noted (PMID: 27044324). In summary, TRIM37 is definitively associated with autosomal recessive mulibrey nanism. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Peroxisomal Disorders GCEP on May 1, 2020 (SOP Version 7).
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Dermatologic; Endocrine; Gastrointestinal; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic
Intervention: Cardiovascular; Oncologic
Rationale: Surveillance and early detection of and treatment for malignancy (Wilms tumors, as well a number of other cancer types have been reported) may decrease morbidity and mortality; Awareness of cardiovascular anomalies (including structural anomalies, as well as pericardial constriction and congestive heart failure) may be beneficial in order to allow early diagnosis and treatment
Comments: The condition may involve multiple malformations
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TRIM37 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015294.6. 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 | 3 | 217 | 1 | 221 | ||
| missense | 4 | 187 | 4 | 1 | 196 | |
| nonsense | 16 | 24 | 40 | |||
| start loss | 0 | |||||
| frameshift | 25 | 27 | 52 | |||
| splice donor/acceptor (+/-2bp) | 1 | 24 | 2 | 27 | ||
| Total | 42 | 79 | 192 | 221 | 2 | 536 |
Highest pathogenic variant AF is 0.0003123168
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056109.1 | 24 | MANE Select | |
| Ensembl | ENSP00000262294.7 | 24 | MANE Select | |
| RefSeq | NP_001005207.1 | 25 | Standard | |
| RefSeq | NP_001307916.1 | 23 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ubiquitin mediated proteolysis - Homo sapiens (human)
- Immune System
- Adaptive Immune System
- Antigen processing: Ubiquitination & Proteasome degradation
- Class I MHC mediated antigen processing & presentation
Biological Process
- negative regulation of transcription by RNA polymerase II
- negative regulation of NF-kappaB transcription factor activity
- histone H2A monoubiquitination
- histone H2A-K119 monoubiquitination
- negative regulation of centriole replication
Molecular Function
- chromatin binding
- ubiquitin-protein transferase activity
- tumor necrosis factor receptor binding
- protein binding
- zinc ion binding
Cellular Component
- cytoplasm
- peroxisome
- cytosol
- aggresome
- ESC/E(Z) complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262294
- Coding exons
- 24
- Length
- 124284
- Individuals with no LoFs
- 125461
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 287
- Defined
- 125748
- p
- 0.00114
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.820 | 476 | 529 | 0.900 | 0.0000286 | 6356 |
| Missense (PolyPhen) | 97 | 151.53 | 0.64016 | 1798 | ||
| Synonymous | -0.0639 | 177 | 176 | 1.01 | 0.00000899 | 1791 |
| Loss of Function | 3.85 | 29 | 61.6 | 0.471 | 0.00000367 | 685 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00065 | 0.00065 | rare |
| Finnish | 0.0091 | 0.0091 | notable |
| European (Non-Finnish) | 0.00046 | 0.00045 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00082 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase required to prevent centriole reduplication (PubMed:15885686, PubMed:23769972). Probably acts by ubiquitinating positive regulators of centriole reduplication (PubMed:23769972). Mediates monoubiquitination of 'Lys-119' of histone H2A (H2AK119Ub), a specific tag for epigenetic transcriptional repression: associates with some Polycomb group (PcG) multiprotein PRC2-like complex and mediates repression of target genes (PubMed:25470042). Has anti-HIV activity (PubMed:24317724). {ECO:0000269|PubMed:15885686, ECO:0000269|PubMed:23769972, ECO:0000269|PubMed:24317724, ECO:0000269|PubMed:25470042}.;
- Disease
- DISEASE: Mulibrey nanism (MUL) [MIM:253250]: An autosomal recessive growth disorder characterized by severe growth failure of prenatal onset, constrictive pericardium and progressive cardiomyopathy, facial dysmorphism, and failure of sexual maturation. Additional clinical features include hepatomegaly, muscle hypotonia, J-shaped sella turcica, yellowish dots in the ocular fundi, hypoplasia of various endocrine glands, insulin resistance with type 2 diabetes, and an increased risk for Wilms' tumor. {ECO:0000269|PubMed:10888877, ECO:0000269|PubMed:12754710, ECO:0000269|PubMed:15108285, ECO:0000269|PubMed:15885686, ECO:0000269|PubMed:17100991, ECO:0000269|PubMed:17551331, ECO:0000269|PubMed:21865362, ECO:0000269|PubMed:23385855}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.289
Intolerance Scores
- LoFtool
- 0.884
- RVIS EVS
- -0.22
- RVIS percentile EVS
- 37.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.928
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |