Aliases for IQSEC3 Gene

Aliases for IQSEC3 Gene

  • IQ Motif And Sec7 Domain ArfGEF 3 2 3 5
  • IQ Motif And SEC7 Domain-Containing Protein 3 3 4
  • IQ Motif And Sec7 Domain 3 2 3
  • KIAA1110 2 4
  • MGC30156 2
  • IQSEC3 5

External Ids for IQSEC3 Gene

Previous GeneCards Identifiers for IQSEC3 Gene

  • GC12P000057
  • GC12P000176

Summaries for IQSEC3 Gene

GeneCards Summary for IQSEC3 Gene

IQSEC3 (IQ Motif And Sec7 Domain ArfGEF 3) is a Protein Coding gene. Diseases associated with IQSEC3 include Periodontosis and Temtamy Syndrome. Among its related pathways are Endocytosis. Gene Ontology (GO) annotations related to this gene include ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is IQSEC2.

UniProtKB/Swiss-Prot Summary for IQSEC3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IQSEC3 Gene

Genomics for IQSEC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for IQSEC3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J000065 Promoter/Enhancer 1.1 Ensembl ENCODE dbSUPER 600.7 -0.1 -143 1.6 IKZF1 PRDM1 REST RAD21 ZBTB26 MIER1 EHMT2 ZFHX2 SIN3A GABPB1 IQSEC3 lnc-SLC6A12-5 HSALNG0088442
GH12J000067 Enhancer 0.3 ENCODE dbSUPER 600.7 -1.1 -1117 0.2 IQSEC3 lnc-SLC6A12-5 HSALNG0088442
GH12J000386 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 12.6 +321.8 321774 4.1 SP1 CREB1 GATAD2A TEAD4 ZNF629 SIX5 IKZF1 ZNF692 POLR2A BACH1 CCDC77 KDM5A lnc-CCDC77-1 WASH8P RAD52 IQSEC3 ENSG00000261799 LOC105369594 piR-45012-097 SLC6A13
GH12J000164 Enhancer 0.9 Ensembl ENCODE dbSUPER 26.3 +97.8 97834 1.6 ZIC2 ZFHX2 ZNF223 GLIS1 KLF1 EGR2 L3MBTL2 GLIS2 ENSG00000256694 IQSEC3 SLC6A12 LOC105369592 LOC574538
GH12J000163 Enhancer 0.7 Ensembl ENCODE 26.2 +96.1 96095 1.1 ZNF692 PRDM1 PATZ1 ZNF600 ZNF341 ZBTB17 ZNF189 ZFP69B ZNF366 BCL11B IQSEC3 SLC6A12 ENSG00000256694 LOC574538
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IQSEC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IQSEC3

Top Transcription factor binding sites by QIAGEN in the IQSEC3 gene promoter:
  • Brachyury
  • Egr-4
  • Elk-1
  • FOXO3b
  • Nkx2-5
  • NRSF form 1
  • NRSF form 2
  • Pax-5

Genomic Locations for IQSEC3 Gene

Genomic Locations for IQSEC3 Gene
111,689 bases
Plus strand
111,696 bases
Plus strand

Genomic View for IQSEC3 Gene

Genes around IQSEC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IQSEC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IQSEC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IQSEC3 Gene

Proteins for IQSEC3 Gene

  • Protein details for IQSEC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    IQ motif and SEC7 domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • A6NIF2
    • A6NKV9
    • Q8TB43

    Protein attributes for IQSEC3 Gene

    1182 amino acids
    Molecular mass:
    127621 Da
    Quaternary structure:
    • Interacts with DLG1 and DLG4 (By similarity). Interacts with GPHN (By similarity).

    Alternative splice isoforms for IQSEC3 Gene


neXtProt entry for IQSEC3 Gene

Post-translational modifications for IQSEC3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for IQSEC3 Gene

Domains & Families for IQSEC3 Gene

Gene Families for IQSEC3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for IQSEC3 Gene

  • Pleckstrin-like
  • SEC7-like domain

Suggested Antigen Peptide Sequences for IQSEC3 Gene

GenScript: Design optimal peptide antigens:
  • IQ motif and SEC7 domain-containing protein 3 (IQEC3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the BRAG family.
  • Belongs to the BRAG family.
genes like me logo Genes that share domains with IQSEC3: view

Function for IQSEC3 Gene

Molecular function for IQSEC3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a guanine nucleotide exchange factor (GEF) for ARF1.

Phenotypes From GWAS Catalog for IQSEC3 Gene

Gene Ontology (GO) - Molecular Function for IQSEC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005086 ARF guanyl-nucleotide exchange factor activity IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with IQSEC3: view
genes like me logo Genes that share phenotypes with IQSEC3: view

Animal Models for IQSEC3 Gene

MGI Knock Outs for IQSEC3:
  • Iqsec3 Iqsec3<tm3b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IQSEC3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for IQSEC3 Gene

Localization for IQSEC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IQSEC3 Gene

Cytoplasm. Cell junction, synapse, postsynaptic density.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IQSEC3 gene
Compartment Confidence
cytosol 5
nucleus 4
plasma membrane 3
mitochondrion 1
endosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for IQSEC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0014069 postsynaptic density ISS --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with IQSEC3: view

Pathways & Interactions for IQSEC3 Gene

PathCards logo

SuperPathways for IQSEC3 Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with IQSEC3: view

Pathways by source for IQSEC3 Gene

1 KEGG pathway for IQSEC3 Gene

Gene Ontology (GO) - Biological Process for IQSEC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030036 actin cytoskeleton organization IBA 21873635
GO:0032012 regulation of ARF protein signal transduction IEA --
genes like me logo Genes that share ontologies with IQSEC3: view

No data available for SIGNOR curated interactions for IQSEC3 Gene

Drugs & Compounds for IQSEC3 Gene

(3) Drugs for IQSEC3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with IQSEC3: view

Transcripts for IQSEC3 Gene

mRNA/cDNA for IQSEC3 Gene

4 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IQSEC3

Alternative Splicing Database (ASD) splice patterns (SP) for IQSEC3 Gene

No ASD Table

Relevant External Links for IQSEC3 Gene

GeneLoc Exon Structure for

Expression for IQSEC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for IQSEC3 Gene

mRNA differential expression in normal tissues according to GTEx for IQSEC3 Gene

This gene is overexpressed in Brain - Cerebellum (x7.4), Brain - Cerebellar Hemisphere (x6.3), Brain - Cortex (x5.7), Brain - Frontal Cortex (BA9) (x4.7), and Brain - Anterior cingulate cortex (BA24) (x4.4).

Protein differential expression in normal tissues from HIPED for IQSEC3 Gene

This gene is overexpressed in Fetal gut (28.3), Frontal cortex (13.6), and Retina (13.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for IQSEC3 Gene

Protein tissue co-expression partners for IQSEC3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IQSEC3

SOURCE GeneReport for Unigene cluster for IQSEC3 Gene:


mRNA Expression by UniProt/SwissProt for IQSEC3 Gene:

Tissue specificity: Expressed specifically in the adult brain, predominantly in the cerebral cortex and the olfactory bulb, but not in the fetal brain. Expressed only in mature neurons, but not in undifferentiated neural stem precursor cells (NSPCs), nor in glioma cells.

Evidence on tissue expression from TISSUES for IQSEC3 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with IQSEC3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for IQSEC3 Gene

Orthologs for IQSEC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for IQSEC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia IQSEC3 30 31
  • 95.93 (n)
(Canis familiaris)
Mammalia IQSEC3 30 31
  • 89.25 (n)
(Bos Taurus)
Mammalia IQSEC3 30 31
  • 87.11 (n)
(Mus musculus)
Mammalia Iqsec3 30 17 31
  • 84.87 (n)
(Rattus norvegicus)
Mammalia Iqsec3 30
  • 84.5 (n)
(Monodelphis domestica)
Mammalia IQSEC3 31
  • 74 (a)
(Ornithorhynchus anatinus)
Mammalia IQSEC3 31
  • 49 (a)
(Gallus gallus)
Aves IQSEC3 30 31
  • 73.88 (n)
(Anolis carolinensis)
Reptilia IQSEC3 31
  • 63 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia iqsec3 30
  • 66.6 (n)
(Danio rerio)
Actinopterygii iqsec3b 31
  • 62 (a)
LOC798516 30
  • 59.49 (n)
iqsec3a 31
  • 55 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta siz 31
  • 25 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 53 (a)
Species where no ortholog for IQSEC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for IQSEC3 Gene

Gene Tree for IQSEC3 (if available)
Gene Tree for IQSEC3 (if available)
Evolutionary constrained regions (ECRs) for IQSEC3: view image

Paralogs for IQSEC3 Gene

(5) SIMAP similar genes for IQSEC3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with IQSEC3: view

Variants for IQSEC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IQSEC3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
692309 Uncertain Significance: Fetal akinesia sequence; Arthrogryposis multiplex congenita 138,421(+) T/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
692310 Uncertain Significance: Fetal akinesia sequence; Arthrogryposis multiplex congenita 175,030(+) G/A SYNONYMOUS_VARIANT
717712 Benign: not provided 138,470(+) G/A SYNONYMOUS_VARIANT
718779 Benign: not provided 138,744(+) C/T MISSENSE_VARIANT
732536 Likely Benign: not provided 67,206(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for IQSEC3 Gene

Structural Variations from Database of Genomic Variants (DGV) for IQSEC3 Gene

Variant ID Type Subtype PubMed ID
dgv1325n100 CNV gain+loss 25217958
dgv1326n100 CNV gain 25217958
dgv1327n100 CNV gain+loss 25217958
dgv1328n100 CNV gain 25217958
dgv1329n100 CNV gain 25217958
dgv1330n100 CNV gain 25217958
dgv1331n100 CNV gain 25217958
dgv2240n54 CNV loss 21841781
dgv2241n54 CNV loss 21841781
dgv241e214 CNV gain 21293372
dgv429e212 CNV loss 25503493
dgv430e212 CNV gain 25503493
dgv745n106 CNV duplication 24896259
dgv76e215 CNV deletion 23714750
dgv87n21 CNV loss 19592680
esv1788942 CNV insertion 17803354
esv1944737 CNV deletion 18987734
esv24198 CNV gain+loss 19812545
esv2445422 CNV insertion 19546169
esv2661929 CNV deletion 23128226
esv2668905 CNV deletion 23128226
esv3386480 CNV duplication 20981092
esv3580005 CNV loss 25503493
esv3628219 CNV loss 21293372
esv3628220 CNV gain 21293372
esv3628221 CNV gain 21293372
esv3628222 CNV loss 21293372
esv3628223 CNV gain 21293372
esv3628224 CNV loss 21293372
esv3628226 CNV gain 21293372
nsv1035539 CNV gain 25217958
nsv1035587 CNV gain 25217958
nsv1041720 CNV gain 25217958
nsv1045572 CNV gain 25217958
nsv1050434 CNV loss 25217958
nsv1069628 CNV deletion 25765185
nsv1070078 CNV deletion 25765185
nsv1075437 CNV duplication 25765185
nsv1076386 CNV duplication 25765185
nsv1121481 CNV deletion 24896259
nsv1121845 CNV deletion 24896259
nsv1122685 CNV deletion 24896259
nsv1130662 CNV deletion 24896259
nsv1141219 CNV deletion 24896259
nsv1151681 CNV deletion 26484159
nsv428269 CNV gain+loss 18775914
nsv468943 CNV gain 19166990
nsv468947 CNV gain 19166990
nsv470252 CNV gain 18288195
nsv556845 CNV loss 21841781
nsv556846 CNV loss 21841781
nsv556849 CNV loss 21841781
nsv556852 CNV gain 21841781
nsv556853 CNV gain 21841781
nsv556854 CNV loss 21841781
nsv556855 CNV loss 21841781
nsv556856 CNV loss 21841781
nsv556857 CNV gain 21841781
nsv567 CNV insertion 18451855
nsv568 CNV insertion 18451855
nsv821041 CNV duplication 20802225
nsv826169 CNV gain 20364138
nsv826170 CNV gain 20364138
nsv826171 CNV gain 20364138
nsv826172 CNV gain 20364138
nsv832301 CNV gain+loss 17160897
nsv832302 CNV gain 17160897
nsv952779 CNV deletion 24416366
nsv983261 CNV duplication 23825009

Variation tolerance for IQSEC3 Gene

Residual Variation Intolerance Score: 52% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.51; 77.64% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IQSEC3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for IQSEC3 Gene

Disorders for IQSEC3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for IQSEC3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
  • periodontitis, juvenile
temtamy syndrome
  • temtys
cantu syndrome
  • hypertrichotic osteochondrodysplasia
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for IQSEC3

genes like me logo Genes that share disorders with IQSEC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IQSEC3 Gene

Publications for IQSEC3 Gene

  1. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  2. Identification of a neuron-specific human gene, KIAA1110, that is a guanine nucleotide exchange factor for ARF1. (PMID: 17981261) Hattori Y … Toda M (Biochemical and biophysical research communications 2007) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. IQ Motif and SEC7 Domain-containing Protein 3 (IQSEC3) Interacts with Gephyrin to Promote Inhibitory Synapse Formation. (PMID: 27002143) Um JW … Ko J (The Journal of biological chemistry 2016) 3
  5. Genomic association analysis identifies multiple loci influencing antihypertensive response to an angiotensin II receptor blocker. (PMID: 22566498) Turner ST … Boerwinkle E (Hypertension (Dallas, Tex. : 1979) 2012) 3

Products for IQSEC3 Gene

Sources for IQSEC3 Gene