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    ATRX alpha thalassemia/mental retardation syndrome X-linked [ Homo sapiens (human) ]

    Gene ID: 546, updated on 6-Aug-2015
    Official Symbol
    ATRXprovided by HGNC
    Official Full Name
    alpha thalassemia/mental retardation syndrome X-linkedprovided by HGNC
    Primary source
    HGNC:HGNC:886
    See related
    Ensembl:ENSG00000085224; HPRD:02069; MIM:300032; MIM:300504; Vega:OTTHUMG00000022686
    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
    JMS; SHS; XH2; XNP; ATR2; SFM1; MRX52; RAD54; MRXHF1; RAD54L; ZNF-HX
    Summary
    The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. This protein is found to undergo cell cycle-dependent phosphorylation, which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at interphase and chromosomal segregation in mitosis. Mutations in this gene are associated with an X-linked mental retardation (XLMR) syndrome most often accompanied by alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2013]
    Orthologs
    See ATRX in Epigenomics, MapViewer
    Location:
    Xq21.1
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    107 current GRCh38.p2 (GCF_000001405.28) X NC_000023.11 (77504878..77786269, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (76760356..77041755, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 pseudogene Neighboring gene fibroblast growth factor 16 Neighboring gene fatty acid binding protein 5 pseudogene 15 Neighboring gene magnesium transporter 1 Neighboring gene cytochrome c oxidase subunit VIIb

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Acquired hemoglobin H disease
    MedGen: C0585216 OMIM: 300448 GeneReviews: Not available
    Compare labs
    ATR-X syndrome Compare labs
    Mental retardation-hypotonic facies syndrome X-linked, 1
    MedGen: C0796003 OMIM: 309580 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-07-31)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-31)

    ClinGen Genome Curation PagePubMed
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC2094

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA helicase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA translocase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    chromo shadow domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    helicase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    methylated histone binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    DNA damage response, signal transduction by p53 class mediator ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    DNA duplex unwinding TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA methylation TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA recombination TAS
    Traceable Author Statement
    more info
    PubMed 
    DNA repair IEA
    Inferred from Electronic Annotation
    more info
     
    DNA replication-independent nucleosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Sertoli cell development IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to hydroxyurea ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    multicellular organism growth IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of telomeric RNA transcription from RNA pol II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of nuclear cell cycle DNA replication ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of telomere maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    post-embryonic forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription, DNA-templated TAS
    Traceable Author Statement
    more info
    PubMed 
    replication fork processing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    seminiferous tubule development IEA
    Inferred from Electronic Annotation
    more info
     
    spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    PML body IEA
    Inferred from Electronic Annotation
    more info
     
    SWI/SNF superfamily-type complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear heterochromatin TAS
    Traceable Author Statement
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    telomeric heterochromatin ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Preferred Names
    transcriptional regulator ATRX
    Names
    ATP-dependent helicase ATRX
    DNA dependent ATPase and helicase
    X-linked helicase II
    X-linked nuclear protein
    Zinc finger helicase
    alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)
    helicase 2, X-linked
    mental retardation, X-linked 52
    NP_000480.3
    NP_612114.2

    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_008838.2 RefSeqGene

      Range
      4953..286344
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000489.4NP_000480.3  transcriptional regulator ATRX isoform 1

      See identical proteins and their annotated locations for NP_000480.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA732359, AB102641, AC233305, AK297183, DA791316, U72937
      Consensus CDS
      CCDS14434.1
      UniProtKB/TrEMBL
      A4LAA3
      UniProtKB/TrEMBL
      B4DLW1
      UniProtKB/Swiss-Prot
      P46100
      Related
      ENSP00000362441, OTTHUMP00000024265, ENST00000373344, OTTHUMT00000058860
      Conserved Domains (4) summary
      cd00046
      Location:15881750
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:20172163
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15631889
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:167270
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    2. NM_138270.3NP_612114.2  transcriptional regulator ATRX isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment within the coding region when compared to variant 1. The translation remains in-frame, and thus results in an isoform (2) that lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AA732359, AB102641, AC233305, DA791316, U72938
      Consensus CDS
      CCDS14435.1
      UniProtKB/Swiss-Prot
      P46100
      Related
      ENSP00000378967, OTTHUMP00000024266, ENST00000395603, OTTHUMT00000058861
      Conserved Domains (4) summary
      cd00046
      Location:15501712
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19792125
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15251851
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:129232
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

    Reference GRCh38.p2 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p2 Primary Assembly

      Range
      77504878..77786269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005262157.3XP_005262214.2  

      Conserved Domains (4) summary
      cd00046
      Location:15201682
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19492095
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:14951821
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:128231
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    2. XM_006724666.2XP_006724729.1  

      Conserved Domains (4) summary
      cd00046
      Location:15491711
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19782124
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15241850
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:128231
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    3. XM_005262153.3XP_005262210.2  

      Conserved Domains (4) summary
      cd00046
      Location:15871749
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:20162162
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15621888
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:166269
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    4. XM_005262154.3XP_005262211.2  

      Conserved Domains (4) summary
      cd00046
      Location:15591721
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19882134
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15341860
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:167270
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    5. XM_005262155.3XP_005262212.2  

      Conserved Domains (4) summary
      cd00046
      Location:15491711
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19782124
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15241850
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:128231
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    6. XM_005262156.3XP_005262213.2  

      Conserved Domains (4) summary
      cd00046
      Location:15331695
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19622108
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:15081834
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:112215
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    7. XM_006724667.2XP_006724730.1  

      Conserved Domains (4) summary
      cd00046
      Location:14951657
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      cd00079
      Location:19242070
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      pfam00176
      Location:14701796
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:74177
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)
    8. XM_006724668.2XP_006724731.1  

      Conserved Domains (3) summary
      cd00046
      Location:15881750
      DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
      pfam00176
      Location:15631870
      SNF2_N; SNF2 family N-terminal domain
      cd11726
      Location:167270
      ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

    RNA

    1. XR_938400.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018934.2 Alternate CHM1_1.1

      Range
      76653073..76934456
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_138271.1: Suppressed sequence

      Description
      NM_138271.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.