Gene Gene information from NCBI Gene database.
Entrez ID 5994
Gene name Regulatory factor X associated protein
Gene symbol RFXAP
Synonyms (NCBI Gene)
MHC2D4
Chromosome 13
Chromosome location 13q13.3
Summary 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 a
SNPs SNP information provided by dbSNP.
3
SNP ID Visualize variation Clinical significance Consequence
rs137853098 C>T Pathogenic Stop gained, coding sequence variant
rs754240018 T>A,G Pathogenic Stop gained, missense variant, coding sequence variant
rs1313207845 C>T Pathogenic Coding sequence variant, stop gained
miRNA miRNA information provided by mirtarbase database.
247
miRTarBase ID miRNA Experiments Reference
MIRT711792 hsa-miR-106a-5p HITS-CLIP 19536157
MIRT711791 hsa-miR-106b-5p HITS-CLIP 19536157
MIRT711790 hsa-miR-17-5p HITS-CLIP 19536157
MIRT711789 hsa-miR-20a-5p HITS-CLIP 19536157
MIRT711788 hsa-miR-20b-5p HITS-CLIP 19536157
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
14
GO ID Ontology Definition Evidence Reference
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA 9118943, 9806546
GO:0001228 Function DNA-binding transcription activator activity, RNA polymerase II-specific IDA 9118943, 9806546
GO:0003677 Function DNA binding IEA
GO:0005515 Function Protein binding IPI 10938133, 20732328, 25752541, 26496610, 28514442, 33961781
GO:0005634 Component Nucleus IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
601861 9988 ENSG00000133111
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O00287
Protein name Regulatory factor X-associated protein (RFX-associated protein) (RFX DNA-binding complex 36 kDa subunit)
Protein function Part of the RFX complex that binds to the X-box of MHC II promoters.
PDB 2KW3
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF15289 RFXA_RFXANK_bdg 140 267 Regulatory factor X-associated C-terminal binding domain Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitous.
Sequence
MEAQGVAEGAGPGAASGVPHPAALAPAAAPTLAPASVAAAASQFTLLVMQPCAGQDEAAA
PGGSVGAGKPVRYLCEGAGDGEEEAGEDEADLLDTSDPPGGGESAASLEDLEDEETHSGG
EGSSGGARRRGSGGGSMSKTCTYEGCSETTSQVAKQRKPWMCKKHRNKMYKDKYKKKKSD
QALNCGGTASTGSAGNVKLEESADNILSIVKQRTGSFGDRPARPTLLEQVLNQKRLSLLR
SPEVVQFLQKQQQLLNQQVLEQRQQQF
PGTSM
Sequence length 272
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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
7
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
MHC class II deficiency Pathogenic; Likely pathogenic rs1388967331, rs1249595284, rs2138212278, rs1224857205, rs2138213000, rs754240018, rs775250354, rs2057955936, rs749368415, rs1313207845 RCV001380175
RCV001380092
RCV001844513
RCV001959135
RCV002053870
View all (5 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MHC class II deficiency 1 Pathogenic rs775250354 RCV005632170
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MHC class II deficiency 4 Likely pathogenic; Pathogenic rs754240018, rs1250669587, rs2500443582, rs775250354, rs137853098, rs2500443426, rs2500443932, rs1415196376, rs1313207845 RCV005008122
RCV004576884
RCV004576885
RCV004576886
RCV004576887
View all (4 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
BARE LYMPHOCYTE SYNDROME 2 Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial prostate cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
RFXAP-related disorder Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute otitis media Otitis media HPO_DG
★☆☆☆☆
Found in Text Mining only
Agammaglobulinemia Agammaglobulinemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Autoimmune hemolytic anemia Autoimmune hemolytic anemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Bare Lymphocyte Syndrome Bare Lymphocyte Syndrome BEFREE 16337482, 22390233
★☆☆☆☆
Found in Text Mining only
Bare lymphocyte syndrome 2 Bare Lymphocyte Syndrome BEFREE 10825209, 15655668, 16337482, 22390233
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2 Bare lymphocyte syndrome Pubtator 25445815 Associate
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2 Bare Lymphocyte Syndrome CLINVAR_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2 Bare Lymphocyte Syndrome ORPHANET_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bare lymphocyte syndrome 2 Bare Lymphocyte Syndrome CTD_human_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Bare Lymphocyte Syndrome, Type II, Complementation Group D Bare Lymphocyte Syndrome GENOMICS_ENGLAND_DG 9806639
★☆☆☆☆
Found in Text Mining only