IQGAP3

protein-coding

IQ motif containing GTPase activating protein 3, the group of IQ motif containing GTPase activating protein family

Gene summary

Enables calmodulin binding activity and myosin VI light chain binding activity. Predicted to be involved in mitotic actomyosin contractile ring assembly actin filament organization. Predicted to act upstream of or within several processes, including G1/S transition of mitotic cell cycle; intracellular signaling cassette; and regulation of gene expression. Predicted to be located in cytosol. Predicted to be active in cell cortex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_178229.5

Inheritance

ClinVar variants

U:276B:45

Top phenotype

IQGAP3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr1:156,525,405-156,572,604

External References & Databases

Ensembl (ENSG00000183856)

Transcript & Mutation Effects

hg38 • Region Span ~47.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hereditary peripheral neuropathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0020127

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IQGAP3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 252

IQGAP3-related disorderTotal: 34

not providedTotal: 22

Motor and sensory neuropathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178229.5. 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	17 clinvar	3 clinvar	25
missense			254 clinvar	19 clinvar	6 clinvar	279
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	0	276	36	9	321

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178229.5	RefSeq	NP_839943.3	38	MANE Select
ENST00000361170.7	Ensembl	ENSP00000354451.2	38	MANE Select
ENST00000491900.1	Ensembl	ENSP00000436603.1	36	Standard
ENST00000862862.1	Ensembl	ENSP00000532921.1	38	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
iqgap3	Danio rerio	Structure: trunk Quality: truncated abnormal

Gene / Model

Organism

Observed Phenotype

iqgap3

Danio rerio

Structure: trunk

Quality: truncated

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of actin cytoskeleton - Homo sapiens (human)
miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
Signal Transduction
RHO GTPases activate IQGAPs

Biological Process

G1/S transition of mitotic cell cycle
activation of MAPK activity
Ras protein signal transduction
regulation of cell size
positive regulation of gene expression

Molecular Function

calmodulin binding
Rho GTPase binding
myosin VI light chain binding

Cellular Component

cytosol
cell-cell junction
lateral plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361170
Coding exons: 38
Length: 47200
Individuals with no LoFs: 125049
Homozygous LoFs: 1
Heterozygous LoFs: 698
Defined: 125748
p: 0.00278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.642	869	924	0.941	0.0000543	10560
Missense (PolyPhen)		287	317.21	0.90477		3688
Synonymous	1.71	328	370	0.887	0.0000205	3261
Loss of Function	2.81	67	96.8	0.692	0.00000563	988

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.0016	0.0016	notable
Ashkenazi Jewish	0.0044	0.0044	notable
East Asian	0.0016	0.0016	notable
Finnish	0.0032	0.0032	notable
European (Non-Finnish)	0.0035	0.0034	notable
South Asian	0.0023	0.0023	notable
Other	0.0031	0.0031	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.220

Intolerance Scores

LoFtool: 0.641
RVIS EVS: -0.38
RVIS percentile EVS: 28.02

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.888

Gene Damage Prediction

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