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Aliases for IQSEC3 Gene

Aliases for IQSEC3 Gene

  • IQ Motif And Sec7 Domain 3 2 3 5
  • KIAA1110 4

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 3) is a Protein Coding gene. Among its related pathways are Endocytosis. GO annotations related to this gene include ARF guanyl-nucleotide exchange factor activity. An important paralog of this gene is IQSEC2.

UniProtKB/Swiss-Prot for IQSEC3 Gene

  • Acts as a guanine nucleotide exchange factor (GEF) for ARF1.

Additional gene information for IQSEC3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IQSEC3 Gene

Genomics for IQSEC3 Gene

Regulatory Elements for IQSEC3 Gene

Enhancers for IQSEC3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H000163 0.7 ENCODE 25.6 +96.0 96015 0.2 MAZ ZEB2 BCL11B ZFP69B ZNF366 ZNF692 ZNF341 GLIS1 PATZ1 ZNF600 IQSEC3 ENSG00000256694 LOC574538
GH12H000188 1.6 FANTOM5 Ensembl ENCODE dbSUPER 11.1 +122.3 122264 1.9 CTCF ZNF777 RB1 ARID4B EBF1 ZIC2 RAD21 ZFHX2 GLIS2 CTBP1 IQSEC3 ENSG00000256540 GC12P000187 ENSG00000255671
GH12H000162 0.6 ENCODE 26.2 +96.3 96322 0.3 MAZ ZEB2 BCL11B ZFP69B ZNF366 ZNF692 ZNF341 PATZ1 ZNF600 PRDM1 IQSEC3 ENSG00000256694 LOC574538
GH12H000386 1.1 ENCODE 12.6 +321.7 321729 4 PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF207 CCDC77 KDM5A RAD52 ENSG00000255825 DDX11L8 ENSG00000261799 IQSEC3 ENSG00000250132 PIR47780
GH12H000144 1 ENCODE dbSUPER 13.8 +78.0 77992 3 ELF3 SAP130 MAX ZNF644 RAD21 TEAD3 ZNF316 MAFK ZNF3 TFE3 IQSEC3 ENSG00000255671 LOC101929384 SLC6A12 SLC6A13 LOC102723544 LOC574538 LOC105379613
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around IQSEC3 on UCSC Golden Path with GeneCards custom track

Promoters for IQSEC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000047492 -65 201 MXI1 REST ZBTB26

Genomic Locations for IQSEC3 Gene

Genomic Locations for IQSEC3 Gene
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.

    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

Suggested Antigen Peptide Sequences for IQSEC3 Gene

GenScript: Design optimal peptide antigens:

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 --
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:

Animal Model Products

Clone Products

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


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
plasma membrane 3
cytosol 3
nucleus 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for IQSEC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0045211 postsynaptic membrane IEA --
GO:0060077 inhibitory synapse IEA --
genes like me logo Genes that share ontologies with IQSEC3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for IQSEC3 Gene

Pathways & Interactions for IQSEC3 Gene

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

Interacting Proteins 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 --
GO:0032012 regulation of ARF protein signal transduction IEA --
GO:0043547 positive regulation of GTPase activity 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

Unigene Clusters for IQSEC3 Gene

IQ motif and Sec7 domain 3:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for IQSEC3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for IQSEC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of IQSEC3 Gene:


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(4.6)
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 33 34
  • 95.93 (n)
(Canis familiaris)
Mammalia IQSEC3 33 34
  • 89.25 (n)
(Bos Taurus)
Mammalia IQSEC3 33 34
  • 87.11 (n)
(Mus musculus)
Mammalia Iqsec3 33 16 34
  • 84.87 (n)
(Rattus norvegicus)
Mammalia Iqsec3 33
  • 84.5 (n)
(Monodelphis domestica)
Mammalia IQSEC3 34
  • 74 (a)
(Ornithorhynchus anatinus)
Mammalia IQSEC3 34
  • 49 (a)
(Gallus gallus)
Aves IQSEC3 33 34
  • 73.88 (n)
(Anolis carolinensis)
Reptilia IQSEC3 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia iqsec3 33
  • 66.6 (n)
(Danio rerio)
Actinopterygii iqsec3b 34
  • 62 (a)
LOC798516 33
  • 59.49 (n)
iqsec3a 34
  • 55 (a)
fruit fly
(Drosophila melanogaster)
Insecta siz 34
  • 25 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
Species where no ortholog for IQSEC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

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 from dbSNP and Humsavar for IQSEC3 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000167210 -- 113,955(+) ACCAG(A/G)TAATT intron-variant, upstream-variant-2KB
rs1000218657 -- 178,135(+) TGCAC(A/C)GGTGT intron-variant, nc-transcript-variant, utr-variant-3-prime
rs1000418167 -- 109,216(+) TCTGA(C/T)AAAGC intron-variant
rs1000503249 -- 177,228(+) AGGAC(A/G)GGCAG intron-variant, utr-variant-3-prime
rs1000656219 -- 175,233(+) CTGCA(A/G)ATCTG intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime

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

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

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)

Relevant External Links 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

Relevant External Links for IQSEC3

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for IQSEC3 Gene.

No data available for MalaCards , 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 60
  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 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60
  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 60

Products for IQSEC3 Gene

Sources for IQSEC3 Gene

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