MICALL1

protein-coding

MICAL like 1, the group of LIM domain containing

Gene summary

Enables several functions, including identical protein binding activity; phosphatidic acid binding activity; and small GTPase binding activity. Involved in several processes, including plasma membrane tubulation; protein localization to endosome; and slow endocytic recycling. Located in several cellular components, including cilium; endosome; and microtubule organizing center. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_033386.4

Inheritance

—

ClinVar variants

U:171B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr22:37,905,657-37,942,822

External References & Databases

Ensembl (ENSG00000100139)

Transcript & Mutation Effects

hg38 • Region Span ~37.2 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 MICALL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 165

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033386.4. 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			1 clinvar	2 clinvar		3
missense			160 clinvar	6 clinvar		166
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	171	8	0	179

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033386.4	RefSeq	NP_203744.1	16	MANE Select
ENST00000215957.10	Ensembl	ENSP00000215957.6	16	MANE Select
NM_001410818.1	RefSeq	NP_001397747.1	17	Standard
NM_001410819.1	RefSeq	NP_001397748.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein targeting to membrane
endocytosis
receptor-mediated endocytosis
neuron projection development
slow endocytic recycling

Molecular Function

protein binding
Rab GTPase binding
identical protein binding
cadherin binding
metal ion binding

Cellular Component

early endosome
late endosome
trans-Golgi network
extrinsic component of membrane
late endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000215957
Coding exons: 16
Length: 37166
Individuals with no LoFs: 125704
Homozygous LoFs: 0
Heterozygous LoFs: 44
Defined: 125748
p: 0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.976	444	506	0.878	0.0000311	5530
Missense (PolyPhen)		132	183.87	0.7179		2041
Synonymous	0.942	196	214	0.918	0.0000138	1790
Loss of Function	2.69	17	33.9	0.501	0.00000152	431

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00020	rare
South Asian	0.000098	0.000098	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. On endosome membranes, may act as a downstream effector of Rab proteins recruiting cytosolic proteins to regulate membrane tubulation. May be involved in a late step of receptor-mediated endocytosis regulating for instance endocytosed-EGF receptor trafficking. Alternatively, may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. May indirectly play a role in neurite outgrowth. {ECO:0000269|PubMed:19864458, ECO:0000269|PubMed:20801876, ECO:0000269|PubMed:21795389, ECO:0000269|PubMed:23596323}.;

Recessive Scores

pRec: 0.0874

Intolerance Scores

LoFtool: 0.535
RVIS EVS: -0.79
RVIS percentile EVS: 12.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.625

Gene Damage Prediction

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