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Aliases for IQSEC2 Gene

Aliases for IQSEC2 Gene

  • IQ Motif And Sec7 Domain 2 2 3 5
  • Mental Retardation, X-Linked 78 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
  • Brefeldin A Resistant Arf-Guanine Nucleotide Exchange Factor 1 3
  • Mental Retardation, X-Linked 1 (Non-Dysmorphic) 2
  • IQ Motif And SEC7 Domain-Containing Protein 2 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 mental retardation. 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 Non-Syndromic X-Linked Intellectual Disability. 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 IQSEC1.

Gene Wiki entry for IQSEC2 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for IQSEC2 Gene

Genomics for IQSEC2 Gene

Regulatory Elements for IQSEC2 Gene

Enhancers for IQSEC2 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
GH0XF053373 0.9 Ensembl ENCODE 12.7 -53.2 -53242 1.4 HDAC1 ARNT CREB3L1 PTRF GLIS2 GATA2 ZNF366 SCRT2 ZBTB11 USF2 RPSAP62 ENSG00000207408 IQSEC2 RIBC1 SMC1A ENSG00000233250 HSD17B10 PIR40105 LOC101060056
GH0XF053481 0.6 Ensembl 12.2 -160.7 -160663 0.8 CTCF KLF1 ZNF654 RAD21 OSR2 SMC3 ZNF143 PRDM10 SETDB1 ENSG00000207408 RPSAP62 IQSEC2 ENSG00000233250 HSD17B10 RIBC1 SMC1A GC0XP053462 VTRNA3-1P GC0XM053556
GH0XF053256 0.4 FANTOM5 3.6 +64.4 64425 0.5 KLF1 RFX1 GLIS1 ZIC2 KDM5C IQSEC2 FAM156A RIBC1 GC0XP053261
GH0XF053126 0.8 FANTOM5 3.2 +195.0 195035 0.4 ZNF316 ZNF211 NFE2 TRIM28 NFE2L2 FAM156A GPR173 IQSEC2 XAGE5 FAM156B TSPYL2 RNU7-37P ENSG00000235224
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around IQSEC2 on UCSC Golden Path with GeneCards custom track

Promoters for IQSEC2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001917313 850 2201 CTCF SUZ12 ZNF493 KLF17 ZIC2 HIC1 ZNF121 ZFHX2 GLIS2 POLR2A

Genomic Location for IQSEC2 Gene

53,227,454 bp from pter
53,321,350 bp from pter
93,897 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

    1478 amino acids
    Molecular mass:
    161736 Da
    Quaternary structure:
    No Data Available

    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

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 IQ domain.
  • Belongs to the BRAG family.
  • Contains 1 IQ domain.
  • Contains 1 PH domain.
  • Contains 1 SEC7 domain.
  • Belongs to the BRAG family.
genes like me logo Genes that share domains with IQSEC2: view

Function for IQSEC2 Gene

Gene Ontology (GO) - Molecular Function for IQSEC2 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 IQSEC2: view

Phenotypes for IQSEC2 Gene

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

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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

Jensen Localization Image for IQSEC2 Gene COMPARTMENTS Subcellular localization image for IQSEC2 gene
Compartment Confidence
cytosol 3
endoplasmic reticulum 1
mitochondrion 1
nucleus 1
peroxisome 1
plasma membrane 1

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:0043547 positive regulation of GTPase activity IEA --
GO:0051968 positive regulation of synaptic transmission, glutamatergic IEA --
GO:1900454 positive regulation of long term synaptic depression IEA --
genes like me logo Genes that share ontologies with IQSEC2: view

No data available for SIGNOR curated interactions for IQSEC2 Gene

Transcripts for IQSEC2 Gene

Unigene Clusters for IQSEC2 Gene

IQ motif and Sec7 domain 2:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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 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, PaxDb, 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.
genes like me logo Genes that share expression patterns with IQSEC2: view

Primer Products

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 35
  • 100 (a)
(Canis familiaris)
Mammalia IQSEC2 35
  • 98 (a)
LOC491895 34
  • 94.88 (n)
(Bos Taurus)
Mammalia IQSEC2 34 35
  • 94.67 (n)
(Mus musculus)
Mammalia Iqsec2 34 16 35
  • 92.88 (n)
(Rattus norvegicus)
Mammalia Iqsec2 34
  • 92.67 (n)
(Ornithorhynchus anatinus)
Mammalia IQSEC2 35
  • 80 (a)
(Monodelphis domestica)
Mammalia IQSEC2 35
  • 65 (a)
(Anolis carolinensis)
Reptilia IQSEC2 35
  • 72 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia iqsec2 34
  • 70.69 (n)
(Danio rerio)
Actinopterygii iqsec2 34 35
  • 67.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta siz 35
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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)

Paralogs for IQSEC2 Gene

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

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 Sequence Context AA Info Type
VAR_063742 Mental retardation, X-linked 1 (MRX1) [MIM:309530]
VAR_063743 Mental retardation, X-linked 1 (MRX1) [MIM:309530]
VAR_063744 Mental retardation, X-linked 1 (MRX1) [MIM:309530]
VAR_063745 Mental retardation, X-linked 1 (MRX1) [MIM:309530]
rs267607186 Pathogenic 53,247,131(-) GCCAG(C/T)GGTAC nc-transcript-variant, reference, missense

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)

Relevant External Links 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

(6) MalaCards diseases for IQSEC2 Gene - From: Orphanet, DISEASES, and GeneCards


  • 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}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for IQSEC2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with IQSEC2: view

No data available for Genatlas for IQSEC2 Gene

Publications for IQSEC2 Gene

  1. Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability. (PMID: 20473311) Shoubridge C. … Gecz J. (Nat. Genet. 2010) 2 3 4 64
  2. 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 Res. 1998) 2 3 4 64
  3. Novel Missense Mutation A789V in IQSEC2 Underlies X-Linked Intellectual Disability in the MRX78 Family. (PMID: 26793055) Kalscheuer V.M. … Harvey R.J. (Front Mol Neurosci 2015) 2 3 64
  4. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross M.T. … Bentley D.R. (Nature 2005) 3 4 64
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64

Products for IQSEC2 Gene

Sources for IQSEC2 Gene

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