MICALL2

protein-coding

MICAL like 2, the group of LIM domain containing

Gene summary

Enables filamin binding activity. Involved in obsolete positive regulation of protein targeting to mitochondrion. Predicted to be located in several cellular components, including bicellular tight junction; recycling endosome; and stress fiber. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_182924.4

Inheritance

—

ClinVar variants

P:1U:249B:54

Top phenotype

Joubert syndrome 1

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr7:1,428,465-1,459,470

External References & Databases

Ensembl (ENSG00000164877)

Transcript & Mutation Effects

hg38 • Region Span ~31.0 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 MICALL2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 250

not providedTotal: 37

Joubert syndrome 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182924.4. 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			5 clinvar	11 clinvar	11 clinvar	27
missense	1 clinvar		239 clinvar	21 clinvar	11 clinvar	272
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	1	0	249	32	22	304

Highest pathogenic variant AF is 0.0000054938714

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182924.4	RefSeq	NP_891554.1	17	MANE Select
ENST00000297508.8	Ensembl	ENSP00000297508.7	17	MANE Select
ENST00000413446.5	Ensembl	ENSP00000405415.1	10	Standard
ENST00000873414.1	Ensembl	ENSP00000543473.1	17	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
micall2b	Danio rerio	Structure: whole organism Quality: increased speed abnormal

Gene / Model

Organism

Observed Phenotype

micall2b

Danio rerio

Structure: whole organism

Quality: increased speed

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Tight junction - Homo sapiens (human)

Biological Process

actin filament polymerization
neuron projection development
actin cytoskeleton reorganization
endocytic recycling
substrate adhesion-dependent cell spreading

Molecular Function

protein binding
Rab GTPase binding
filamin binding
actinin binding
metal ion binding

Cellular Component

stress fiber
cytosol
plasma membrane
cell-cell junction
bicellular tight junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297508
Coding exons: 17
Length: 31038
Individuals with no LoFs: 125360
Homozygous LoFs: 1
Heterozygous LoFs: 104
Defined: 125465
p: 0.000419

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.99	675	544	1.24	0.0000356	5650
Missense (PolyPhen)		180	160.87	1.1189		1719
Synonymous	-4.07	323	242	1.33	0.0000174	1883
Loss of Function	-0.264	38	36.3	1.05	0.00000178	428

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00054	0.00049	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.00045	0.00044	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00036	0.00035	rare
South Asian	0.00089	0.00085	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Effector of small Rab GTPases which is involved in junctional complexes assembly through the regulation of cell adhesion molecules transport to the plasma membrane and actin cytoskeleton reorganization. Regulates the endocytic recycling of occludins, claudins and E-cadherin to the plasma membrane and may thereby regulate the establishment of tight junctions and adherens junctions. In parallel, may regulate actin cytoskeleton reorganization directly through interaction with F-actin or indirectly through actinins and filamins. Most probably involved in the processes of epithelial cell differentiation, cell spreading and neurite outgrowth (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0834

Intolerance Scores

LoFtool: 0.725
RVIS EVS: 1.39
RVIS percentile EVS: 94.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.120

Gene Damage Prediction

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