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RFXANK regulatory factor X associated ankyrin containing protein [ Homo sapiens (human) ]

Gene ID: 8625, updated on 21-Mar-2023

Summary

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Official Symbol
RFXANKprovided by HGNC
Official Full Name
regulatory factor X associated ankyrin containing proteinprovided by HGNC
Primary source
HGNC:HGNC:9987
See related
Ensembl:ENSG00000064490 MIM:603200; AllianceGenome:HGNC:9987
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BLS; RFX-B; ANKRA1; F14150_1
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 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. This protein contains ankyrin repeats involved in protein-protein interactions. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group B. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in thyroid (RPKM 13.0), bone marrow (RPKM 11.7) and 25 other tissues See more
Orthologs
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Genomic context

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See RFXANK in Genome Data Viewer
Location:
19p13.11
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19192258..19201866)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19328750..19338416)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19303067..19312675)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene BORCS8-MEF2B readthrough Neighboring gene myocyte enhancer factor 2B Neighboring gene BLOC-1 related complex subunit 8 Neighboring gene Sharpr-MPRA regulatory region 11890 Neighboring gene nuclear receptor 2C2 associated protein Neighboring gene Sharpr-MPRA regulatory region 3423 Neighboring gene neurocan

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. MHC Class II Deficiency with Normal CD4+ T Cell Counts: A Case Report. Abolnezhadian F, et al. Iran J Allergy Asthma Immunol, 2018 Dec 4. PMID 30644704
  2. Major Histocompatibility Complex Class II Deficiency due to a Novel Mutation in RFXANK in a Child of Mexican Descent. Clarridge K, et al. J Clin Immunol, 2016 Jan. PMID 26634365, Free PMC Article
  3. Major histocompatibility complex class II expression deficiency caused by a RFXANK founder mutation: a survey of 35 patients. Ouederni M, et al. Blood, 2011 Nov 10. PMID 21908431
  4. The 752delG26 mutation in the RFXANK gene associated with major histocompatibility complex class II deficiency: evidence for a founder effect in the Moroccan population. Naamane H, et al. Eur J Pediatr, 2010 Sep. PMID 20414676
  5. New functions of the major histocompatibility complex class II-specific transcription factor RFXANK revealed by a high-resolution mutagenesis study. Krawczyk M, et al. Mol Cell Biol, 2005 Oct. PMID 16166641, Free PMC Article

See all (37) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural basis for the recognition of RFX7 by ANKRA2 and RFXANK.
    Title: Structural basis for the recognition of RFX7 by ANKRA2 and RFXANK.
  2. this study reports an 8 month-old girl with MHC class II deficiency with a novel homozygous mutation in RFXANK gene and normal CD4+ T cell counts, diagnosed by whole exome sequencing and negative HLA-DR proteins on peripheral blood mononuclear cell in flow cytometry
    Title: MHC Class II Deficiency with Normal CD4+ T Cell Counts: A Case Report.
  3. these data identify a novel caspase-2-interacting factor, RFXANK, and indicate a potential non-apoptotic role for the enzyme in the control of MHC class II gene regulation.
    Title: A caspase-2-RFXANK interaction and its implication for MHC class II expression.
  4. mutation results in Bare Lymphocyte Syndrome, Type 2 in a child of Mexican descent
    Title: Major Histocompatibility Complex Class II Deficiency due to a Novel Mutation in RFXANK in a Child of Mexican Descent.
  5. genetic, clinical, and immunologic features of 35 patients from 30 unrelated kindreds from North Africa sharing the same RFXANK founder mutation, a 26-bp deletion called I5E6-25_I5E6 + 1)
    Title: Major histocompatibility complex class II expression deficiency caused by a RFXANK founder mutation: a survey of 35 patients.
  6. Findings confirm the association between the high frequency of the combined immunodeficiency and the defect in MHC class II expression and provides strong evidence for a founder effect of the 752delG26 mutation in the North African population.
    Title: The 752delG26 mutation in the RFXANK gene associated with major histocompatibility complex class II deficiency: evidence for a founder effect in the Moroccan population.
  7. RFXAP and RFXB have roles in relieving autoinhibition of RFX5
    Title: Assembly of the RFX complex on the MHCII promoter: role of RFXAP and RFXB in relieving autoinhibition of RFX5.
  8. analysis of RFXANK domains and function
    Title: New functions of the major histocompatibility complex class II-specific transcription factor RFXANK revealed by a high-resolution mutagenesis study.
  9. in vivo effects of mutations on the expression of the RFXANK RNA and protein
    Title: Novel mutations in the RFXANK gene: RFX complex containing in-vitro-generated RFXANK mutant binds the promoter without transactivating MHC II.
  10. ANKRA, RFXANK, and CIITA are novel targets of class IIa HDACs which may deacetylases play a role in regulating MHCII expression
    Title: Identification of the ankyrin repeat proteins ANKRA and RFXANK as novel partners of class IIa histone deacetylases.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
MHC class II deficiency
MedGen: C2931418 OMIM: 209920 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC138628

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone deacetylase binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Ras protein signal transduction IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of MHC class II biosynthetic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intercellular bridge IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA-binding protein RFXANK
Names
RFX-Bdelta4
ankyrin repeat family A protein 1
ankyrin repeat-containing regulatory factor X-associated protein
regulatory factor X subunit B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007432.1 RefSeqGene

    Range
    5001..14671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_102

mRNA and Protein(s)

  1. NM_001278727.2 → NP_001265656.1  DNA-binding protein RFXANK isoform c

    See identical proteins and their annotated locations for NP_001265656.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, as compared to variant 1. The resulting isoform (c) lacks an internal segment, as compared to isoform a.
    Source sequence(s)
    AF094760, AW411190, BC114558
    Consensus CDS
    CCDS62611.1
    UniProtKB/Swiss-Prot
    O14593
    Related
    ENSP00000409138.2, ENST00000456252.7
    Conserved Domains (2) summary
    sd00045
    Location:101 → 132
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:106 → 196
    Ank_2; Ankyrin repeats (3 copies)

  2. NM_001278728.2 → NP_001265657.1  DNA-binding protein RFXANK isoform b

    See identical proteins and their annotated locations for NP_001265657.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, and has an alternate splice site and lacks an in-frame exon in the coding region, as compared to variant 1. The resulting isoform (b) lacks an internal single aa and an internal segment, as compared to isoform a. Variants 2 and 4 encode the same isoform c.
    Source sequence(s)
    AF105428, AW411190, BG740813
    Consensus CDS
    CCDS12396.1
    UniProtKB/Swiss-Prot
    O14593
    UniProtKB/TrEMBL
    A0A024R7P0
    Related
    ENSP00000376138.3, ENST00000392324.8
    Conserved Domains (3) summary
    cd00204
    Location:95 → 215
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:105 → 194
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:100 → 131
    ANK; ANK repeat [structural motif]

  3. NM_001370233.1 → NP_001357162.1  DNA-binding protein RFXANK isoform a

    Status: REVIEWED

    Source sequence(s)
    AC002126, AC003110
    Consensus CDS
    CCDS12395.1
    UniProtKB/Swiss-Prot
    Q6FGA8
    UniProtKB/TrEMBL
    A0A024R7M1
    Related
    ENSP00000384572.3, ENST00000407360.7
    Conserved Domains (3) summary
    COG0666
    Location:73 → 258
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  4. NM_001370234.1 → NP_001357163.1  DNA-binding protein RFXANK isoform c

    Status: REVIEWED

    Source sequence(s)
    AC002126, AC003110
    Consensus CDS
    CCDS62611.1
    Conserved Domains (2) summary
    sd00045
    Location:101 → 132
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:106 → 196
    Ank_2; Ankyrin repeats (3 copies)

  5. NM_001370235.1 → NP_001357164.1  DNA-binding protein RFXANK isoform d

    Status: REVIEWED

    Source sequence(s)
    AC002126, AC003110
    Conserved Domains (3) summary
    COG0666
    Location:72 → 257
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:122 → 153
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:127 → 217
    Ank_2; Ankyrin repeats (3 copies)

  6. NM_001370236.1 → NP_001357165.1  DNA-binding protein RFXANK isoform d

    Status: REVIEWED

    Source sequence(s)
    AC002126, AC003110
    Conserved Domains (3) summary
    COG0666
    Location:72 → 257
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:122 → 153
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:127 → 217
    Ank_2; Ankyrin repeats (3 copies)

  7. NM_001370237.1 → NP_001357166.1  DNA-binding protein RFXANK isoform e

    Status: REVIEWED

    Source sequence(s)
    AC002126, AC003110
    Conserved Domains (3) summary
    PTZ00322
    Location:59 → 248
    PTZ00322; 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional
    sd00045
    Location:122 → 153
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:127 → 217
    Ank_2; Ankyrin repeats (3 copies)

  8. NM_001370238.1 → NP_001357167.1  DNA-binding protein RFXANK isoform f

    Status: REVIEWED

    Source sequence(s)
    AC002126, AC003110
    Conserved Domains (4) summary
    PHA02798
    Location:171 → 278
    PHA02798; ankyrin-like protein; Provisional
    COG0666
    Location:35 → 218
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  9. NM_003721.4 → NP_003712.1  DNA-binding protein RFXANK isoform a

    See identical proteins and their annotated locations for NP_003712.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF094760, AW411190, BM682278
    Consensus CDS
    CCDS12395.1
    UniProtKB/Swiss-Prot
    O14593, Q6FGA8
    UniProtKB/TrEMBL
    A0A024R7M1
    Related
    ENSP00000305071.2, ENST00000303088.9
    Conserved Domains (3) summary
    COG0666
    Location:73 → 258
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  10. NM_134440.3 → NP_604389.1  DNA-binding protein RFXANK isoform b

    See identical proteins and their annotated locations for NP_604389.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate splice site and lacks an in-frame exon in the coding region, as compared to transcript variant 1. The resulting isoform (b) lacks an internal single aa and an internal segment, as compared to isoform a. Variants 2 and 4 encode the same isoform c.
    Source sequence(s)
    AF105428, AW411190, BM682278, CX871218
    Consensus CDS
    CCDS12396.1
    UniProtKB/Swiss-Prot
    O14593
    UniProtKB/TrEMBL
    A0A024R7P0
    Conserved Domains (3) summary
    cd00204
    Location:95 → 215
    ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...
    pfam12796
    Location:105 → 194
    Ank_2; Ankyrin repeats (3 copies)
    sd00045
    Location:100 → 131
    ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    19192258..19201866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005260134.6 → XP_005260191.1  DNA-binding protein RFXANK isoform X5

    See identical proteins and their annotated locations for XP_005260191.1

    UniProtKB/Swiss-Prot
    O14593, Q6FGA8
    UniProtKB/TrEMBL
    A0A024R7M1
    Conserved Domains (3) summary
    COG0666
    Location:73 → 258
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  2. XM_047439590.1 → XP_047295546.1  DNA-binding protein RFXANK isoform X2

    Conserved Domains (3) summary
    PTZ00322
    Location:59 → 248
    PTZ00322; 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional
    sd00045
    Location:122 → 153
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:127 → 217
    Ank_2; Ankyrin repeats (3 copies)

  3. XM_005260137.5 → XP_005260194.1  DNA-binding protein RFXANK isoform X6

    See identical proteins and their annotated locations for XP_005260194.1

    Conserved Domains (3) summary
    COG0666
    Location:72 → 257
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:122 → 153
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:127 → 217
    Ank_2; Ankyrin repeats (3 copies)

  4. XM_047439586.1 → XP_047295542.1  DNA-binding protein RFXANK isoform X1

    Conserved Domains (4) summary
    PHA02798
    Location:171 → 278
    PHA02798; ankyrin-like protein; Provisional
    COG0666
    Location:35 → 218
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  5. XM_047439589.1 → XP_047295545.1  DNA-binding protein RFXANK isoform X2

    Conserved Domains (3) summary
    PTZ00322
    Location:59 → 248
    PTZ00322; 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional
    sd00045
    Location:122 → 153
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:127 → 217
    Ank_2; Ankyrin repeats (3 copies)

  6. XM_047439593.1 → XP_047295549.1  DNA-binding protein RFXANK isoform X4

  7. XM_047439587.1 → XP_047295543.1  DNA-binding protein RFXANK isoform X1

    Conserved Domains (4) summary
    PHA02798
    Location:171 → 278
    PHA02798; ankyrin-like protein; Provisional
    COG0666
    Location:35 → 218
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  8. XM_047439594.1 → XP_047295550.1  DNA-binding protein RFXANK isoform X6

  9. XM_047439588.1 → XP_047295544.1  DNA-binding protein RFXANK isoform X1

    Conserved Domains (4) summary
    PHA02798
    Location:171 → 278
    PHA02798; ankyrin-like protein; Provisional
    COG0666
    Location:35 → 218
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    sd00045
    Location:123 → 154
    ANK; ANK repeat [structural motif]
    pfam12796
    Location:128 → 218
    Ank_2; Ankyrin repeats (3 copies)

  10. XM_047439591.1 → XP_047295547.1  DNA-binding protein RFXANK isoform X3

  11. XM_047439592.1 → XP_047295548.1  DNA-binding protein RFXANK isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19328750..19338416
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322479.1 → XP_054178454.1  DNA-binding protein RFXANK isoform X6

  2. XM_054322478.1 → XP_054178453.1  DNA-binding protein RFXANK isoform X5

  3. XM_054322472.1 → XP_054178447.1  DNA-binding protein RFXANK isoform X1

  4. XM_054322475.1 → XP_054178450.1  DNA-binding protein RFXANK isoform X2

  5. XM_054322477.1 → XP_054178452.1  DNA-binding protein RFXANK isoform X4

  6. XM_054322473.1 → XP_054178448.1  DNA-binding protein RFXANK isoform X1

  7. XM_054322480.1 → XP_054178455.1  DNA-binding protein RFXANK isoform X6

  8. XM_054322474.1 → XP_054178449.1  DNA-binding protein RFXANK isoform X1

  9. XM_054322476.1 → XP_054178451.1  DNA-binding protein RFXANK isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14593.2 GenPept UniProtKB/Swiss-Prot:O14593

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