IQGAP2

IQ motif containing GTPase activating protein 2, the group of IQ motif containing GTPase activating protein family

Basic information

Region (hg38): 5:76403285-76708132

Links

ENSG00000145703 ∙ NCBI:10788 ∙ OMIM:605401 ∙ HGNC:6111 ∙ Uniprot:Q13576 ∙ 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 IQGAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQGAP2 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				1	5	6
missense			84	2	6	92
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23	1		24
Total	0	0	108	4	11

Variants in IQGAP2

This is a list of pathogenic ClinVar variants found in the IQGAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-76403565-C-A		not specified	Uncertain significance (Jun 29, 2023)
5-76403579-C-A			Benign (Apr 16, 2018)
5-76461580-C-T			Likely benign (Feb 12, 2018)
5-76461582-A-T		not specified	Uncertain significance (Mar 25, 2024)
5-76461612-A-G		not specified	Uncertain significance (Jul 12, 2023)
5-76461620-C-T		not specified	Uncertain significance (May 15, 2024)
5-76461638-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-76461639-A-T		not specified	Uncertain significance (May 10, 2024)
5-76562422-A-T		not specified	Uncertain significance (Jul 25, 2023)
5-76562437-C-T		not specified	Uncertain significance (Jul 17, 2023)
5-76562458-G-A		not specified	Uncertain significance (Jan 10, 2023)
5-76562470-A-T		not specified	Uncertain significance (Sep 23, 2023)
5-76562518-A-T		not specified	Uncertain significance (Jul 13, 2022)
5-76562544-C-T		not specified	Uncertain significance (Jan 11, 2023)
5-76570598-C-T		not specified	Uncertain significance (Nov 06, 2015)
5-76570605-C-T		not specified	Uncertain significance (Oct 27, 2021)
5-76570616-G-A		not specified	Uncertain significance (Nov 10, 2021)
5-76570634-A-C		not specified	Uncertain significance (Oct 24, 2023)
5-76575702-C-G		not specified	Uncertain significance (Aug 13, 2021)
5-76575730-A-G		not specified	Uncertain significance (Oct 27, 2021)
5-76588909-G-A			Benign (Oct 11, 2018)
5-76588914-T-A		not specified	Uncertain significance (Dec 14, 2023)
5-76588934-C-A		not specified	Uncertain significance (Dec 08, 2023)
5-76588940-A-G		not specified	Uncertain significance (Sep 01, 2021)
5-76590438-C-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQGAP2	protein_coding	protein_coding	ENST00000274364	36	304884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.50e-27	0.993	125474	0	274	125748	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	718	815	0.881	0.0000423	10359
Missense in Polyphen		239	288.46	0.82853		3587
Synonymous	0.362	302	310	0.974	0.0000173	2889
Loss of Function	3.16	56	88.0	0.636	0.00000455	1123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00158	0.00157
Ashkenazi Jewish	0.00617	0.00617
East Asian	0.00152	0.00152
Finnish	0.000878	0.000878
European (Non-Finnish)	0.000809	0.000800
Middle Eastern	0.00152	0.00152
South Asian	0.000611	0.000588
Other	0.00199	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to activated CDC42 and RAC1 but does not seem to stimulate their GTPase activity. Associates with calmodulin.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);G13 Signaling Pathway;Neutrophil degranulation;Signal Transduction;Innate Immune System;Immune System;RHO GTPases activate IQGAPs;RHO GTPase Effectors;Signaling by Rho GTPases;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.252

Intolerance Scores

• loftool: 0.492
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.06

Haploinsufficiency Scores

• pHI: 0.560
• hipred: Y
• hipred_score: 0.706
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.785

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Iqgap2
• Phenotype: liver/biliary system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: iqgap2
• Affected structure: glomerular basement membrane
• Phenotype tag: abnormal
• Phenotype quality: increased width

Gene ontology

• Biological process: signal transduction;negative regulation of GTPase activity;Arp2/3 complex-mediated actin nucleation;neutrophil degranulation;thrombin-activated receptor signaling pathway
• Cellular component: cytoplasm;cytosol;plasma membrane;microvillus;cell surface;actin cytoskeleton;lamellipodium;filopodium;secretory granule membrane;extracellular exosome
• Molecular function: actin binding;GTPase inhibitor activity;calmodulin binding;phosphatidylinositol-3,4,5-trisphosphate binding;Rho GTPase binding;Rac GTPase binding;actin filament binding;Arp2/3 complex binding