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 th... See more...

Aliases for RFXAP Gene

Aliases for RFXAP Gene

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

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 Severe Combined Immunodeficiency. 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 Summary for RFXAP Gene

Gene Wiki entry for RFXAP Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RFXAP Gene

Genomics for RFXAP Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RFXAP Gene
GeneHancer (GH) Identifier GH Type GH
Score
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 CraniofacialAtlas 600.7 +0.6 579 3.2 HNRNPL CTCF ZNF692 POLR2A BACH1 FOXA1 LARP7 PRDM1 ZNF143 RBFOX2 RFXAP EXOSC8 SUPT20H lnc-RFXAP-2 SMAD9
GH13J036997 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 40.1 +180.9 180878 5 ZNF221 SP1 HNRNPL GATAD2A CTCF TEAD4 PRDM10 REST ZNF629 TFE3 EXOSC8 ALG5 lnc-ALG5-1 RFXAP SUPT20H SPART-AS1 SMAD9 CSNK1A1L lnc-ALG5-2
GH13J036127 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 14.3 -688.4 -688431 4.4 ZSCAN4 POLR2A PATZ1 ZNF501 ZNF341 ZNF561 ZNF140 KLF9 SP2 RAD21 DCLK1 RFXAP SOHLH2 EXOSC8 CCDC169 SUPT20H piR-41525-145 MAB21L1
GH13J036673 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 14.5 -145.0 -145021 1.6 TEAD4 PRDM10 ZNF692 ZIC2 PATZ1 EZH2 ZNF341 ZNF561 SP2 ZBTB10 SERTM1 RFXAP SPART-AS1 HSALNG0096391 LOC102723490
GH13J036343 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 9.7 -473.7 -473658 4.1 GATAD2A CTCF TEAD4 PRDM10 ZNF629 IKZF1 ZNF692 BACH1 TARDBP FOXA1 SPART SPART-AS1 SOHLH2 CCDC169 RFXAP piR-38580-075 CCDC169-SOHLH2
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFXAP

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

Genomic Locations for RFXAP Gene

Genomic Locations for RFXAP Gene
chr13:36,819,222-36,829,104
(GRCh38/hg38)
Size:
9,883 bases
Orientation:
Plus strand
chr13:37,393,339-37,403,740
(GRCh37/hg19)
Size:
10,402 bases
Orientation:
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:
    O00287-RFXAP_HUMAN
    Recommended name:
    Regulatory factor X-associated protein
    Protein Accession:
    O00287
    Secondary Accessions:
    • B2R9T8
    • Q5VZM6
    • Q8TC40

    Protein attributes for RFXAP Gene

    Size:
    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

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RFXAP Gene

GenScript: Design optimal peptide antigens:
  • RFX DNA-binding complex 36 kDa subunit (RFXAP_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O00287

UniProtKB/Swiss-Prot:

RFXAP_HUMAN :
  • The C-terminal domain is necessary for the RFX complex formation.
Domain:
  • 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:0000976 contributes_to transcription regulatory region sequence-specific DNA binding IDA 9806546
GO:0003677 DNA binding TAS,IBA 21873635
GO:0003700 DNA-binding transcription factor activity NAS --
GO:0003713 transcription coactivator activity TAS,IDA 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

CRISPR Products

Inhibitory RNA Products

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

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

COMPARTMENTS
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 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 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 21873635
GO:0005667 transcription factor complex IPI 9806546
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 21873635
GO:0045944 positive regulation of transcription by RNA polymerase II IDA, IMP 9118943
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 :
3 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

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

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

No ASD Table

Relevant External Links for RFXAP Gene

GeneLoc Exon Structure for
RFXAP

Expression for RFXAP Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Liver (Hepatobiliary System)

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RFXAP

SOURCE GeneReport for Unigene cluster for RFXAP Gene:

Hs.24422

mRNA Expression by UniProt/SwissProt for RFXAP Gene:

O00287-RFXAP_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for RFXAP Gene

  • Blood(4.5)
  • Nervous system(4.3)
  • Lymph node(2.1)

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

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

No data available for 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
Chimpanzee
(Pan troglodytes)
Mammalia RFXAP 30 31
  • 99.14 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RFXAP 30 31
  • 88.74 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RFXAP 30 31
  • 87.58 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rfxap 30
  • 83.73 (n)
Mouse
(Mus musculus)
Mammalia Rfxap 30 17 31
  • 78.22 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RFXAP 31
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RFXAP 31
  • 48 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RFXAP 31
  • 75 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.30365 30
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.20047 30
Zebrafish
(Danio rerio)
Actinopterygii rfxap 31
  • 50 (a)
OneToOne
Dr.12444 30
Species where no ortholog for RFXAP was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for RFXAP (if available)
TreeFam:
Gene Tree for RFXAP (if available)
Aminode:
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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFXAP Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
636400 Uncertain Significance: not provided 36,819,716(+) G/A MISSENSE_VARIANT
636582 Uncertain Significance: not provided 36,819,591(+) C/A SYNONYMOUS_VARIANT
643242 Uncertain Significance: Bare lymphocyte syndrome 2 36,819,371(+) G/T MISSENSE_VARIANT
644661 Uncertain Significance: Bare lymphocyte syndrome 2 36,819,486(+) A/G SYNONYMOUS_VARIANT
645743 Uncertain Significance: Bare lymphocyte syndrome 2 36,819,593(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for RFXAP Gene

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)
RFXAP
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFXAP

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

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

Disorder Aliases PubMed IDs
bare lymphocyte syndrome, type ii
  • bls, type ii
severe combined immunodeficiency
  • combined t and b cell inborn immunodeficiency
retinitis pigmentosa 48
  • rp48
immune deficiency disease
  • primary immunodeficiency disease
bare lymphocyte syndrome, type i
  • bls, type i
- elite association - COSMIC cancer census association via MalaCards
Search RFXAP in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RFXAP_HUMAN
  • 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 23
  2. 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 23
  3. 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
  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 23
  5. Transcriptional silencing of RFXAP in MHC class II-deficiency. (PMID: 18336911) van Eggermond MC … van den Elsen PJ (Molecular immunology 2008) 3 23

Products for RFXAP Gene

Sources for RFXAP Gene