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AFF2 ALF transcription elongation factor 2 [ Homo sapiens (human) ]

Gene ID: 2334, updated on 5-Mar-2024

Summary

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Official Symbol
AFF2provided by HGNC
Official Full Name
ALF transcription elongation factor 2provided by HGNC
Primary source
HGNC:HGNC:3776
See related
Ensembl:ENSG00000155966 MIM:300806; AllianceGenome:HGNC:3776
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FMR2; MRX2; OX19; FMR2P; FRAXE; XLID109
Summary
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]
Expression
Biased expression in placenta (RPKM 3.7), bone marrow (RPKM 2.5) and 8 other tissues See more
Orthologs
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Genomic context

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Location:
Xq28
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (148500617..149000663)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (146765203..147266230)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (147582137..148082193)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene HAX1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30008 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:147507788-147508643 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:147522255-147522928 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:147522929-147523603 Neighboring gene origin of replication in 5' region of AFF2/FMR2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:147582797-147583674 Neighboring gene RPL7L1 pseudogene 11 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:147636485-147637684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30009 Neighboring gene fragile site, folic acid type, rare, fra(X)(q28) E Neighboring gene RN7SK pseudogene 267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:148228003-148228504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:148228505-148229004 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:148264804-148265396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30014 Neighboring gene uncharacterized LOC122319696 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:148517664-148518235 Neighboring gene uncharacterized LOC107985667 Neighboring gene Sharpr-MPRA regulatory region 6851

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Nuclear expression of AFF2 C-terminus is a sensitive and specific ancillary marker for DEK::AFF2 carcinoma of the sinonasal tract. Kuo YJ, et al. Mod Pathol, 2022 Nov. PMID 35701667
  2. Development and validation in 500 female samples of a TP-PCR assay to identify AFF2 GCC expansions. Silva C, et al. Sci Rep, 2021 Jul 19. PMID 34282157, Free PMC Article
  3. Partial AFF2 microduplication in a patient with auditory processing disorder, emotional impairment and macrosomia. da Rocha NB, et al. Am J Med Genet A, 2014 Dec. PMID 25256661
  4. Excess variants in AFF2 detected by massively parallel sequencing of males with autism spectrum disorder. Mondal K, et al. Hum Mol Genet, 2012 Oct 1. PMID 22773736, Free PMC Article
  5. Microdeletion of Xq28 involving the AFF2 (FMR2) gene in two unrelated males with developmental delay. Sahoo T, et al. Am J Med Genet A, 2011 Dec. PMID 22065534

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ALKBH5/YTHDF2-mediated m6A modification of circAFF2 enhances radiosensitivity of colorectal cancer by inhibiting Cullin neddylation.
    Title: ALKBH5/YTHDF2-mediated m6A modification of circAFF2 enhances radiosensitivity of colorectal cancer by inhibiting Cullin neddylation.
  2. [AF4/FMR2 and IL-10 gene single nucleotide polymorphisms are correlated with disease susceptibility and immune infiltration in ankylosing spondylitis].
    Title: [AF4/FMR2 and IL-10 gene single nucleotide polymorphisms are correlated with disease susceptibility and immune infiltration in ankylosing spondylitis].
  3. Nuclear expression of AFF2 C-terminus is a sensitive and specific ancillary marker for DEK::AFF2 carcinoma of the sinonasal tract.
    Title: Nuclear expression of AFF2 C-terminus is a sensitive and specific ancillary marker for DEK::AFF2 carcinoma of the sinonasal tract.
  4. Simultaneous Screening of the FRAXA and FRAXE Loci for Rapid Detection of FMR1 CGG and/or AFF2 CCG Repeat Expansions by Triplet-Primed PCR.
    Title: Simultaneous Screening of the FRAXA and FRAXE Loci for Rapid Detection of FMR1 CGG and/or AFF2 CCG Repeat Expansions by Triplet-Primed PCR.
  5. Development and validation in 500 female samples of a TP-PCR assay to identify AFF2 GCC expansions.
    Title: Development and validation in 500 female samples of a TP-PCR assay to identify AFF2 GCC expansions.
  6. DEK-AFF2 Carcinoma of the Sinonasal Region and Skull Base: Detailed Clinicopathologic Characterization of a Distinctive Entity.
    Title: DEK-AFF2 Carcinoma of the Sinonasal Region and Skull Base: Detailed Clinicopathologic Characterization of a Distinctive Entity.
  7. Circ-AFF2/miR-650/CNP axis promotes proliferation, inflammatory response, migration, and invasion of rheumatoid arthritis synovial fibroblasts.
    Title: Circ-AFF2/miR-650/CNP axis promotes proliferation, inflammatory response, migration, and invasion of rheumatoid arthritis synovial fibroblasts.
  8. AFF2/FMR2 regulates the transcription and toxicity of expanded G4C2 repeats in human C9ORF72-ALS/FTD neurons.
    Title: Transcription elongation factor AFF2/FMR2 regulates expression of expanded GGGGCC repeat-containing C9ORF72 allele in ALS/FTD.
  9. Partial AFF2 microduplication in a patient with auditory processing disorder, emotional impairment and macrosomia.
    Title: Partial AFF2 microduplication in a patient with auditory processing disorder, emotional impairment and macrosomia.
  10. FMR2 is an upstream regulator of FOS and JUN, and further link deregulation of the immediate early response genes to the pathology of ID- and FRAXE-associated ID in particular.
    Title: Loss of FMR2 further emphasizes the link between deregulation of immediate early response genes FOS and JUN and intellectual disability.
Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
FRAXE
MedGen: C0751157 OMIM: 309548 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-12-08)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-12-08)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of AF4/FMR2 family, member 2 (AFF2) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables G-quadruplex RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables G-quadruplex RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in brain development TAS
Traceable Author Statement
more info
 PubMed 
involved_in learning or memory IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within nuclear speck organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of RNA splicing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nuclear speck IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
NOT part_of super elongation complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
AF4/FMR2 family member 2
Names
protein FMR-2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_016313.2 RefSeqGene

    Range
    4999..505045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001169122.2 → NP_001162593.1  AF4/FMR2 family member 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC002368, AC231841, L76569, U48436
    Consensus CDS
    CCDS78510.1
    UniProtKB/Swiss-Prot
    P51816
    Related
    ENSP00000345459.4, ENST00000342251.7
    Conserved Domains (1) summary
    pfam05110
    Location:19 → 1273
    AF-4; AF-4 proto-oncoprotein

  2. NM_001169123.2 → NP_001162594.1  AF4/FMR2 family member 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC002368, AC231841, BC132683, U48436
    UniProtKB/Swiss-Prot
    P51816
    Conserved Domains (1) summary
    pfam05110
    Location:19 → 1298
    AF-4; AF-4 proto-oncoprotein

  3. NM_001169124.2 → NP_001162595.1  AF4/FMR2 family member 2 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has multiple differences, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC002368, AC231841, BC143744, U48436
    Consensus CDS
    CCDS76040.1
    UniProtKB/Swiss-Prot
    P51816
    Related
    ENSP00000359486.6, ENST00000370457.9
    Conserved Domains (1) summary
    pfam05110
    Location:19 → 1273
    AF-4; AF-4 proto-oncoprotein

  4. NM_001169125.2 → NP_001162596.1  AF4/FMR2 family member 2 isoform 5

    See identical proteins and their annotated locations for NP_001162596.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AC002368, AC231841, BC143740, U48436
    UniProtKB/Swiss-Prot
    P51816
    Conserved Domains (1) summary
    pfam05110
    Location:19 → 1269
    AF-4; AF-4 proto-oncoprotein

  5. NM_001170628.1 → NP_001164099.1  AF4/FMR2 family member 2 isoform 6

    See identical proteins and their annotated locations for NP_001164099.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple differences, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (6) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC002368, AC231841, AK301927
    Consensus CDS
    CCDS55521.1
    UniProtKB/Swiss-Prot
    P51816
    Related
    ENSP00000286437.5, ENST00000286437.7
    Conserved Domains (1) summary
    pfam05110
    Location:18 → 949
    AF-4; AF-4 proto-oncoprotein

  6. NM_002025.4 → NP_002016.2  AF4/FMR2 family member 2 isoform 1

    See identical proteins and their annotated locations for NP_002016.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC002368, AC231841, BC132683, BC143744, L76569
    Consensus CDS
    CCDS14684.1
    UniProtKB/Swiss-Prot
    A2RTY4, B4DXD5, B7WNQ1, B7ZLD6, B7ZLD9, O43786, O60215, P51816, P78407, Q13521, Q14323, Q7Z2F7, Q7Z400, Q9UNA5
    Related
    ENSP00000359489.2, ENST00000370460.7
    Conserved Domains (1) summary
    pfam05110
    Location:19 → 1308
    AF-4; AF-4 proto-oncoprotein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    148500617..149000663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    146765203..147266230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51816.4 GenPept UniProtKB/Swiss-Prot:P51816

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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