RFX5

Protein identityUniProt · HPA

UniProt accession

P48382

Gene

RFX5

Ensembl

ENSG00000143390

Chromosome

1

Canonical length

616 aa

Protein class

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

Subcellular location

Nucleoplasm,Vesicles

Quaternary structure

Homodimer

OverviewNCBI Gene

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 BLS. The molecular defects in complementation groups B, C, and D all lead to a deficiency in RFX, a nuclear protein complex that binds to the X box of MHC-II promoters. The lack of RFX binding activity in complementation group C results from mutations in the RFX5 gene encoding the 75-kD subunit of RFX (Steimle et al., 1995). RFX5 is the fifth member of the growing family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif. Multiple alternatively spliced transcript variants have been found but the full-length natures of only two have been determined. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

616 residues, UniProt reviewed canonical sequence.

>P48382|RFX5
     1  MAEDEPDAKS PKTGGRAPPG GAEAGEPTTL LQRLRGTISK AVQNKVEGIL QDVQKFSDND
    61  KLYLYLQLPS GPTTGDKSSE PSTLSNEEYM YAYRWIRNHL EEHTDTCLPK QSVYDAYRKY
   121  CESLACCRPL STANFGKIIR EIFPDIKARR LGGRGQSKYC YSGIRRKTLV SMPPLPGLDL
   181  KGSESPEMGP EVTPAPRDEL VEAACALTCD WAERILKRSF SSIVEVARFL LQQHLISARS
   241  AHAHVLKAMG LAEEDEHAPR ERSSKPKNGL ENPEGGAHKK PERLAQPPKD LEARTGAGPL
   301  ARGERKKSVV ESSAPGANNL QVNALVARLP LLLPRAPRSL IPPIPVSPPI LAPRLSSGAL
   361  KVATLPLSSR AGAPPAAVPI INMILPTVPA LPGPGPGPGR APPGGLTQPR GTENREVGIG
   421  GDQGPHDKGV KRTAEVPVSE ASGQAPPAKA AKQDIEDTAS DAKRKRGRPR KKSGGSGERN
   481  STPLKSAAAM ESAQSSRLPW ETWGSGGEGN SAGGAERPGP MGEAEKGAVL AQGQGDGTVS
   541  KGGRGPGSQH TKEAEDKIPL VPSKVSVIKG SRSQKEAFPL AKGEVDTAPQ GNKDLKEHVL
   601  QSSLSQEHKD PKATPP

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against RFX5 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)

0.63

Highest tissue expression

67 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about RFX5.

Disease | AllUniProt

Conditions RFX5 is implicated in, by any mechanism.

• MHC class II deficiency 3 (MHC2D3) MIM:620816
• MHC class II deficiency 5 (MHC2D5) MIM:620818

Disease | GeneticClinVar

51 pathogenic / likely-pathogenic of 475 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• MHC class II deficiency
• MHC class II deficiency 3
• MHC class II deficiency 5
• RFX5-related disorder

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)

1.1

gnomAD pLI

0

gnomAD missense Z

0.48

DepMap mean gene effect

-0.25

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• negative regulation of transcription by RNA polymerase II
• 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 transcription activator activity, RNA polymerase II-specific
• DNA-binding transcription factor activity, RNA polymerase II-specific
• RNA polymerase II cis-regulatory region sequence-specific DNA binding
• RNA polymerase II transcription regulatory region sequence-specific DNA binding
• sequence-specific DNA binding
• sequence-specific double-stranded DNA binding
• transcription coregulator binding

Cellular components

• chromatin
• nucleoplasm
• nucleus
• RNA polymerase II transcription regulator complex

Protein domainsUniProt · Pfam · InterPro

• DNA-binding RFX-type winged-helix domain
• Winged helix-like DNA-binding domain superfamily
• Winged helix DNA-binding domain superfamily
• RFX-like DNA-binding protein
• RFX DNA-binding domain
• RFX5 N-terminal domain
• RFX5, C-terminal
• RFX5 DNA-binding domain

KeywordsUniProt

• Acetylation
• Activator
• DNA-binding
• Nucleus
• Phosphoprotein
• SCID
• Transcription
• Transcription regulation

InteractionsUniProt · HPA

Protein binding partners of RFX5 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• RFXANK
• RFXAP