BOLA3

protein-coding

bolA 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

NM_212552.3

Inheritance

AR

ClinVar variants

P:8U:51B:13

Top phenotype

Multiple mitochondrial dysfunctions syndrome 2 with hyperglycinemia

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr2:74,135,400-74,147,912

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~12.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

multiple mitochondrial dysfunctions syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013675

Submitter: G2P

multiple mitochondrial dysfunctions syndrome 2SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013675

Submitter: Orphanet

mitochondrial diseaseDEFINITIVE

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).

multiple mitochondrial dysfunctions syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013675

Submitter: Labcorp Genetics (formerly Invitae)

multiple mitochondrial dysfunctions syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013675

Submitter: Genomics England PanelApp

multiple mitochondrial dysfunctions syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013675

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Multiple mitochondrial dysfunctions syndrome 2 with hyperglycinemiaAR

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

Refs: 11156534; 21944046; 22562699; 24334290Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BOLA3 variants in ClinVar

5 Conditions Cataloged
not providedTotal: 63
Inborn genetic diseasesTotal: 27
Multiple mitochondrial dysfunctions syndrome 2Total: 27
not specifiedTotal: 7
BOLA3-related disorderTotal: 5

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
10
clinvar
13
missense
3
clinvar
47
clinvar
3
clinvar
53
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
2
clinvar
1
clinvar
4
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total265113072

Highest pathogenic variant AF is 0.00008648851

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_212552.3RefSeqNP_997717.24MANE Select
ENST00000327428.10EnsemblENSP00000331369.54MANE Select
NM_001035505.2RefSeqNP_001030582.13Standard
ENST00000295326.4EnsemblENSP00000295326.43Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5474859.90.8010.00000327689
Missense (PolyPhen)1116.5520.66456206
Synonymous0.5421619.00.8429.24e-7201
Loss of Function1.5025.930.3373.52e-766

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000970.000097rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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