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Aliases for IQSEC2 Gene

Aliases for IQSEC2 Gene

  • IQ Motif And Sec7 Domain 2 2 3 5
  • Brefeldin A Resistant Arf-Guanine Nucleotide Exchange Factor 1 2 3
  • Mental Retardation, X-Linked 18 2 3
  • Brefeldin A Resistant Arf-Guanine Nucleotide Exchange Factor 1b 3
  • Brefeldin A Resistant Arf-Guanine Nucleotide Exchange Factor 1c 3
  • Mental Retardation, X-Linked 1 (Non-Dysmorphic) 2
  • IQ Motif And SEC7 Domain-Containing Protein 2 3
  • Mental Retardation, X-Linked 78 2
  • IQ-ArfGEF 3
  • KIAA0522 4
  • BRAG1 3
  • MRX18 3
  • MRX78 3
  • MRX1 3

External Ids for IQSEC2 Gene

Previous HGNC Symbols for IQSEC2 Gene

  • MRX1
  • MRX78
  • MRX18

Previous GeneCards Identifiers for IQSEC2 Gene

  • GC0XM053146
  • GC0XM050327

Summaries for IQSEC2 Gene

Entrez Gene Summary for IQSEC2 Gene

  • This gene encodes a guanine nucleotide exchange factor for the ARF family of small GTP-binding proteins. The encoded protein is a component of the postsynaptic density at excitatory synapses, and may play a critical role in cytoskeletal and synaptic organization through the activation of selected ARF substrates including ARF1 and ARF6. Mutations in this gene have been implicated in nonsyndromic X-linked cognitive disability. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2011]

GeneCards Summary for IQSEC2 Gene

IQSEC2 (IQ Motif And Sec7 Domain 2) is a Protein Coding gene. Diseases associated with IQSEC2 include Severe Intellectual Disability-Progressive Postnatal Microcephaly-Midline Stereotypic Hand Movements Syndrome and X-Linked Non-Specific Intellectual Disability. 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 IQSEC1.

UniProtKB/Swiss-Prot for IQSEC2 Gene

  • Is a guanine nucleotide exchange factor for the ARF GTP-binding proteins.

Gene Wiki entry for IQSEC2 Gene

Additional gene information for IQSEC2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IQSEC2 Gene

Genomics for IQSEC2 Gene

GeneHancer (GH) Regulatory Elements for IQSEC2 Gene

Promoters and enhancers for IQSEC2 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
GH0XJ053279 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.3 +40.3 40266 3.7 HDGF GLI4 ZNF121 GLIS2 ZFP91 ATF7 ZNF263 SP3 REST ZNF610 IQSEC2 FAM156B ACTG1P10 KDM5C KANTR ENSG00000233250 PHF8 KDM5C-IT1 HUWE1 TSPYL2
GH0XJ053320 Promoter 1.5 EPDnew Ensembl 650.7 +0.6 649 1.8 CTCF ZNF777 SUZ12 ZNF493 KLF17 ZIC2 HIC1 ZNF335 ZNF121 ZFHX2 IQSEC2 TSPYL2 KANTR GC0XP053261
GH0XJ053374 Enhancer 1.1 Ensembl ENCODE 12.7 -53.3 -53319 1.3 HDGF ATF1 ARNT TCF12 GLIS2 GATA2 ATF7 CAVIN1 NCOA1 ZNF592 ENSG00000207408 IQSEC2 RPSAP62 RIBC1 SMC1A ENSG00000233250 HSD17B10 PIR40105 LOC101060056
GH0XJ052933 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.1 +386.4 386411 2.1 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 YY1 POLR2B ZNF213 E2F8 ACTG1P10 FAM156B KDM5C SSXP5 SSX7 RPSAP62 XAGE1B XAGE1A ENSG00000233250 SMC1A
GH0XJ053440 Enhancer 1.3 FANTOM5 Ensembl ENCODE 1.7 -120.0 -119951 2.6 ARID4B KLF17 SIN3A ZNF335 GLIS2 SCRT2 ZNF416 RCOR1 FOS KLF13 HSD17B10 HUWE1 KANTR ACTG1P10 FAM156B IQSEC2 KDM5C TSPYL2 FAM156A GC0XM053456
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IQSEC2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the IQSEC2 gene promoter:
  • Nkx2-5
  • POU2F1a
  • POU2F1
  • CP2
  • HEN1
  • NF-1
  • NF-1/L
  • AREB6
  • Pax-4a

Genomic Locations for IQSEC2 Gene

Genomic Locations for IQSEC2 Gene
95,523 bases
Minus strand
88,465 bases
Minus strand

Genomic View for IQSEC2 Gene

Genes around IQSEC2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IQSEC2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IQSEC2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IQSEC2 Gene

Proteins for IQSEC2 Gene

  • Protein details for IQSEC2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    IQ motif and SEC7 domain-containing protein 2
    Protein Accession:
    Secondary Accessions:
    • B3KT97
    • C7SDG1
    • O60275
    • Q5JUX1

    Protein attributes for IQSEC2 Gene

    1488 amino acids
    Molecular mass:
    162784 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA25448.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAA25448.1; Type=Frameshift; Positions=1468; Evidence={ECO:0000305}; Sequence=CAI42091.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for IQSEC2 Gene

    Alternative splice isoforms for IQSEC2 Gene


neXtProt entry for IQSEC2 Gene

Post-translational modifications for IQSEC2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for IQSEC2 Gene

Domains & Families for IQSEC2 Gene

Gene Families for IQSEC2 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for IQSEC2 Gene

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 IQSEC2: view

Function for IQSEC2 Gene

Molecular function for IQSEC2 Gene

UniProtKB/Swiss-Prot Function:
Is a guanine nucleotide exchange factor for the ARF GTP-binding proteins.

Gene Ontology (GO) - Molecular Function for IQSEC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005086 ARF guanyl-nucleotide exchange factor activity IMP 26793055
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with IQSEC2: view
genes like me logo Genes that share phenotypes with IQSEC2: view

Human Phenotype Ontology for IQSEC2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for IQSEC2 Gene

Localization for IQSEC2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for IQSEC2 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 IQSEC2 gene
Compartment Confidence
cytosol 3
plasma membrane 1
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for IQSEC2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with IQSEC2: view

Pathways & Interactions for IQSEC2 Gene

SuperPathways for IQSEC2 Gene

SuperPathway Contained pathways
1 Endocytosis
genes like me logo Genes that share pathways with IQSEC2: view

Pathways by source for IQSEC2 Gene

1 KEGG pathway for IQSEC2 Gene

Gene Ontology (GO) - Biological Process for IQSEC2 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:0065009 regulation of molecular function IEA --
genes like me logo Genes that share ontologies with IQSEC2: view

No data available for SIGNOR curated interactions for IQSEC2 Gene

Drugs & Compounds for IQSEC2 Gene

No Compound Related Data Available

Transcripts for IQSEC2 Gene

mRNA/cDNA for IQSEC2 Gene

Unigene Clusters for IQSEC2 Gene

IQ motif and Sec7 domain 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for IQSEC2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8
SP1: - -
SP3: -

Relevant External Links for IQSEC2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for IQSEC2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for IQSEC2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for IQSEC2 Gene

This gene is overexpressed in Brain - Cortex (x4.4).

Protein differential expression in normal tissues from HIPED for IQSEC2 Gene

This gene is overexpressed in Brain (12.7), Breast (10.5), Peripheral blood mononuclear cells (10.0), Urine (8.7), Cervix (8.2), Platelet (8.1), and Frontal cortex (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for IQSEC2 Gene

NURSA nuclear receptor signaling pathways regulating expression of IQSEC2 Gene:


SOURCE GeneReport for Unigene cluster for IQSEC2 Gene:


mRNA Expression by UniProt/SwissProt for IQSEC2 Gene:

Tissue specificity: Expressed in brain, kidney and small intestine. Weakly expressed in placenta, pancreas, ovary, prostate and liver.

Evidence on tissue expression from TISSUES for IQSEC2 Gene

  • Nervous system(4.4)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for IQSEC2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • salivary gland
  • skull
  • tooth
  • lung
  • rib
  • rib cage
  • pelvis
  • testicle
  • urinary bladder
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with IQSEC2: view

No data available for Protein tissue co-expression partners for IQSEC2 Gene

Orthologs for IQSEC2 Gene

This gene was present in the common ancestor of animals.

Orthologs for IQSEC2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia IQSEC2 34
  • 100 (a)
(Canis familiaris)
Mammalia IQSEC2 34
  • 98 (a)
LOC491895 33
  • 94.88 (n)
(Bos Taurus)
Mammalia IQSEC2 34 33
  • 94.67 (n)
(Mus musculus)
Mammalia Iqsec2 16 34 33
  • 92.88 (n)
(Rattus norvegicus)
Mammalia Iqsec2 33
  • 92.67 (n)
(Ornithorhynchus anatinus)
Mammalia IQSEC2 34
  • 80 (a)
(Monodelphis domestica)
Mammalia IQSEC2 34
  • 65 (a)
(Anolis carolinensis)
Reptilia IQSEC2 34
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia iqsec2 33
  • 70.69 (n)
(Danio rerio)
Actinopterygii iqsec2 34 33
  • 67.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta siz 34
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
Species where no ortholog for IQSEC2 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)
  • chicken (Gallus gallus)
  • 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 IQSEC2 Gene

Gene Tree for IQSEC2 (if available)
Gene Tree for IQSEC2 (if available)
Evolutionary constrained regions (ECRs) for IQSEC2: view image

Paralogs for IQSEC2 Gene

(4) SIMAP similar genes for IQSEC2 Gene using alignment to 2 proteins:

  • L8E757_HUMAN
genes like me logo Genes that share paralogs with IQSEC2: view

Variants for IQSEC2 Gene

Sequence variations from dbSNP and Humsavar for IQSEC2 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1037744173 uncertain-significance, Mental retardation, X-linked 1 53,320,481(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1057518993 likely-pathogenic, Autism, Severe intellectual deficiency 53,243,367(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs1057519497 uncertain-significance, Specific learning disability 53,320,525(-) C/G coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1057520858 pathogenic, not provided, Mental retardation, X-linked 1 53,243,445(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs1057521782 likely-benign, not specified, Mental retardation, X-linked 1 53,234,480(-) C/T 3_prime_UTR_variant, coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for IQSEC2 Gene

Variant ID Type Subtype PubMed ID
esv2740175 CNV deletion 23290073
nsv435891 CNV deletion 17901297
nsv472494 CNV novel sequence insertion 20440878

Variation tolerance for IQSEC2 Gene

Residual Variation Intolerance Score: 3.99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.83; 34.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IQSEC2 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 IQSEC2 Gene

Disorders for IQSEC2 Gene

MalaCards: The human disease database

(11) MalaCards diseases for IQSEC2 Gene - From: HGMD, ClinVar, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
severe intellectual disability-progressive postnatal microcephaly-midline stereotypic hand movements syndrome
  • iqsec2-related syndromic intellectual disability
x-linked non-specific intellectual disability
  • x-linked non-syndromic intellectual disability
alacrima, achalasia, and mental retardation syndrome
  • aamr
  • iqsec2-related epilepsy
chromosome xp11.23-p11.22 duplication syndrome
  • microduplication xp11.22-p11.23 syndrome
- elite association - COSMIC cancer census association via MalaCards


  • Mental retardation, X-linked 1 (MRX1) [MIM:309530]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269 PubMed:20473311, ECO:0000269 PubMed:26793055}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for IQSEC2

genes like me logo Genes that share disorders with IQSEC2: view

No data available for Genatlas for IQSEC2 Gene

Publications for IQSEC2 Gene

  1. Novel Missense Mutation A789V in IQSEC2 Underlies X-Linked Intellectual Disability in the MRX78 Family. (PMID: 26793055) Kalscheuer VM … Harvey RJ (Frontiers in molecular neuroscience 2015) 2 3 4 58
  2. Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability. (PMID: 20473311) Shoubridge C … Gécz J (Nature genetics 2010) 2 3 4 58
  3. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  4. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for IQSEC2 Gene

Sources for IQSEC2 Gene

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