Gene Gene information from NCBI Gene database.
Entrez ID 5993
Gene name Regulatory factor X5
Gene symbol RFX5
Synonyms (NCBI Gene)
MHC2D3MHC2D5
Chromosome 1
Chromosome location 1q21.3
Summary A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BL
SNPs SNP information provided by dbSNP.
7
SNP ID Visualize variation Clinical significance Consequence
rs137853099 C>T Pathogenic, uncertain-significance 5 prime UTR variant, missense variant, coding sequence variant
rs748270285 C>T Pathogenic Splice acceptor variant
rs1557831362 G>A Pathogenic Coding sequence variant, synonymous variant
rs1571256140 ->G Likely-pathogenic Coding sequence variant, frameshift variant
rs1571260017 T>- Pathogenic Coding sequence variant, frameshift variant
miRNA miRNA information provided by mirtarbase database.
246
miRTarBase ID miRNA Experiments Reference
MIRT026061 hsa-miR-196a-5p Sequencing 20371350
MIRT032137 hsa-let-7d-5p Sequencing 20371350
MIRT042366 hsa-miR-484 CLASH 23622248
MIRT439779 hsa-miR-218-5p HITS-CLIP 23212916
MIRT439779 hsa-miR-218-5p HITS-CLIP 23212916
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
23
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0000785 Component Chromatin ISA
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA 9806546
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
601863 9986 ENSG00000143390
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P48382
Protein name DNA-binding protein RFX5 (Regulatory factor X 5)
Protein function Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding between RFX and NF-Y. RFX binds the X1 box of MHC-II promoters.
PDB 2KW3 , 3V30
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF18326 RFX5_N 28 86 RFX5 N-terminal domain Domain
PF02257 RFX_DNA_binding 89 168 RFX DNA-binding domain Domain
PF14621 RFX5_DNA_bdg 396 614 RFX5 DNA-binding domain Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitous.
Sequence
MAEDEPDAKSPKTGGRAPPGGAEAGEPTTLLQRLRGTISKAVQNKVEGILQDVQKFSDND
KLYLYLQLPSGPTTGDKSSEPSTLSN
EEYMYAYRWIRNHLEEHTDTCLPKQSVYDAYRKY
CESLACCRPLSTANFGKIIREIFPDIKARRLGGRGQSKYCYSGIRRKT
LVSMPPLPGLDL
KGSESPEMGPEVTPAPRDELVEAACALTCDWAERILKRSFSSIVEVARFLLQQHLISARS
AHAHVLKAMGLAEEDEHAPRERSSKPKNGLENPEGGAHKKPERLAQPPKDLEARTGAGPL
ARGERKKSVVESSAPGANNLQVNALVARLPLLLPRAPRSLIPPIPVSPPILAPRLSSGAL
KVATLPLSSRAGAPPAAVPIINMILPTVPALPGPGPGPGRAPPGGLTQPRGTENREVGIG
GDQGPHDKGVKRTAEVPVSEASGQAPPAKAAKQDIEDTASDAKRKRGRPRKKSGGSGERN
STPLKSAAAMESAQSSRLPWETWGSGGEGNSAGGAERPGPMGEAEKGAVLAQGQGDGTVS
KGGRGPGSQHTKEAEDKIPLVPSKVSVIKGSRSQKEAFPLAKGEVDTAPQGNKDLKEHVL
QSSLSQEHKDPKAT
PP
Sequence length 616
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Antigen processing and presentation
Tuberculosis
Primary immunodeficiency
 
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
398
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
MHC class II deficiency Likely pathogenic; Pathogenic rs1183832067, rs1650858382, rs992795118, rs1196551559, rs2102065180, rs758904746, rs1489967497, rs763938154, rs1557832711, rs367771361, rs1650653829, rs2529047720, rs1233130743, rs1228361094, rs2529019649
View all (19 more)
RCV001376181
RCV001385734
RCV001991699
RCV001959732
RCV002045058
RCV001889093
RCV001930685
RCV001965705
RCV001886213
RCV002238570
RCV002308617
RCV002469980
RCV003074905
RCV003091009
RCV002814977
RCV002881149
RCV003006010
RCV003031560
RCV003029913
RCV003155824
RCV005061379
RCV005104298
RCV003479550
RCV003524116
RCV003525261
RCV003636152
RCV003637013
RCV003637033
RCV003638058
RCV003638044
RCV003840150
RCV003853665
RCV000804318
RCV000802772
RCV000818355
RCV001219865
MHC class II deficiency 3 Likely pathogenic; Pathogenic rs1196551559, rs758904746, rs1233130743, rs556806561, rs748270285, rs2102068023, rs2529017348, rs1571256140 RCV005031925
RCV005042463
RCV004565683
RCV004562199
RCV004562201
RCV000008086
RCV004566480
RCV004561798
MHC class II deficiency 5 Likely pathogenic; Pathogenic rs1196551559, rs758904746 RCV005031925
RCV005042463
RFX5-related disorder Likely pathogenic; Pathogenic rs367771361, rs1363575527 RCV003399668
RCV003399673
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
MHC class II deficiency 1 Uncertain significance; Conflicting classifications of pathogenicity rs1557830458, rs2233846, rs769690666 RCV005630337
RCV005408043
RCV005408797
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Anodontia Associate 20013806
Bare lymphocyte syndrome 2 Associate 25445815, 9177217
Carcinogenesis Associate 31188160
Carcinoma Hepatocellular Associate 31188160, 32883983, 35291486
Carcinoma Non Small Cell Lung Associate 31096145
Colorectal Neoplasms Associate 20013806
Genetic Diseases Inborn Associate 12498778
Malocclusion Angle Class II Associate 12498778, 16848795, 7744245
Malocclusion Angle Class II Inhibit 29527204
Neoplasms Associate 20013806, 36045400