BOLA3
protein-codingbolA family member 3, the group of Mitochondrial iron-sulfur assembly components
Gene summary
This gene encodes a protein that plays an essential role in the production of iron-sulfur (Fe-S) clusters for the normal maturation of lipoate-containing 2-oxoacid dehydrogenases, and for the assembly of the mitochondrial respiratory chain complexes. Mutation in this gene has been associated with multiple mitochondrial dysfunctions syndrome-2. Two alternatively spliced transcript variants encoding different isoforms with distinct subcellular localization have been reported for this gene (PMID:21944046). [provided by RefSeq, Dec 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013675
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013675
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *BOLA3* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of July 24, 2023. The *BOLA3* gene encodes bola family member 3, a mitochondrial iron-sulfur (Fe-S) cluster assembly factor involved in iron-sulfur cluster biogenesis. Iron-sulfur clusters are necessary for electron transport through oxidative phosphorylation (OXPHOS) as well for other cellular proteins, including for normal maturation of lipoate-containing enzymes and for assembly of OXPHOS complexes. The *BOLA3* gene was first reported in relation to autosomal recessive primary mitochondrial disease in 2011 (PMID: 21944046). While various names have been given to the constellation of features seen in those with *BOLA3*-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *BOLA3* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included three variants from five individuals from three publications (PMIDs: 21944046, 22562699, 24334290). More cases are reported in the medical literature (PMIDs: 26741492, 30302924, 29353736, 29654549, 32742935, 35803560) but not included in this curation as the maximum case level score was reached. Affected individuals are variably affected although onset tends to be infantile and early death may occur. Most reported individuals have leukodystrophy and seizures, but additional clinical features include neurodegeneration, spasticity, contractures, lethargy, myoclonus, ataxia, choreoathetoid movements, irritability, intellectual disability, developmental delay, developmental regression, hypertrophic or dilated cardiomyopathy, feeding difficulty, failure to thrive, vomiting, diarrhea, hepatomegaly, respiratory insufficiency, and optic atrophy. Brain imaging has shown changes in white matter, midbrain, cerebral/cerebellar atrophy, and cervical spine. Lab abnormalities include lactic acidosis, elevated glucose, elevated plasma glycine, elevated tricarboxylic acid (TCA) cycle metabolites on urine organic acids, and decreased activity of 2-oxoacid dehydrogenases and the glycine cleavage enzyme. Muscle biopsies have shown variable decreased activities of OXPHOS complexes I, II, II + III, and IV (also decreased in fibroblasts) and decreased pyruvate dehydrogenase complex activity. Some individuals have normal OXPHOS complex activities. Variants reported include nonsense, missense, and frameshift. Loss of function is the mechanism of disease. This gene-disease association is also supported by known biochemical function (PMID: 33340416). In summary, there is definitive evidence to support this gene-disease relationship, including that more than three years have elapsed since the first proposal of the association. No convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on July 24, 2023 (SOP Version 9).
Inheritance Pattern: AR
Disease ID:MONDO:0013675
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013675
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0013675
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BOLA3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_212552.3. 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 | 3 | 10 | 13 | |||
| missense | 3 | 47 | 3 | 53 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 1 | 4 | ||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 2 | 6 | 51 | 13 | 0 | 72 |
Highest pathogenic variant AF is 0.00008648851
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_997717.2 | 4 | MANE Select | |
| Ensembl | ENSP00000331369.5 | 4 | MANE Select | |
| RefSeq | NP_001030582.1 | 3 | Standard | |
| Ensembl | ENSP00000295326.4 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- biological_process
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- molecular_function
Cellular Component
- mitochondrion
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000327428
- Coding exons
- 4
- Length
- 12597
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125748
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.547 | 48 | 59.9 | 0.801 | 0.00000327 | 689 |
| Missense (PolyPhen) | 11 | 16.552 | 0.66456 | 206 | ||
| Synonymous | 0.542 | 16 | 19.0 | 0.842 | 9.24e-7 | 201 |
| Loss of Function | 1.50 | 2 | 5.93 | 0.337 | 3.52e-7 | 66 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000097 | 0.000097 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as a mitochondrial iron-sulfur (Fe-S) cluster assembly factor that facilitates (Fe-S) cluster insertion into a subset of mitochondrial proteins. Probably acts together with NFU1 (PubMed:27532772). {ECO:0000250|UniProtKB:P39724, ECO:0000305|PubMed:27532772}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- LoFtool
- 0.269
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |