MICU2
protein-codingmitochondrial calcium uptake 2, the group of EF-hand domain containing
Gene summary
Enables calcium ion binding activity; calcium ion sensor activity; and protein heterodimerization activity. Involved in calcium import into the mitochondrion; cellular response to calcium ion; and negative regulation of mitochondrial calcium ion concentration. Located in mitochondrial intermembrane space. Part of uniplex complex. Is active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jun 2026]
- EFHA1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~111.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *MICU2* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of October 19, 2023. *MICU2* encodes mitochondrial calcium uptake protein 2. This is a subunit of the mitochondrial uniporter complex, a multi-subunit calcium channel of the mitochondrial inner membrane. *MICU2* is involved in calcium import into the mitochondrion and negative regulation of mitochondrial calcium ion concentration by regulating calcium channel opening. The *MICU2* gene has been reported in relation to autosomal recessive primary mitochondrial disease in one case to date in 2017 (PMID: 29053821). This was an 11-year-old girl with cognitive delay and intellectual disability. Brain MRI showed gliosis and T2 hyperintense foci in both cerebral hemisphere in a subcortical distribution. She had a similarly affected brother who also had abnormal eye movements. Although the phenotype is nonspecific, there was a homozygous nonsense variant in *MICU2* present in these two siblings, and given the calcium flux abnormalities noted in patient cells, this GCEP elected to include this family in this curation. While various names could be given to the constellation of features seen in those with *MICU2*-related disease, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *MICU2* 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. As described above, this curation includes one proband with a homozygous nonsense variant from one publication (PMID: 29053821). This gene-disease association is also supported by the known biochemical function of *MICU2* that is shared with *MICU1*, a gene with a definitive association to primary mitochondrial disease (PMID: 26903221). It is also supported by experimental data including mitochondrial calcium uptake studies with either shRNA or siRNA knockdown in HeLa cells (PMIDs: 26903221, 24560927) and knockout mice (PMID: 29073106). In summary, there is limited evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, 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 October 19, 2023 (SOP Version 9).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MICU2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152726.3. 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 | 1 | 1 | 2 | |||
| missense | 57 | 7 | 64 | |||
| nonsense | 1 | 1 | 2 | |||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 64 | 9 | 0 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689939.1 | 12 | MANE Select | |
| Ensembl | ENSP00000371811.4 | 12 | MANE Select | |
| Ensembl | ENSP00000431792.2 | 9 | Standard | |
| Ensembl | ENSP00000573460.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Transport of small molecules
- Mitochondrial calcium ion transport
- Processing of SMDT1
Biological Process
- mitochondrial calcium ion transmembrane transport
- calcium import into the mitochondrion
- mitochondrial calcium ion homeostasis
- positive regulation of mitochondrial calcium ion concentration
- negative regulation of mitochondrial calcium ion concentration
Molecular Function
- calcium ion binding
- protein binding
- protein heterodimerization activity
Cellular Component
- mitochondrion
- mitochondrial inner membrane
- mitochondrial intermembrane space
- calcium channel complex
- uniplex complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000382374
- Coding exons
- 12
- Length
- 111518
- Individuals with no LoFs
- 124856
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 890
- Defined
- 125748
- p
- 0.00355
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.311 | 234 | 221 | 1.06 | 0.0000109 | 2844 |
| Missense (PolyPhen) | 50 | 62.574 | 0.79906 | 846 | ||
| Synonymous | -1.27 | 90 | 75.9 | 1.19 | 0.00000372 | 766 |
| Loss of Function | -0.515 | 29 | 26.2 | 1.11 | 0.00000140 | 310 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0027 | 0.0026 | notable |
| Latino/Admixed American | 0.0041 | 0.0040 | notable |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00050 | 0.00049 | rare |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.0055 | 0.0055 | notable |
| South Asian | 0.0015 | 0.0014 | notable |
| Other | 0.0045 | 0.0044 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Key regulator of mitochondrial calcium uniporter (MCU) required to limit calcium uptake by MCU when cytoplasmic calcium is low (PubMed:24503055, PubMed:24560927, PubMed:26903221). MICU1 and MICU2 form a disulfide-linked heterodimer that stimulate and inhibit MCU activity, depending on the concentration of calcium (PubMed:24560927). MICU2 acts as a gatekeeper of MCU that senses calcium level via its EF-hand domains: prevents channel opening at resting calcium, avoiding energy dissipation and cell-death triggering (PubMed:24560927). {ECO:0000269|PubMed:24503055, ECO:0000269|PubMed:24560927, ECO:0000269|PubMed:26387864, ECO:0000269|PubMed:26903221}.;
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |