MICU3

protein-coding

mitochondrial calcium uptake family member 3, the group of EF-hand domain containing

Gene summary

Enables calcium ion sensor activity and protein heterodimerization activity. Involved in calcium import into the mitochondrion and cellular response to calcium ion. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

EFHA2

MANE transcript

NM_181723.3

Inheritance

—

ClinVar variants

U:111B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr8:17,027,238-17,122,642

External References & Databases

Ensembl (ENSG00000155970)

Transcript & Mutation Effects

hg38 • Region Span ~95.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MICU3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 106

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181723.3. 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						0
missense			105 clinvar	3 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	111	3	0	114

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 62 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181723.3	RefSeq	NP_859074.1	14	MANE Select
ENST00000318063.10	Ensembl	ENSP00000321455.5	14	MANE Select
NM_001349810.2	RefSeq	NP_001336739.1	14	Standard
NM_001413217.1	RefSeq	NP_001400146.1	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

Molecular Function

calcium ion binding

Cellular Component

mitochondrial inner membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318063
Coding exons: 14
Length: 95407
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125735
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.219	228	238	0.960	0.0000125	3406
Missense (PolyPhen)		38	55.922	0.67951		788
Synonymous	-1.80	99	78.7	1.26	0.00000383	993
Loss of Function	1.49	17	25.1	0.678	0.00000121	362

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00061	0.00058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00027	0.00025	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in mitochondrial calcium uptake. {ECO:0000250}.;

Intolerance Scores

RVIS EVS: -0.74
RVIS percentile EVS: 13.94

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