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    AFF3 ALF transcription elongation factor 3 [ Homo sapiens (human) ]

    Gene ID: 3899, updated on 5-Mar-2024

    Summary

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    Official Symbol
    AFF3provided by HGNC
    Official Full Name
    ALF transcription elongation factor 3provided by HGNC
    Primary source
    HGNC:HGNC:6473
    See related
    Ensembl:ENSG00000144218 MIM:601464; AllianceGenome:HGNC:6473
    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
    KINS; LAF4; MLLT2-like
    Summary
    This gene encodes a tissue-restricted nuclear transcriptional activator that is preferentially expressed in lymphoid tissue. Isolation of this protein initially defined a highly conserved LAF4/MLLT2 gene family of nuclear transcription factors that may function in lymphoid development and oncogenesis. In some ALL patients, this gene has been found fused to the gene for MLL. Multiple alternatively spliced transcript variants that encode different proteins have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in prostate (RPKM 4.8), lymph node (RPKM 3.7) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2q11.2
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (99545419..100142590, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (100004081..100601540, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (100161881..100759052, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16281 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99952564-99953104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99953733-99954234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:99954235-99954734 Neighboring gene thioredoxin domain containing 9 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:100019841-100021040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11808 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:100056357-100057026 Neighboring gene eukaryotic translation initiation factor 5B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:100092059-100092722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:100106417-100107302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16289 Neighboring gene REV1 DNA directed polymerase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100146131-100146758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100170377-100170925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100170926-100171473 Neighboring gene NANOG hESC enhancer GRCh37_chr2:100171857-100172363 Neighboring gene NANOG hESC enhancer GRCh37_chr2:100188674-100189175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100218069-100218631 Neighboring gene uncharacterized LOC124906051 Neighboring gene uncharacterized LOC105373504 Neighboring gene MPRA-validated peak3800 silencer Neighboring gene MPRA-validated peak3801 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:100483776-100484975 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:100521553-100522052 Neighboring gene Sharpr-MPRA regulatory region 9249 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:100735506-100736449 Neighboring gene fragile site, folic acid type, rare, fra(2)(q11.2) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16290 Neighboring gene long intergenic non-protein coding RNA 1104 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:100865373-100866572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:100871469-100871968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:100907393-100908033 Neighboring gene LON peptidase N-terminal domain and ring finger 2

    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. Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants. Inoue Y, et al. Clin Genet, 2023 May. PMID 36576140
    2. A novel variant in AFF3 underlying isolated syndactyly. Khan H, et al. Clin Genet, 2023 Mar. PMID 36273379
    3. Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort. Ali Y, et al. Genet Res (Camb), 2021. PMID 34104118, Free PMC Article
    4. AFF3 upregulation mediates tamoxifen resistance in breast cancers. Shi Y, et al. J Exp Clin Cancer Res, 2018 Oct 16. PMID 30326937, Free PMC Article
    5. Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes. Barton A, et al. Hum Mol Genet, 2009 Jul 1. PMID 19359276, Free PMC Article

    See all (54) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants.
      Title: Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants.
    2. A novel variant in AFF3 underlying isolated syndactyly.
      Title: A novel variant in AFF3 underlying isolated syndactyly.
    3. Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort.
      Title: Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort.
    4. Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.
      Title: Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.
    5. AFF3 was overexpressed in tamoxifen-resistant tumors. AFF3 overexpression in breast cancer cells resulted in tamoxifen resistance, whereas RNA interference-mediated gene knockdown reversed this phenotype.
      Title: AFF3 upregulation mediates tamoxifen resistance in breast cancers.
    6. Data identified AFF3 as an interactive protein with beclin1 and suggest that AFF3 is probably a key regulator of Beclin-1.
      Title: Integrating multiple omics data for the discovery of potential Beclin-1 interactions in breast cancer.
    7. Both the AFF3 and NTM triglyceride associations were replicated among Multi-ethnic Study of Atherosclerosis study participants (P = 1.00 x 10(-7) and 8.00 x 10(-5), respectively).
      Title: Genome-wide linkage and positional association analyses identify associations of novel AFF3 and NTM genes with triglycerides: the GenSalt study.
    8. FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat.
      Title: FRA2A is a CGG repeat expansion associated with silencing of AFF3.
    9. Significant evidence for association of AFF3 rs10865035 with systgemic lupus erythmatgosus was detected.
      Title: Association of AFF1 rs340630 and AFF3 rs10865035 polymorphisms with systemic lupus erythematosus in a Chinese population.
    10. overexpression of AFF2/3/4 interferes with the organization and/or biogenesis of nuclear speckles.
      Title: Functional characterization of the AFF (AF4/FMR2) family of RNA-binding proteins: insights into the molecular pathology of FRAXE intellectual disability.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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
    KINSSHIP syndrome
    MedGen: C5543317 OMIM: 619297 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome wide association study identifies a novel putative mammographic density locus at 1q12-q21.
    EBI GWAS Catalog
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    EBI GWAS Catalog
    New susceptibility loci associated with kidney disease in type 1 diabetes.
    EBI GWAS Catalog
    Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
    EBI GWAS Catalog
    Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
    EBI GWAS Catalog

    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

    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 DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryonic hindlimb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to tumor necrosis factor IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 3
    Names
    MLLT2-related protein
    lymphoid nuclear protein 4
    lymphoid nuclear protein related to AF4
    protein LAF-4

    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_052835.1 RefSeqGene

      Range
      4994..602165
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001025108.2 → NP_001020279.1  AF4/FMR2 family member 3 isoform 2

      See identical proteins and their annotated locations for NP_001020279.1

      Status: REVIEWED

      Source sequence(s)
      AC010736, AC018690, AC073118, AC092667, AC093373, KF456685
      Consensus CDS
      CCDS33258.1
      UniProtKB/Swiss-Prot
      P51826
      UniProtKB/TrEMBL
      Q8NAP7
      Related
      ENSP00000386834.1, ENST00000409579.5
      Conserved Domains (1) summary
      pfam05110
      Location:48 → 1245
      AF-4; AF-4 proto-oncoprotein

    2. NM_001386135.1 → NP_001373064.1  AF4/FMR2 family member 3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC010736, AC018690, AC073118, AC092667, AC093373, KF456685
      Consensus CDS
      CCDS42723.1
      UniProtKB/Swiss-Prot
      B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5
      Related
      ENSP00000500419.1, ENST00000672756.2
      Conserved Domains (2) summary
      pfam05110
      Location:20 → 473
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:965 → 1225
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    3. NM_002285.3 → NP_002276.2  AF4/FMR2 family member 3 isoform 1

      See identical proteins and their annotated locations for NP_002276.2

      Status: REVIEWED

      Source sequence(s)
      AC010736, AC018690, AC073118, AC092667, AC093373, KF456685
      Consensus CDS
      CCDS42723.1
      UniProtKB/Swiss-Prot
      B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5
      Related
      ENSP00000317421.4, ENST00000317233.8
      Conserved Domains (2) summary
      pfam05110
      Location:20 → 473
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:965 → 1225
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      99545419..100142590 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444286.1 → XP_047300242.1  AF4/FMR2 family member 3 isoform X13

    2. XM_047444281.1 → XP_047300237.1  AF4/FMR2 family member 3 isoform X8

    3. XM_047444283.1 → XP_047300239.1  AF4/FMR2 family member 3 isoform X10

      UniProtKB/Swiss-Prot
      B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5

    4. XM_047444280.1 → XP_047300236.1  AF4/FMR2 family member 3 isoform X8

    5. XM_047444279.1 → XP_047300235.1  AF4/FMR2 family member 3 isoform X6

    6. XM_011511169.4 → XP_011509471.2  AF4/FMR2 family member 3 isoform X2

      Conserved Domains (1) summary
      pfam05110
      Location:177 → 1373
      AF-4; AF-4 proto-oncoprotein

    7. XM_024452883.2 → XP_024308651.1  AF4/FMR2 family member 3 isoform X1

      Conserved Domains (1) summary
      pfam05110
      Location:177 → 1374
      AF-4; AF-4 proto-oncoprotein

    8. XM_047444278.1 → XP_047300234.1  AF4/FMR2 family member 3 isoform X5

    9. XM_047444277.1 → XP_047300233.1  AF4/FMR2 family member 3 isoform X4

    10. XM_011511171.4 → XP_011509473.2  AF4/FMR2 family member 3 isoform X3

      Conserved Domains (1) summary
      pfam05110
      Location:177 → 1358
      AF-4; AF-4 proto-oncoprotein

    11. XM_011511170.3 → XP_011509472.1  AF4/FMR2 family member 3 isoform X7

      Conserved Domains (1) summary
      pfam05110
      Location:100 → 1297
      AF-4; AF-4 proto-oncoprotein

    12. XM_047444284.1 → XP_047300240.1  AF4/FMR2 family member 3 isoform X11

    13. XM_047444285.1 → XP_047300241.1  AF4/FMR2 family member 3 isoform X12

    14. XM_005263943.5 → XP_005264000.2  AF4/FMR2 family member 3 isoform X10

      See identical proteins and their annotated locations for XP_005264000.2

      UniProtKB/Swiss-Prot
      B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5
      Related
      ENSP00000387207.1, ENST00000409236.6
      Conserved Domains (2) summary
      pfam05110
      Location:20 → 473
      AF-4; AF-4 proto-oncoprotein
      pfam18876
      Location:965 → 1225
      AF-4_C; AF-4 proto-oncoprotein C-terminal region

    15. XM_047444282.1 → XP_047300238.1  AF4/FMR2 family member 3 isoform X9

    16. XM_011511174.4 → XP_011509476.1  AF4/FMR2 family member 3 isoform X8

      See identical proteins and their annotated locations for XP_011509476.1

      UniProtKB/Swiss-Prot
      P51826
      Conserved Domains (1) summary
      pfam05110
      Location:48 → 1245
      AF-4; AF-4 proto-oncoprotein

    17. XM_047444287.1 → XP_047300243.1  AF4/FMR2 family member 3 isoform X13

    18. XM_047444289.1 → XP_047300245.1  AF4/FMR2 family member 3 isoform X17

    19. XM_017004085.3 → XP_016859574.1  AF4/FMR2 family member 3 isoform X15

    20. XM_047444288.1 → XP_047300244.1  AF4/FMR2 family member 3 isoform X16

    21. XM_005263945.5 → XP_005264002.1  AF4/FMR2 family member 3 isoform X14

      Conserved Domains (1) summary
      pfam05110
      Location:24 → 889
      AF-4; AF-4 proto-oncoprotein

    22. XM_047444290.1 → XP_047300246.1  AF4/FMR2 family member 3 isoform X20

    23. XM_017004087.3 → XP_016859576.1  AF4/FMR2 family member 3 isoform X21

    24. XM_011511179.4 → XP_011509481.1  AF4/FMR2 family member 3 isoform X19

      Conserved Domains (1) summary
      pfam05110
      Location:88 → 858
      AF-4; AF-4 proto-oncoprotein

    25. XM_011511178.4 → XP_011509480.1  AF4/FMR2 family member 3 isoform X18

      Conserved Domains (1) summary
      pfam05110
      Location:89 → 859
      AF-4; AF-4 proto-oncoprotein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      100004081..100601540 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341993.1 → XP_054197968.1  AF4/FMR2 family member 3 isoform X8

    2. XM_054341990.1 → XP_054197965.1  AF4/FMR2 family member 3 isoform X6

    3. XM_054341989.1 → XP_054197964.1  AF4/FMR2 family member 3 isoform X5

    4. XM_054341988.1 → XP_054197963.1  AF4/FMR2 family member 3 isoform X4

    5. XM_054341986.1 → XP_054197961.1  AF4/FMR2 family member 3 isoform X2

    6. XM_054341987.1 → XP_054197962.1  AF4/FMR2 family member 3 isoform X3

    7. XM_054341985.1 → XP_054197960.1  AF4/FMR2 family member 3 isoform X1

    8. XM_054341994.1 → XP_054197969.1  AF4/FMR2 family member 3 isoform X8

    9. XM_054341991.1 → XP_054197966.1  AF4/FMR2 family member 3 isoform X7

    10. XM_054341992.1 → XP_054197967.1  AF4/FMR2 family member 3 isoform X8

    11. XM_054341998.1 → XP_054197973.1  AF4/FMR2 family member 3 isoform X11

    12. XM_054341995.1 → XP_054197970.1  AF4/FMR2 family member 3 isoform X8

    13. XM_054341999.1 → XP_054197974.1  AF4/FMR2 family member 3 isoform X12

    14. XM_054341997.1 → XP_054197972.1  AF4/FMR2 family member 3 isoform X10

      UniProtKB/Swiss-Prot
      B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5

    15. XM_054341996.1 → XP_054197971.1  AF4/FMR2 family member 3 isoform X9

    16. XM_054342000.1 → XP_054197975.1  AF4/FMR2 family member 3 isoform X13

    17. XM_054342004.1 → XP_054197979.1  AF4/FMR2 family member 3 isoform X17

    18. XM_054342001.1 → XP_054197976.1  AF4/FMR2 family member 3 isoform X15

    19. XM_054342003.1 → XP_054197978.1  AF4/FMR2 family member 3 isoform X16

    20. XM_054342002.1 → XP_054197977.1  AF4/FMR2 family member 3 isoform X14

    21. XM_054342008.1 → XP_054197983.1  AF4/FMR2 family member 3 isoform X21

    22. XM_054342007.1 → XP_054197982.1  AF4/FMR2 family member 3 isoform X20

    23. XM_054342006.1 → XP_054197981.1  AF4/FMR2 family member 3 isoform X19

    24. XM_054342005.1 → XP_054197980.1  AF4/FMR2 family member 3 isoform X18

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51826.3 GenPept UniProtKB/Swiss-Prot:P51826

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