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Aliases for AFF2 Gene

Aliases for AFF2 Gene

  • AF4/FMR2 Family Member 2 2 3 3 5
  • Fragile X E Mental Retardation Syndrome Protein 3 4
  • Fragile X Mental Retardation 2 Protein 3 4
  • Protein FMR-2 3 4
  • FMR2P 3 4
  • FMR2 3 4
  • OX19 3 4
  • Fragile X Mental Retardation 2 2
  • AF4/FMR2 Family, Member 2 2
  • Protein Ox19 4
  • FRAXE 3
  • MRX2 3

External Ids for AFF2 Gene

Previous HGNC Symbols for AFF2 Gene

  • FMR2

Previous GeneCards Identifiers for AFF2 Gene

  • GC0XP147288
  • GC0XP147389
  • GC0XP147582
  • GC0XP136538

Summaries for AFF2 Gene

Entrez Gene Summary for AFF2 Gene

  • This gene encodes a putative transcriptional activator that is a member of the AF4\FMR2 gene family. This gene is associated with the folate-sensitive fragile X E locus on chromosome X. A repeat polymorphism in the fragile X E locus results in silencing of this gene causing Fragile X E syndrome. Fragile X E syndrome is a form of nonsyndromic X-linked cognitive disability. In addition, this gene contains 6-25 GCC repeats that are expanded to >200 repeats in the disease state. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jul 2016]

GeneCards Summary for AFF2 Gene

AFF2 (AF4/FMR2 Family Member 2) is a Protein Coding gene. Diseases associated with AFF2 include Mental Retardation, X-Linked, Associated With Fragile Site Fraxe and Fragile X Syndrome. Gene Ontology (GO) annotations related to this gene include G-quadruplex RNA binding. An important paralog of this gene is AFF3.

UniProtKB/Swiss-Prot for AFF2 Gene

  • RNA-binding protein. Might be involved in alternative splicing regulation through an interaction with G-quartet RNA structure.

Gene Wiki entry for AFF2 Gene

Additional gene information for AFF2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AFF2 Gene

Genomics for AFF2 Gene

GeneHancer (GH) Regulatory Elements for AFF2 Gene

Promoters and enhancers for AFF2 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
GH0XJ148500 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 650.7 +0.5 482 1.8 ZNF398 ZBTB8A ZNF335 ZFHX2 GLIS2 ZBTB48 GLIS1 ZNF341 ZBTB26 ZBTB17 AFF2 ENSG00000237741 AFF2-IT1
GH0XJ148371 Promoter/Enhancer 0.7 EPDnew ENCODE 650.1 -129.2 -129195 0.2 AFF2 PIR37036 RPL7L1P11
GH0XJ148310 Enhancer 0.8 ENCODE dbSUPER 6.4 -189.6 -189590 2 MAX JUNB BATF GABPA POLR2A ETV6 RUNX3 MYC AFF2 PIR32877 PIR52149 PIR52150 GC0XP148356 GC0XP148357 GC0XP148358 GC0XP148359 GC0XP148360 GC0XP148362
GH0XJ148379 Enhancer 0.9 Ensembl ENCODE 4.4 -119.4 -119381 2.9 PKNOX1 BATF RELA ZNF143 ZNF207 ATF7 IKZF2 CREM RUNX3 SMARCA5 AFF2 PIR37036 RPL7L1P11
GH0XJ148198 Promoter 0.5 Ensembl 6.1 -301.8 -301818 0.4 GC0XM148198 LOC100129661 AFF2 GC0XM148184
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around AFF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the AFF2 gene promoter:
  • Nkx2-5
  • POU2F1a
  • POU2F1
  • Elk-1
  • HTF
  • S8
  • Nkx3-1 v1
  • Nkx3-1
  • Nkx3-1 v2
  • Nkx3-1 v3

Genomic Locations for AFF2 Gene

Genomic Locations for AFF2 Gene
500,045 bases
Plus strand
500,055 bases
Plus strand

Genomic View for AFF2 Gene

Genes around AFF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AFF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AFF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AFF2 Gene

Proteins for AFF2 Gene

  • Protein details for AFF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    AF4/FMR2 family member 2
    Protein Accession:
    Secondary Accessions:
    • A2RTY4
    • B4DXD5
    • B7WNQ1
    • B7ZLD6
    • B7ZLD9
    • O43786
    • O60215
    • P78407
    • Q13521
    • Q14323
    • Q7Z2F7
    • Q7Z400
    • Q9UNA5

    Protein attributes for AFF2 Gene

    1311 amino acids
    Molecular mass:
    144771 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for AFF2 Gene

neXtProt entry for AFF2 Gene

Post-translational modifications for AFF2 Gene

  • Ubiquitination at Lys404
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for AFF2 Gene

Domains & Families for AFF2 Gene

Gene Families for AFF2 Gene

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

Protein Domains for AFF2 Gene


Suggested Antigen Peptide Sequences for AFF2 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the AF4 family.
  • Belongs to the AF4 family.
genes like me logo Genes that share domains with AFF2: view

Function for AFF2 Gene

Molecular function for AFF2 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding protein. Might be involved in alternative splicing regulation through an interaction with G-quartet RNA structure.

Phenotypes From GWAS Catalog for AFF2 Gene

Gene Ontology (GO) - Molecular Function for AFF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002151 G-quadruplex RNA binding ISS --
GO:0003690 NOT double-stranded DNA binding IBA --
GO:0003700 NOT DNA binding transcription factor activity IBA --
GO:0003723 RNA binding IEA --
genes like me logo Genes that share ontologies with AFF2: view

Phenotypes for AFF2 Gene

genes like me logo Genes that share phenotypes with AFF2: view

Human Phenotype Ontology for AFF2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for AFF2 Gene

miRTarBase miRNAs that target AFF2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AFF2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for AFF2 Gene

Localization for AFF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AFF2 Gene

Nucleus speckle. Note=When splicing is inhibited, accumulates in enlarged speckles.

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 AFF2 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for AFF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IEA --
GO:0008023 NOT transcription elongation factor complex IBA --
GO:0016607 nuclear speck IEA,IDA 19136466
GO:0032783 NOT ELL-EAF complex IBA --
genes like me logo Genes that share ontologies with AFF2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for AFF2 Gene

Pathways & Interactions for AFF2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for AFF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006397 mRNA processing IEA --
GO:0007420 brain development TAS 8673086
GO:0007611 learning or memory IEA --
GO:0008380 RNA splicing IEA --
GO:0010468 regulation of gene expression IMP 23562910
genes like me logo Genes that share ontologies with AFF2: view

No data available for Pathways by source and SIGNOR curated interactions for AFF2 Gene

Drugs & Compounds for AFF2 Gene

(1) Drugs for AFF2 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with AFF2: view

Transcripts for AFF2 Gene

Unigene Clusters for AFF2 Gene

AF4/FMR2 family, member 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for AFF2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for AFF2 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1: -
SP2: - - -
SP3: - - -

Relevant External Links for AFF2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for AFF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AFF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for AFF2 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x6.9), Brain - Cerebellum (x4.9), and Pituitary (x4.3).

Protein differential expression in normal tissues from HIPED for AFF2 Gene

This gene is overexpressed in Lung (51.0) and Heart (18.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for AFF2 Gene

Protein tissue co-expression partners for AFF2 Gene

NURSA nuclear receptor signaling pathways regulating expression of AFF2 Gene:


SOURCE GeneReport for Unigene cluster for AFF2 Gene:


mRNA Expression by UniProt/SwissProt for AFF2 Gene:

Tissue specificity: Brain (most abundant in hippocampus and amygdala), placenta and lung.

Evidence on tissue expression from TISSUES for AFF2 Gene

  • Nervous system(4.6)
  • Spleen(2.1)
  • Blood(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for AFF2 Gene

Germ Layers:
  • ectoderm
  • integumentary
  • nervous
  • skeleton
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • head
  • nose
  • skull
  • skin
genes like me logo Genes that share expression patterns with AFF2: view

Orthologs for AFF2 Gene

This gene was present in the common ancestor of animals.

Orthologs for AFF2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia AFF2 34
  • 97 (a)
(Canis familiaris)
Mammalia AFF2 34
  • 90 (a)
(Mus musculus)
Mammalia Aff2 34
  • 89 (a)
(Bos Taurus)
Mammalia AFF2 34
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 60 (a)
-- 34
  • 60 (a)
(Monodelphis domestica)
Mammalia AFF2 34
  • 52 (a)
(Gallus gallus)
Aves AFF2 34 33
  • 68.7 (n)
(Anolis carolinensis)
Reptilia AFF2 34
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia aff2 33
  • 64.83 (n)
(Danio rerio)
Actinopterygii LOC100330019 33
  • 61.63 (n)
aff2 34
  • 52 (a)
fruit fly
(Drosophila melanogaster)
Insecta lilli 34
  • 15 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4989 34
  • 16 (a)
Species where no ortholog for AFF2 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)
  • rat (Rattus norvegicus)
  • 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 AFF2 Gene

Gene Tree for AFF2 (if available)
Gene Tree for AFF2 (if available)
Evolutionary constrained regions (ECRs) for AFF2: view image

Paralogs for AFF2 Gene

Paralogs for AFF2 Gene

(2) SIMAP similar genes for AFF2 Gene using alignment to 2 proteins:

  • F8W6J4_HUMAN
genes like me logo Genes that share paralogs with AFF2: view

Variants for AFF2 Gene

Sequence variations from dbSNP and Humsavar for AFF2 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1057518785 uncertain-significance, Congenital microcephaly, Hirsutism, Intellectual disability, moderate, Muscular hypotonia, Myopia, Short stature, Synophrys 148,967,634(+) A/G coding_sequence_variant, missense_variant
rs145907183 uncertain-significance, Inborn genetic diseases 148,953,627(+) G/C coding_sequence_variant, missense_variant
rs149653283 uncertain-significance, not provided, not specified 148,966,964(+) A/C coding_sequence_variant, missense_variant
rs200306870 benign, not specified, not provided 148,837,681(+) C/A coding_sequence_variant, intron_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for AFF2 Gene

Variant ID Type Subtype PubMed ID
nsv7144 CNV deletion 18451855
nsv7142 CNV insertion 18451855
nsv527473 CNV gain 19592680
nsv525908 CNV gain 19592680
nsv523386 CNV gain 19592680
nsv515740 CNV gain 19592680
nsv476153 CNV novel sequence insertion 20440878
nsv1141851 CNV insertion 24896259
nsv1120593 CNV tandem duplication 24896259
nsv1117919 CNV tandem duplication 24896259
nsv1112491 CNV deletion 24896259
esv3577502 CNV gain 25503493
esv3574948 CNV loss 25503493
esv3574947 CNV loss 25503493
esv3574946 CNV loss 25503493
esv3574945 CNV loss 25503493
esv3391393 CNV insertion 20981092
esv3309946 CNV mobile element insertion 20981092
esv2740817 CNV deletion 23290073
esv2740590 CNV deletion 23290073
esv2740588 CNV deletion 23290073
esv1732096 CNV insertion 17803354
esv1682218 CNV insertion 17803354
esv1401412 CNV insertion 17803354
esv1373270 CNV insertion 17803354
esv1297644 CNV insertion 17803354
esv1254777 CNV insertion 17803354
esv1234642 CNV insertion 17803354
dgv1327e201 CNV deletion 23290073

Variation tolerance for AFF2 Gene

Residual Variation Intolerance Score: 4.88% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.41; 27.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for AFF2 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AFF2 Gene

Disorders for AFF2 Gene

MalaCards: The human disease database

(16) MalaCards diseases for AFF2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, x-linked, associated with fragile site fraxe
  • fraxe mental retardation syndrome
fragile x syndrome
  • fxs
epidemic typhus
  • sylvatic typhus
endemic typhus
  • cat flea rickettsiosis
brill-zinsser disease
  • brill zinsser disease
- elite association - COSMIC cancer census association via MalaCards
Search AFF2 in MalaCards View complete list of genes associated with diseases


  • Mental retardation, X-linked, associated with fragile site FRAXE (MRFRAXE) [MIM:309548]: A form of mild to moderate mental retardation associated with learning difficulties, communication deficits, attention problems, hyperactivity, and autistic behavior. It is associated with a fragile site on chromosome Xq28. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269 PubMed:19136466, ECO:0000269 PubMed:21739600}. Note=The disease is caused by mutations affecting the gene represented in this entry. It is caused either by silencing of the AFF2 gene as a consequence of a CCG expansion located upstream of this gene or by deletion within the gene. Loss of AFF2 expression is correlated with FRAXE CCG(N) expansion. Normal individuals have 6-35 copies of the repeat, whereas cytogenetically positive, developmentally delayed males have more than 200 copies and show methylation of the associated CPG island.

Additional Disease Information for AFF2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with AFF2: view

No data available for Genatlas for AFF2 Gene

Publications for AFF2 Gene

  1. FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure. (PMID: 19136466) Bensaid M … Bardoni B (Nucleic acids research 2009) 3 4 22 58
  2. Expansion mutation frequency and CGG/GCC repeat polymorphism in FMR1 and FMR2 genes in an Indian population. (PMID: 11119302) Sharma D … Thelma BK (Genetic epidemiology 2001) 3 22 44 58
  3. Expression of the murine homologue of FMR2 in mouse brain and during development. (PMID: 9467002) Chakrabarti L … Davies KE (Human molecular genetics 1998) 3 4 22 58
  4. Identification of the gene FMR2, associated with FRAXE mental retardation. (PMID: 8673085) Gecz J … Mulley JC (Nature genetics 1996) 3 4 22 58
  5. Identification of FMR2, a novel gene associated with the FRAXE CCG repeat and CpG island. (PMID: 8673086) Gu Y … Nelson DL (Nature genetics 1996) 3 4 22 58

Products for AFF2 Gene

Sources for AFF2 Gene

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