IQSEC3 Gene

Name IQ motif and Sec7 domain 3
Description Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including activation of GTPase activity; postsynapse organization; and regulation of small GTPase mediated signal transduction. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Mar 2025]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n IQSEC3 is a brain‐enriched guanine nucleotide exchange factor (GEF) for ARF GTPases that has emerged as a key orchestrator of inhibitory synapse development and function. Several studies have demonstrated that IQSEC3 localizes specifically to inhibitory (GABAergic and glycinergic) postsynaptic sites through its direct interaction with the scaffold protein gephyrin, thereby promoting the formation, maturation, and maintenance of inhibitory synapses."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " In addition, gain- and loss-of-function analyses have shown that modulation of IQSEC3’s ARF-GEF activity affects synapse density and size, ultimately impacting neuronal network excitability, seizure susceptibility, and cognitive functions, such as hippocampus-dependent fear memory formation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Furthermore, its expression is subject to activity-dependent regulation—for example, by the transcription factor Npas4 in somatostatin-expressing interneurons—highlighting an important role in adaptive synaptic plasticity."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " Moreover, genomic investigations have implicated IQSEC3 as a candidate gene in neuromuscular and neurodevelopmental phenotypes, while evolutionary analyses position it within a cytohesin-derived clade of ARF-GEFs, underscoring its specialized function in the central nervous system."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Ji Won Um, Gayoung Choii, Dongseok Park, et al. "}, {"type": "b", "children": [{"type": "t", "text": "IQ Motif and SEC7 Domain-containing Protein 3 (IQSEC3) Interacts with Gephyrin to Promote Inhibitory Synapse Formation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M115.712893"}], "href": "https://doi.org/10.1074/jbc.M115.712893"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27002143"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27002143"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Ji Won Um "}, {"type": "b", "children": [{"type": "t", "text": "Synaptic functions of the IQSEC family of ADP-ribosylation factor guanine nucleotide exchange factors."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neurosci Res (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.neures.2016.06.007"}], "href": "https://doi.org/10.1016/j.neures.2016.06.007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27369185"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27369185"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Seungjoon Kim, Hyeonho Kim, Dongseok Park, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Loss of IQSEC3 Disrupts GABAergic Synapse Maintenance and Decreases Somatostatin Expression in the Hippocampus."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2020.01.053"}], "href": "https://doi.org/10.1016/j.celrep.2020.01.053"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32049026"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32049026"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Dongwook Kim, Hyeji Jung, Yoshinori Shirai, et al. "}, {"type": "b", "children": [{"type": "t", "text": "IQSEC3 Deletion Impairs Fear Memory Through Upregulation of Ribosomal S6K1 Signaling in the Hippocampus."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biol Psychiatry (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.biopsych.2021.12.016"}], "href": "https://doi.org/10.1016/j.biopsych.2021.12.016"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35219498"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35219498"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Seungjoon Kim, Dongseok Park, Jinhu Kim, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Npas4 regulates IQSEC3 expression in hippocampal somatostatin interneurons to mediate anxiety-like behavior."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2021.109417"}], "href": "https://doi.org/10.1016/j.celrep.2021.109417"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34289353"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34289353"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Matthias Pergande, Susanne Motameny, Özkan Özdemir, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The genomic and clinical landscape of fetal akinesia."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genet Med (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41436-019-0680-1"}], "href": "https://doi.org/10.1038/s41436-019-0680-1"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31680123"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31680123"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Shweta V Pipaliya, Alexander Schlacht, Christen M Klinger, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Ancient complement and lineage-specific evolution of the Sec7 ARF GEF proteins in eukaryotes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Biol Cell (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1091/mbc.E19-01-0073"}], "href": "https://doi.org/10.1091/mbc.E19-01-0073"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31141460"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31141460"}]}]}]}
Proteins IQEC3_HUMAN
NCBI Gene ID 440073
API
Download Associations
Predicted Functions View IQSEC3's ARCHS4 Predicted Functions.
Co-expressed Genes View IQSEC3's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View IQSEC3's ARCHS4 Predicted Functions.

Functional Associations

IQSEC3 has 3,501 functional associations with biological entities spanning 9 categories (molecular profile, organism, functional term, phrase or reference, disease, phenotype or trait, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 84 datasets.

Click the + buttons to view associations for IQSEC3 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles tissues with high or low expression of IQSEC3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles tissues with high or low expression of IQSEC3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles tissues with high or low expression of IQSEC3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
BioGPS Cell Line Gene Expression Profiles cell lines with high or low expression of IQSEC3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
BioGPS Human Cell Type and Tissue Gene Expression Profiles cell types and tissues with high or low expression of IQSEC3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
CCLE Cell Line Gene CNV Profiles cell lines with high or low copy number of IQSEC3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
CCLE Cell Line Gene Expression Profiles cell lines with high or low expression of IQSEC3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
ChEA Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of IQSEC3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
ChEA Transcription Factor Targets transcription factors binding the promoter of IQSEC3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of IQSEC3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores cellular components containing IQSEC3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing IQSEC3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores cellular components co-occuring with IQSEC3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 cellular components co-occuring with IQSEC3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
COSMIC Cell Line Gene CNV Profiles cell lines with high or low copy number of IQSEC3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
COSMIC Cell Line Gene Mutation Profiles cell lines with IQSEC3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
CTD Gene-Disease Associations diseases associated with IQSEC3 gene/protein from the curated CTD Gene-Disease Associations dataset.
dbGAP Gene-Trait Associations traits associated with IQSEC3 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
DepMap CRISPR Gene Dependency cell lines with fitness changed by IQSEC3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores diseases associated with IQSEC3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores 2025 diseases associated with IQSEC3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores diseases co-occuring with IQSEC3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with IQSEC3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
ENCODE Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at IQSEC3 gene from the ENCODE Histone Modification Site Profiles dataset.
ENCODE Transcription Factor Binding Site Profiles transcription factor binding site profiles with transcription factor binding evidence at the promoter of IQSEC3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
ENCODE Transcription Factor Targets transcription factors binding the promoter of IQSEC3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
ESCAPE Omics Signatures of Genes and Proteins for Stem Cells PubMedIDs of publications reporting gene signatures containing IQSEC3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
GAD Gene-Disease Associations diseases associated with IQSEC3 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
GeneRIF Biological Term Annotations biological terms co-occuring with IQSEC3 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
GeneSigDB Published Gene Signatures PubMedIDs of publications reporting gene signatures containing IQSEC3 from the GeneSigDB Published Gene Signatures dataset.
GEO Signatures of Differentially Expressed Genes for Diseases disease perturbations changing expression of IQSEC3 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.
GEO Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of IQSEC3 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Kinase Perturbations kinase perturbations changing expression of IQSEC3 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Small Molecules small molecule perturbations changing expression of IQSEC3 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations transcription factor perturbations changing expression of IQSEC3 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset.
GEO Signatures of Differentially Expressed Genes for Viral Infections virus perturbations changing expression of IQSEC3 gene from the GEO Signatures of Differentially Expressed Genes for Viral Infections dataset.
GO Biological Process Annotations 2015 biological processes involving IQSEC3 gene from the curated GO Biological Process Annotations 2015 dataset.
GO Cellular Component Annotations 2015 cellular components containing IQSEC3 protein from the curated GO Cellular Component Annotations 2015 dataset.
GO Cellular Component Annotations 2023 cellular components containing IQSEC3 protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Cellular Component Annotations 2025 cellular components containing IQSEC3 protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2015 molecular functions performed by IQSEC3 gene from the curated GO Molecular Function Annotations 2015 dataset.
GTEx eQTL 2025 SNPs regulating expression of IQSEC3 gene from the GTEx eQTL 2025 dataset.
GTEx Tissue Gene Expression Profiles tissues with high or low expression of IQSEC3 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of IQSEC3 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GTEx Tissue Sample Gene Expression Profiles tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the GTEx Tissue Sample Gene Expression Profiles dataset.
GTEx Tissue-Specific Aging Signatures tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset.
GWAS Catalog SNP-Phenotype Associations phenotypes associated with IQSEC3 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations dataset.
GWASdb SNP-Disease Associations diseases associated with IQSEC3 gene in GWAS and other genetic association datasets from the GWASdb SNP-Disease Associations dataset.
GWASdb SNP-Phenotype Associations phenotypes associated with IQSEC3 gene in GWAS datasets from the GWASdb SNP-Phenotype Associations dataset.
Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles cell lines with high or low expression of IQSEC3 gene relative to other cell lines from the Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles dataset.
HMDB Metabolites of Enzymes interacting metabolites for IQSEC3 protein from the curated HMDB Metabolites of Enzymes dataset.
HPA Cell Line Gene Expression Profiles cell lines with high or low expression of IQSEC3 gene relative to other cell lines from the HPA Cell Line Gene Expression Profiles dataset.
HPA Tissue Gene Expression Profiles tissues with high or low expression of IQSEC3 gene relative to other tissues from the HPA Tissue Gene Expression Profiles dataset.
HPA Tissue Sample Gene Expression Profiles tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the HPA Tissue Sample Gene Expression Profiles dataset.
IMPC Knockout Mouse Phenotypes phenotypes of mice caused by IQSEC3 gene knockout from the IMPC Knockout Mouse Phenotypes dataset.
InterPro Predicted Protein Domain Annotations protein domains predicted for IQSEC3 protein from the InterPro Predicted Protein Domain Annotations dataset.
JASPAR Predicted Transcription Factor Targets transcription factors regulating expression of IQSEC3 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset.
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles cell lines with high or low copy number of IQSEC3 gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset.
KnockTF Gene Expression Profiles with Transcription Factor Perturbations transcription factor perturbations changing expression of IQSEC3 gene from the KnockTF Gene Expression Profiles with Transcription Factor Perturbations dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of IQSEC3 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
LOCATE Predicted Protein Localization Annotations cellular components predicted to contain IQSEC3 protein from the LOCATE Predicted Protein Localization Annotations dataset.
MGI Mouse Phenotype Associations 2023 phenotypes of transgenic mice caused by IQSEC3 gene mutations from the MGI Mouse Phenotype Associations 2023 dataset.
MotifMap Predicted Transcription Factor Targets transcription factors regulating expression of IQSEC3 gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset.
MoTrPAC Rat Endurance Exercise Training tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the MoTrPAC Rat Endurance Exercise Training dataset.
NIBR DRUG-seq U2OS MoA Box Gene Expression Profiles drug perturbations changing expression of IQSEC3 gene from the NIBR DRUG-seq U2OS MoA Box dataset.
PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations gene perturbations changing expression of IQSEC3 gene from the PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
PerturbAtlas Signatures of Differentially Expressed Genes for Mouse Gene Perturbations gene perturbations changing expression of IQSEC3 gene from the PerturbAtlas Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
Reactome Pathways 2024 pathways involving IQSEC3 protein from the Reactome Pathways 2024 dataset.
Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles cell types and tissues with high or low DNA methylation of IQSEC3 gene relative to other cell types and tissues from the Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles dataset.
Roadmap Epigenomics Histone Modification Site Profiles histone modification site profiles with high histone modification abundance at IQSEC3 gene from the Roadmap Epigenomics Histone Modification Site Profiles dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of IQSEC3 gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of IQSEC3 gene from the RummaGEO Gene Perturbation Signatures dataset.
SynGO Synaptic Gene Annotations synaptic terms associated with IQSEC3 gene from the SynGO Synaptic Gene Annotations dataset.
TargetScan Predicted Conserved microRNA Targets microRNAs regulating expression of IQSEC3 gene predicted using conserved miRNA seed sequences from the TargetScan Predicted Conserved microRNA Targets dataset.
TargetScan Predicted Nonconserved microRNA Targets microRNAs regulating expression of IQSEC3 gene predicted using nonconserved miRNA seed sequences from the TargetScan Predicted Nonconserved microRNA Targets dataset.
TCGA Signatures of Differentially Expressed Genes for Tumors tissue samples with high or low expression of IQSEC3 gene relative to other tissue samples from the TCGA Signatures of Differentially Expressed Genes for Tumors dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores tissues with high expression of IQSEC3 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of IQSEC3 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores tissues with high expression of IQSEC3 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 tissues with high expression of IQSEC3 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores tissues co-occuring with IQSEC3 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 tissues co-occuring with IQSEC3 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.