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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 3
  • RFX DNA-Binding Complex 36 KDa Subunit 3 4
  • RFX-Associated Protein 3 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 and Bare Lymphocyte Syndrome, Type I. Among its related pathways are Tuberculosis and Primary immunodeficiency. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity 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

Additional gene information for RFXAP Gene

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

Genomics for RFXAP Gene

GeneHancer (GH) Regulatory Elements for RFXAP Gene

Promoters and enhancers for RFXAP 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
GH13J036818 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.7 +0.6 576 2.8 PKNOX1 ATF1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 GLIS2 E2F8 ZNF143 RFXAP EXOSC8 SUPT20H GC13P036843 SMAD9
GH13J036997 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 40.1 +180.9 180880 4.6 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 EXOSC8 ALG5 SUPT20H RFXAP SPART-AS1 SMAD9 CSNK1A1L
GH13J036130 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 11.1 -687.6 -687551 2.7 ZSCAN4 SIN3A KLF14 ZNF335 ZNF121 GLIS2 ZNF366 EGR2 SP3 ZNF398 DCLK1 SOHLH2 EXOSC8 CCDC169 RFXAP SUPT20H NMTRQ-TTG10-1
GH13J036343 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 9.7 -473.6 -473638 4.1 HDGF PKNOX1 SMAD1 FOXA2 SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 SPART SPART-AS1 SOHLH2 CCDC169 RFXAP CCDC169-SOHLH2
GH13J036777 Enhancer 0.8 Ensembl ENCODE 25.4 -40.7 -40724 1.6 ZNF687 NR2F1 SIN3A EBF1 MEF2B DPF2 ZNF585B GLIS1 IKZF1 ZNF24 RFXAP ARL2BPP3 SPART-AS1 LOC102723490 TCEAL4P1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RFXAP on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RFXAP gene promoter:
  • Tal-1beta
  • E47
  • Nkx6-1
  • ISGF-3
  • FOXO1
  • FOXO1a
  • MyoD
  • HNF-1A
  • HNF-1
  • USF1

Genomic Locations for RFXAP Gene

Genomic Locations for RFXAP Gene
10,402 bases
Plus strand
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

Gene Families for RFXAP Gene

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

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

Function for RFXAP Gene

Molecular function for RFXAP Gene

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

Phenotypes From GWAS Catalog for RFXAP Gene

Gene Ontology (GO) - Molecular Function for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IBA --
GO:0003700 DNA binding transcription factor activity 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

Clone 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

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 RFXAP gene
Compartment Confidence
nucleus 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RFXAP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0016607 nuclear speck IDA --
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

Drugs & Compounds for RFXAP Gene

No Compound Related Data Available

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:

Clone 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 CGAP 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, 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.

Evidence on tissue expression from TISSUES for RFXAP Gene

  • Blood(4.4)
  • Nervous system(4.1)

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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • urinary
Head and neck:
  • brain
  • head
  • larynx
  • meninges
  • neck
  • pharynx
  • bronchus
  • lung
  • trachea
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • ureter
  • urethra
  • urinary bladder
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
  • blood
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with RFXAP: view

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 33
  • 99.14 (n)
(Canis familiaris)
Mammalia RFXAP 34 33
  • 88.74 (n)
(Bos Taurus)
Mammalia RFXAP 34 33
  • 87.58 (n)
(Rattus norvegicus)
Mammalia Rfxap 33
  • 83.73 (n)
(Mus musculus)
Mammalia Rfxap 16 34 33
  • 78.22 (n)
(Monodelphis domestica)
Mammalia RFXAP 34
  • 67 (a)
(Gallus gallus)
Aves RFXAP 34
  • 48 (a)
(Anolis carolinensis)
Reptilia RFXAP 34
  • 75 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.20047 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.30365 33
(Danio rerio)
Actinopterygii rfxap 34
  • 50 (a)
Dr.12444 33
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)
Evolutionary constrained regions (ECRs) for RFXAP: view image

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 Variation AA Info Type
rs10976 likely-benign, Bare lymphocyte syndrome 2 36,829,006(+) G/A 3_prime_UTR_variant
rs113555392 uncertain-significance, Bare lymphocyte syndrome 2 36,819,711(+) G/A/C coding_sequence_variant, synonymous_variant
rs11539183 uncertain-significance, Bare lymphocyte syndrome 2 36,828,947(+) A/G 3_prime_UTR_variant
rs137853098 pathogenic, Bare Lymphocyte Syndrome, Type II, Complementation Group D 36,819,520(+) C/T coding_sequence_variant, stop_gained
rs139675642 uncertain-significance, Bare lymphocyte syndrome 2 36,825,493(+) A/G coding_sequence_variant, synonymous_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)

Additional Variant Information for RFXAP 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 RFXAP Gene

Disorders for RFXAP Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
bare lymphocyte syndrome, type ii
  • bls, type ii
bare lymphocyte syndrome, type i
  • bls, type i
severe combined immunodeficiency
  • combined t and b cell inborn immunodeficiency
immune deficiency disease
  • primary immunodeficiency disease
combined immunodeficiency, x-linked
  • cidx
- 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.

Additional Disease Information for RFXAP

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 (The EMBO journal 1997) 2 3 4 22 58
  2. Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex. (PMID: 20732328) Laird KM … Garvie CW (Journal of molecular biology 2010) 3 4 58
  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 SP (Immunogenetics 2010) 3 22 58
  4. Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP. (PMID: 19274739) Briggs L … Garvie CW (Proteins 2009) 3 22 58
  5. Assembly of the RFX complex on the MHCII promoter: role of RFXAP and RFXB in relieving autoinhibition of RFX5. (PMID: 18723135) Garvie CW … Boss JM (Biochimica et biophysica acta 2008) 3 22 58

Products for RFXAP Gene

Sources for RFXAP Gene

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