IQGAP3

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

Basic information

Region (hg38): 1:156525405-156572604

Links

ENSG00000183856 ∙ NCBI:128239 ∙ ∙ HGNC:20669 ∙ Uniprot:Q86VI3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IQGAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQGAP3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	1	5
missense			135	9	3	147
nonsense			2			2
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	138	13	4

Variants in IQGAP3

This is a list of pathogenic ClinVar variants found in the IQGAP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-156526493-C-T		not specified	Uncertain significance (Mar 03, 2022)
1-156526506-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-156526526-A-G		not specified	Uncertain significance (Jan 03, 2024)
1-156526541-T-A		not specified	Uncertain significance (Jan 08, 2024)
1-156526547-T-A		not specified	Uncertain significance (Aug 13, 2021)
1-156526548-T-C		not specified	Uncertain significance (Dec 11, 2024)
1-156526580-T-C		not specified	Uncertain significance (May 30, 2024)
1-156527972-G-A			Uncertain significance (Apr 08, 2021)
1-156527978-T-C		not specified	Uncertain significance (Nov 08, 2022)
1-156528031-G-A		not specified	Uncertain significance (May 03, 2023)
1-156528034-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-156528515-G-T		not specified	Uncertain significance (Dec 06, 2022)
1-156528516-C-G		not specified	Uncertain significance (Mar 13, 2023)
1-156528522-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-156528538-C-G			Uncertain significance (Dec 01, 2022)
1-156528593-T-C		not specified	Uncertain significance (Jun 05, 2024)
1-156528597-C-A		not specified	Uncertain significance (Sep 27, 2024)
1-156528924-G-A		IQGAP3-related disorder	Likely benign (Mar 04, 2019)
1-156528950-G-A		not specified	Uncertain significance (Jun 01, 2023)
1-156528952-A-G		not specified	Uncertain significance (Sep 27, 2022)
1-156528973-C-T		not specified	Uncertain significance (May 27, 2022)
1-156528976-T-A		not specified	Uncertain significance (Dec 01, 2023)
1-156528985-T-C		not specified	Uncertain significance (Mar 03, 2022)
1-156529016-A-C		not specified	Uncertain significance (Sep 16, 2021)
1-156529075-C-T		not specified	Uncertain significance (Dec 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQGAP3	protein_coding	protein_coding	ENST00000361170	38	47200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.40e-33	0.774	125049	1	698	125748	0.00278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.642	869	924	0.941	0.0000543	10560
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00295	0.00295
Ashkenazi Jewish	0.00444	0.00437
East Asian	0.00158	0.00158
Finnish	0.00324	0.00324
European (Non-Finnish)	0.00347	0.00344
Middle Eastern	0.00158	0.00158
South Asian	0.00226	0.00226
Other	0.00311	0.00310

dbNSFP

Source: dbNSFP

• Pathway: 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;RHO GTPase Effectors;Signaling by Rho GTPases;RAC1 signaling pathway;CDC42 signaling events (Consensus)

Recessive Scores

• pRec: 0.220

Intolerance Scores

• loftool: 0.641
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.02

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.492
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Iqgap3

Zebrafish Information Network

• Gene name: iqgap3
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: truncated

Gene ontology

• 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;negative regulation of gene expression;positive regulation of mammary gland epithelial cell proliferation;regulation of GTPase activity;ERK1 and ERK2 cascade;cellular response to organic substance
• Cellular component: cytosol;cell-cell junction;lateral plasma membrane
• Molecular function: calmodulin binding;Rho GTPase binding;myosin VI light chain binding