MICAL3

protein-coding

microtubule associated monooxygenase, calponin and LIM domain containing 3, the group of LIM domain containing|MicroRNA protein coding host genes

Gene summary

Enables actin binding activity and molecular adaptor activity. Involved in actin filament depolymerization. Located in Flemming body; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015241.3

Inheritance

—

ClinVar variants

U:358B:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr22:17,787,649-18,024,561

External References & Databases

Ensembl (ENSG00000243156)

Transcript & Mutation Effects

hg38 • Region Span ~236.9 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 MICAL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 351

not providedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015241.3. 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 clinvar	7 clinvar	2 clinvar	12
missense			344 clinvar	14 clinvar	4 clinvar	362
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	358	21	6	385

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015241.3	RefSeq	NP_056056.2	31	MANE Select
ENST00000441493.7	Ensembl	ENSP00000416015.2	31	MANE Select
NM_001122731.2	RefSeq	NP_001116203.1	20	Standard
NM_001136004.3	RefSeq	NP_001129476.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

exocytosis
cytoskeleton organization
cell cycle
actin filament depolymerization
cell division

Molecular Function

actin binding
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
Rab GTPase binding
metal ion binding
FAD binding

Cellular Component

nucleus
nucleoplasm
spindle
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000441493
Coding exons: 31
Length: 236911
Individuals with no LoFs: 125051
Homozygous LoFs: 0
Heterozygous LoFs: 80
Defined: 125131
p: 0.000320

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.75	1028	1.20e+3	0.858	0.0000777	12907
Missense (PolyPhen)		385	542.31	0.70993		5776
Synonymous	-0.360	519	509	1.02	0.0000352	3993
Loss of Function	7.17	17	90.7	0.188	0.00000489	1069

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00045	rare
Latino/Admixed American	0.00051	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00038	0.00032	rare
European (Non-Finnish)	0.00040	0.00035	rare
South Asian	0.00021	0.00020	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). Seems to act as Rab effector protein and plays a role in vesicle trafficking. Involved in exocytic vesicles tethering and fusion: the monooxygenase activity is required for this process and implicates RAB8A associated with exocytotic vesicles. Required for cytokinesis. Contributes to stabilization and/or maturation of the intercellular bridge independently of its monooxygenase activity. Promotes recruitment of Rab8 and ERC1 to the intercellular bridge, and together these proteins are proposed to function in timely abscission. {ECO:0000269|PubMed:21596566, ECO:0000269|PubMed:24440334}.;

Recessive Scores

pRec: 0.119

Intolerance Scores

RVIS EVS: 0.41
RVIS percentile EVS: 76.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0814

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium