TRIM32
protein-codingtripartite motif containing 32, the group of Tripartite motif family|Ring finger proteins
Gene summary
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. The protein has also been localized to the nucleus, where it interacts with the activation domain of the HIV-1 Tat protein. The Tat protein activates transcription of HIV-1 genes. [provided by RefSeq, Jul 2008]
- LGMD2H
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009683
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009683
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0015229
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009683
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014439
Submitter: ClinGen
*TRIM32* was first asserted in relation to autosomal recessive Bardet-Biedl syndrome in a family reported in 2006 (Chiang et al., PMID: 16606853). The phenotypes were consistent with other forms of Bardet-Biedl syndrome, including obesity, pigmentary retinopathy, polydactyly, hypogonadism, kidney and heart abnormalities, and/or intellectual impairment. *TRIM32* variants have separately been asserted in relation to autosomal recessive limb-girdle muscular dystrophy as early as 2002 (Frosk et al., PMID: 11822024). Per criteria outlined by the ClinGen Lumping & Splitting Working Group, the cases diagnosed as Bardet-Biedl syndrome were found to be distinguishable from the limb-girdle muscular dystrophy cases based on phenotype and disease mechanism, despite their matching mode of inheritance (autosomal recessive). Therefore, a split curation was recommended for Bardet-Biedl syndrome 11 ()MIM# 615988), while *TRIM32* has already been separately curated for autosomal recessive limb-girdle muscular dystrophy (MIM# 254110, MONDO:0015152). This curation includes one missense variant identified in the homozygous state in four affected patients from one consanguineous Israeli Bedouin family in one publication (PMID: 16606853). Interestingly, the variant is located in the B-box-2 domain, in which variants have not yet been observed to be involved in the pathogenesis of limb-girdle muscular dystrophy (PMID: 16606853, PMID: 38304327). The experimental evidence supporting the relationship of *TRIM32* to Bardet-Biedl syndrome includes data from expression studies and animal models. *TRIM32* is also known as *BBS11* and encodes tripartite motif-containing protein 32, an E3 ubiquitin ligase that is responsible for protein degradation (PMID: 19349376) and known to regulate autophagy (PMID: 33802079). *TRIM32* is expressed in a pattern that matches other BBS-related genes (PMID: 11822024). Knockdown of the *trim32* ortholog in zebrafish results in a phenotype consistent with BBS (PMID: 16606853). In summary, *TRIM32* has limited evidence of association with autosomal recessive Bardet-Biedl syndrome 11 (MIM#615988, MONDO:0014439). Additional case evidence will be requried for this gene-disease association to reach a mroe definitive classification. This clinical validity classification was approved by the ClinGen Retina Gene Curation Expert Panel on July 11th, 2024 (SOP version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0014439
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0009683
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0015152
Submitter: ClinGen
TRIM32 was first reported in relation to autosomal recessive limb-girdle muscular dystrophy in 2002 (Frosk et al., PMID:11822024). At least five unique variants (e.g. missense, in-frame indel, nonsense, frameshift, large deletion, etc) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data, segregation data, and experimental data. A founder variant in this gene, D487N, was first characterized by Frosk et al as causative for an LGMD in a Hutterite population, stemming from Eastern Europe. A follow-up publication by Schoser et al (PMID:15786463) observed that Hutterite LGMD probands and German sarcotubular myopathy probands shared this same variant and similar phenotypic features, concluding that both were part of the same spectrum of disorder. Since this initial characterization, several isolated variants have been reported in at least five other probands in four publications (PMIDs: 17994549, 19492423, 19303295, 31309175). In the initial pubication the D487N variant also segregated with disease in 18 additional probands in four families, yielding a maximum LOD score of 7.61. The mechanism for disease appears to be biallelic loss of function, with the disruption of the c-terminal NHL repeats impacting protein interactions and affecting proteins important to the skeletal muscle. However, no exact protein has been implicated. Of note, a variant in the TRIM32 B-box domain has also been implicated in Bardet-Biedl Syndrome. Due to the significant phenotypic and mechanistic differences, this assertion will be assessed separately. This gene-disease association is primarily supported by multiple animal models, with both a TRIM32 Knock-Out model and a D487N Knock-In model recapitulating phenotypes of the human probands such as muscle weakness and atrophy. In summary, TRIM32 is definitively associated with autosomal recessive limb-girdle muscular dystrophy. 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 Limb-Girdle Muscular Dystrophy GCEP on Nov. 5, 2020 (SOP Version 7). This gene curation was re-approved and published on 11/14/24 by the Muscular Dystrophies and Myopathies GCEP to reflect the change in the panel's name from LGMD GCEP to MDM GCEP. As part of this process, the genetic evidence was re-scored in accordance with SOP version 11.
Inheritance Pattern: AR
Disease ID:MONDO:0014439
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009683
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014439
Submitter: G2P
Inheritance Pattern: Unknown
Disease ID:MONDO:0014439
Submitter: Natera
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Dermatologic; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal
Intervention: Endocrine
Rationale: Medical management of obesity with melanocortin-4 receptor (MC4R) agonist (setmelanotide) may be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TRIM32 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012210.4. 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 | 2 | 274 | 276 | |||
| missense | 1 | 6 | 397 | 9 | 1 | 414 |
| nonsense | 12 | 11 | 1 | 24 | ||
| start loss | 0 | |||||
| frameshift | 21 | 30 | 1 | 52 | ||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 34 | 47 | 401 | 283 | 1 | 766 |
Highest pathogenic variant AF is 0.00007620639
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036342.2 | 1 | MANE Select | |
| Ensembl | ENSP00000408292.1 | 1 | MANE Select | |
| RefSeq | NP_001093149.1 | 1 | Standard | |
| RefSeq | NP_001365977.1 | 1 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| trim32 | Danio rerio | Structure: pronephric duct Quality: cystic abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ubiquitin mediated proteolysis - Homo sapiens (human)
- Regulation of innate immune responses to cytosolic DNA
- Innate Immune System
- Immune System
- Adaptive Immune System
Biological Process
- protein polyubiquitination
- tissue homeostasis
- ubiquitin-dependent protein catabolic process
- actin ubiquitination
- response to UV
Molecular Function
- transcription coactivator activity
- RNA binding
- ubiquitin-protein transferase activity
- protein binding
- zinc ion binding
Cellular Component
- nucleus
- cytoplasm
- cytosol
- striated muscle myosin thick filament
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000450136
- Coding exons
- 1
- Length
- 13999
- Individuals with no LoFs
- 125697
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 51
- Defined
- 125748
- p
- 0.000203
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.827 | 335 | 380 | 0.881 | 0.0000245 | 4253 |
| Missense (PolyPhen) | 93 | 125.72 | 0.73972 | 1505 | ||
| Synonymous | 0.619 | 134 | 143 | 0.934 | 0.00000746 | 1392 |
| Loss of Function | 1.98 | 7 | 15.4 | 0.455 | 8.06e-7 | 198 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00029 | 0.00029 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Has an E3 ubiquitin ligase activity. Ubiquitinates DTNBP1 (dysbindin) and promotes its degradation. May ubiquitinate BBS2. May play a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo. Binds specifically to the activation domain of HIV-1 Tat and can also interact with the HIV-2 and EIAV Tat proteins in vivo. {ECO:0000269|PubMed:19349376, ECO:0000269|PubMed:22500027}.;
- Disease
- DISEASE: Limb-girdle muscular dystrophy 2H (LGMD2H) [MIM:254110]: An autosomal recessive degenerative myopathy characterized by pelvic girdle, shoulder girdle and quadriceps muscle weakness. Clinical phenotype and severity are highly variable. Disease progression is slow and most patients remain ambulatory into the sixth decade of life. {ECO:0000269|PubMed:11822024, ECO:0000269|PubMed:17994549}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Bardet-Biedl syndrome 11 (BBS11) [MIM:615988]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:16606853}. Note=The disease is caused by mutations affecting the gene represented in this entry. It has been suggested that TRIM32 might be the E3 ubiquitin ligase for BBS2, a component of the BBSome complex involved in ciliogenesis, that is ubiquitinated and degraded by the proteasome (PubMed:22500027). {ECO:0000269|PubMed:22500027}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.211
- RVIS EVS
- -0.6
- RVIS percentile EVS
- 18.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |