RFXAP

Protein identityUniProt · HPA

UniProt accession

O00287

Gene

RFXAP

Ensembl

ENSG00000133111

Chromosome

13

Canonical length

272 aa

Protein class

Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors

Subcellular location

Nuclear speckles

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

272 residues, UniProt reviewed canonical sequence.

>O00287|RFXAP
     1  MEAQGVAEGA GPGAASGVPH PAALAPAAAP TLAPASVAAA ASQFTLLVMQ PCAGQDEAAA
    61  PGGSVGAGKP VRYLCEGAGD GEEEAGEDEA DLLDTSDPPG GGESAASLED LEDEETHSGG
   121  EGSSGGARRR GSGGGSMSKT CTYEGCSETT SQVAKQRKPW MCKKHRNKMY KDKYKKKKSD
   181  QALNCGGTAS TGSAGNVKLE ESADNILSIV KQRTGSFGDR PARPTLLEQV LNQKRLSLLR
   241  SPEVVQFLQK QQQLLNQQVL EQRQQQFPGT SM

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against RFXAP can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.65

Highest tissue expression

7.7 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about RFXAP.

Disease | AllUniProt

Conditions RFXAP is implicated in, by any mechanism.

• MHC class II deficiency 4 (MHC2D4) MIM:620817

Disease | GeneticClinVar

29 pathogenic / likely-pathogenic of 224 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• MHC class II deficiency
• MHC class II deficiency 4
• MHC class II deficiency 1

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.98

gnomAD pLI

0.02

gnomAD missense Z

1.04

DepMap mean gene effect

-0.09

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• positive regulation of MHC class II biosynthetic process
• positive regulation of transcription by RNA polymerase II
• regulation of transcription by RNA polymerase II

Molecular functions

• DNA binding

Cellular components

• nuclear speck
• nucleus
• RNA polymerase II transcription regulator complex

Protein domainsUniProt · Pfam · InterPro

• Regulatory factor X-associated protein, RFXANK-binding domain
• RFXAP, C-terminal domain superfamily
• Regulatory factor X-associated C-terminal binding domain

KeywordsUniProt

• DNA-binding
• Isopeptide bond
• Nucleus
• Phosphoprotein
• SCID
• Ubl conjugation

InteractionsUniProt · HPA

Protein binding partners of RFXAP in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• RFX5
• RFXANK