MICU2

protein-coding

mitochondrial 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]

Previous symbols:
  • EFHA1

MANE transcript

NM_152726.3

Inheritance

AR

ClinVar variants

U:64B:9

Top phenotype

MICU2-related disorder

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr13:21,492,691-21,604,181

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~111.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial diseaseLIMITED

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

3 Conditions Cataloged
not specifiedTotal: 61
not providedTotal: 6
MICU2-related disorderTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
57
clinvar
7
clinvar
64
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total00649073
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_152726.3RefSeqNP_689939.112MANE Select
ENST00000382374.9EnsemblENSP00000371811.412MANE Select
ENST00000468222.2EnsemblENSP00000431792.29Standard
ENST00000903401.1EnsemblENSP00000573460.113Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.3112342211.060.00001092844
Missense (PolyPhen)5062.5740.79906846
Synonymous-1.279075.91.190.00000372766
Loss of Function-0.5152926.21.110.00000140310

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00270.0026notable
Latino/Admixed American0.00410.0040notable
Ashkenazi Jewish0.000100.000099rare
East Asian0.000500.00049rare
Finnish0.000370.00037rare
European (Non-Finnish)0.00550.0055notable
South Asian0.00150.0014notable
Other0.00450.0044notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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