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Aliases for RFXAP Gene

Aliases for RFXAP Gene

  • Regulatory Factor X Associated Protein 2 3 5
  • Regulatory Factor X-Associated Protein 2
  • RFX DNA-Binding Complex 36 KDa Subunit 4
  • RFX-Associated Protein 4

External Ids for RFXAP Gene

Previous GeneCards Identifiers for RFXAP Gene

  • GC13P035379
  • GC13P031379
  • GC13P036329
  • GC13P035191
  • GC13P036291
  • GC13P037393
  • GC13P018207

Summaries for RFXAP Gene

Entrez Gene Summary for RFXAP Gene

  • Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated ankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group D. Transcript variants utilizing different polyA signals have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for RFXAP Gene

RFXAP (Regulatory Factor X Associated Protein) is a Protein Coding gene. Diseases associated with RFXAP include Bare Lymphocyte Syndrome, Type Ii, Complementation Group C and Severe Combined Immunodeficiency. Among its related pathways are Allograft rejection and Tuberculosis. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and transcription coactivator activity.

UniProtKB/Swiss-Prot for RFXAP Gene

  • Part of the RFX complex that binds to the X-box of MHC II promoters.

Gene Wiki entry for RFXAP Gene

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

Genomics for RFXAP Gene

Regulatory Elements for RFXAP Gene

Enhancers for RFXAP 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
GH13F036777 1.3 Ensembl ENCODE 25.4 -40.7 -40725 1.6 ZNF585B GLIS1 IKZF1 EBF1 RFXAP ARL2BPP3 SPG20-AS1 LOC102723490 TCEAL4P1
GH13F036673 0.6 ENCODE 14.5 -145.2 -145244 0.2 TEAD4 ZIC2 ZNF324 ZFHX2 GLIS2 POLR2A PATZ1 ZNF391 EGR2 ZNF263 RFXAP SPG20-AS1 SERTM1 GAPDHP34
GH13F037209 0.4 ENCODE 13.1 +392.2 392177 3.8 ZNF335 KLF1 JUND ZNF239 ZBTB40 ATF2 RFXAP CSNK1A1L RPS12P24 GC13M037167 RN7SKP1
GH13F036795 0.5 ENCODE 11.9 -23.6 -23565 1.1 PKNOX1 BCL11A TEAD4 POU5F1 KDM1A RFXAP ARL2BPP3 GC13M036798
GH13F036839 0.8 Ensembl 11.7 +20.7 20699 0.2 ZNF680 RFXAP GC13P036843
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RFXAP on UCSC Golden Path with GeneCards custom track

Promoters for RFXAP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001508824 698 3001 ATF1 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 GLIS2 ZNF143 ZNF202 SP5

Genomic Location for RFXAP Gene

36,819,202 bp from pter
36,829,603 bp from pter
10,402 bases
Plus strand

Genomic View for RFXAP Gene

Genes around RFXAP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RFXAP Gene

Proteins for RFXAP Gene

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

    Protein Symbol:
    Recommended name:
    Regulatory factor X-associated protein
    Protein Accession:
    Secondary Accessions:
    • B2R9T8
    • Q5VZM6
    • Q8TC40

    Protein attributes for RFXAP Gene

    272 amino acids
    Molecular mass:
    28232 Da
    Quaternary structure:
    • The RFX heterotetrameric complex consists of 2 molecules of RFX5 and one each of RFXAP and RFX-B/RFXANK; with each subunit representing a separate complementation group. RFX forms cooperative DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with CIITA to form an active transcriptional complex.

    Three dimensional structures from OCA and Proteopedia for RFXAP Gene

neXtProt entry for RFXAP Gene

Post-translational modifications for RFXAP Gene

Other Protein References for RFXAP Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RFXAP Gene

Domains & Families for RFXAP Gene

Protein Domains for RFXAP Gene


Suggested Antigen Peptide Sequences for RFXAP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • The C-terminal domain is necessary for the RFX complex formation.
  • The C-terminal domain is necessary for the RFX complex formation.
genes like me logo Genes that share domains with RFXAP: view

No data available for Gene Families for RFXAP Gene

Function for RFXAP Gene

Molecular function for RFXAP Gene

GENATLAS Biochemistry:
transactivating DNA binding regulatory factor,component AP,36kDa,involved in MHC class II expression,subunit of the RFX complex,interacting with RFX5
UniProtKB/Swiss-Prot Function:
Part of the RFX complex that binds to the X-box of MHC II promoters.

Gene Ontology (GO) - Molecular Function for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding NAS 9118943
GO:0003713 transcription coactivator activity TAS 9118943
genes like me logo Genes that share ontologies with RFXAP: view
genes like me logo Genes that share phenotypes with RFXAP: view

Human Phenotype Ontology for RFXAP Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

Localization for RFXAP Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFXAP Gene

Subcellular locations from

Jensen Localization Image for RFXAP Gene COMPARTMENTS Subcellular localization image for RFXAP gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
genes like me logo Genes that share ontologies with RFXAP: view

Pathways & Interactions for RFXAP Gene

genes like me logo Genes that share pathways with RFXAP: view

Pathways by source for RFXAP Gene

Gene Ontology (GO) - Biological Process for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0045893 positive regulation of transcription, DNA-templated IBA --
genes like me logo Genes that share ontologies with RFXAP: view

No data available for SIGNOR curated interactions for RFXAP Gene

Transcripts for RFXAP Gene

mRNA/cDNA for RFXAP Gene

(1) REFSEQ mRNAs :
(2) Additional mRNA sequences :
(46) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RFXAP Gene

Regulatory factor X-associated protein:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for RFXAP Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RFXAP Gene

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

Protein differential expression in normal tissues from HIPED for RFXAP Gene

This gene is overexpressed in Blymphocyte (23.3), Peripheral blood mononuclear cells (8.8), CD8 Tcells (7.8), and Thyroid (7.1).

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

Protein tissue co-expression partners for RFXAP Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RFXAP Gene:


SOURCE GeneReport for Unigene cluster for RFXAP Gene:


mRNA Expression by UniProt/SwissProt for RFXAP Gene:

Tissue specificity: Ubiquitous.
genes like me logo Genes that share expression patterns with RFXAP: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for RFXAP Gene

Orthologs for RFXAP Gene

This gene was present in the common ancestor of chordates.

Orthologs for RFXAP Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RFXAP 34 35
  • 99.14 (n)
(Canis familiaris)
Mammalia RFXAP 34 35
  • 88.74 (n)
(Bos Taurus)
Mammalia RFXAP 34 35
  • 87.58 (n)
(Rattus norvegicus)
Mammalia Rfxap 34
  • 83.73 (n)
(Mus musculus)
Mammalia Rfxap 34 16 35
  • 78.22 (n)
(Monodelphis domestica)
Mammalia RFXAP 35
  • 67 (a)
(Gallus gallus)
Aves RFXAP 35
  • 48 (a)
(Anolis carolinensis)
Reptilia RFXAP 35
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20047 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.30365 34
(Danio rerio)
Actinopterygii rfxap 35
  • 50 (a)
Dr.12444 34
Species where no ortholog for RFXAP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 RFXAP Gene

Gene Tree for RFXAP (if available)
Gene Tree for RFXAP (if available)

Paralogs for RFXAP Gene

No data available for Paralogs for RFXAP Gene

Variants for RFXAP Gene

Sequence variations from dbSNP and Humsavar for RFXAP Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs137853098 Pathogenic 36,819,520(+) CTGGG(C/T)AGGAC reference, stop-gained
rs754240018 Pathogenic 36,819,680(+) TAGTT(G/T)GGAGG reference, missense
rs10573140 -- 36,821,215(+) TCCTT(-/AAA)AAAAA intron-variant
rs10976 -- 36,829,006(-) AAAAA(C/T)GTTCT utr-variant-3-prime
rs111253172 -- 36,823,223(+) TCACT(G/T)TTACC intron-variant

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

Variant ID Type Subtype PubMed ID
nsv522336 CNV gain 19592680

Variation tolerance for RFXAP Gene

Gene Damage Index Score: 0.98; 20.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RFXAP 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 RFXAP Gene

Disorders for RFXAP Gene

MalaCards: The human disease database

(5) MalaCards diseases for RFXAP Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
bare lymphocyte syndrome, type ii, complementation group c
  • bare lymphocyte syndrome, type ii, complementation group e
severe combined immunodeficiency
  • combined t and b cell inborn immunodeficiency
bare lymphocyte syndrome, type i
  • bare lymphocyte syndrome, type i, due to tap2 deficiency
combined immunodeficiency, x-linked, moderate
  • combined t cell and b cell immunodeficiency
adult syndrome
  • acro-dermato-ungual-lacrimal-tooth syndrome
- elite association - COSMIC cancer census association via MalaCards
Search RFXAP in MalaCards View complete list of genes associated with diseases


  • Bare lymphocyte syndrome 2 (BLS2) [MIM:209920]: A severe combined immunodeficiency disease with early onset. It is characterized by a profound defect in constitutive and interferon-gamma induced MHC II expression, absence of cellular and humoral T-cell response to antigen challenge, hypogammaglobulinemia and impaired antibody production. The consequence include extreme susceptibility to viral, bacterial and fungal infections. {ECO:0000269 PubMed:10072068, ECO:0000269 PubMed:9118943}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RFXAP

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with RFXAP: view

No data available for Genatlas for RFXAP Gene

Publications for RFXAP Gene

  1. RFXAP, a novel subunit of the RFX DNA binding complex is mutated in MHC class II deficiency. (PMID: 9118943) Durand B. … Reith W. (EMBO J. 1997) 2 3 4 22 64
  2. Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex. (PMID: 20732328) Laird K.M. … Garvie C.W. (J. Mol. Biol. 2010) 3 4 64
  3. Coordinate loss of MHC class II expression in the diffuse large B cell lymphoma cell line OCI-Ly2 is due to a novel mutation in RFX-AP. (PMID: 20024540) Bushway M. … Murphy S.P. (Immunogenetics 2010) 3 22 64
  4. Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP. (PMID: 19274739) Briggs L. … Garvie C.W. (Proteins 2009) 3 22 64
  5. Transcriptional silencing of RFXAP in MHC class II-deficiency. (PMID: 18336911) van Eggermond M.C. … van den Elsen P.J. (Mol. Immunol. 2008) 3 22 64

Products for RFXAP Gene

Sources for RFXAP Gene

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