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

    Gene ID: 8625, updated on 2-Nov-2024

    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; MHC2D2; 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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19192258..19201866)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19328750..19338416)
    RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 14338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14339 Neighboring gene myocyte enhancer factor 2B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19271207-19272182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19281232-19281995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19282939-19283545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19285189-19285690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19296281-19296782 Neighboring gene BLOC-1 related complex subunit 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14342 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:19305905-19306056 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:19313199-19313465 Neighboring gene Sharpr-MPRA regulatory region 11890 Neighboring gene nuclear receptor 2C2 associated protein Neighboring gene Sharpr-MPRA regulatory region 3423 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:19324416-19324916 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:19324917-19325417 Neighboring gene neurocan Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14343 Neighboring gene RNA, U6 small nuclear 1028, pseudogene Neighboring gene hyaluronan and proteoglycan link protein 4

    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 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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical, Immunological, and Genetic Findings in Iranian Patients with MHC-II Deficiency: Confirmation of c.162delG RFXANK Founder Mutation in the Iranian Population.
      Title: Clinical, Immunological, and Genetic Findings in Iranian Patients with MHC-II Deficiency: Confirmation of c.162delG RFXANK Founder Mutation in the Iranian Population.
    2. Structural basis for the recognition of RFX7 by ANKRA2 and RFXANK.
      Title: Structural basis for the recognition of RFX7 by ANKRA2 and RFXANK.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    MHC class II deficiency
    MedGen: C2931418 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    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
    		  
    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/TrEMBL
      Q6IB23
      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/TrEMBL
      A0A024R7P0, Q6IB23
      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
      O14593, O95839, Q24JQ1, Q6FGA8
      UniProtKB/TrEMBL
      Q6IB23
      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
      UniProtKB/TrEMBL
      Q6IB23
      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
      UniProtKB/TrEMBL
      Q6IB23
      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
      UniProtKB/TrEMBL
      Q6IB23
      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
      UniProtKB/TrEMBL
      Q6IB23
      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
      UniProtKB/TrEMBL
      Q6IB23
      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, O95839, Q24JQ1, Q6FGA8
      UniProtKB/TrEMBL
      Q6IB23
      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/TrEMBL
      A0A024R7P0, Q6IB23
      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_2024_08

    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, O95839, Q24JQ1, Q6FGA8
      UniProtKB/TrEMBL
      Q6IB23
      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

      UniProtKB/TrEMBL
      Q6IB23
      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

      UniProtKB/Swiss-Prot
      O14593, O95839, Q24JQ1, Q6FGA8

    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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