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

    Gene ID: 546, updated on 20-May-2012

    Summary

    Official Symbol
    ATRXprovided by HGNC
    Official Full Name
    alpha thalassemia/mental retardation syndrome X-linkedprovided by HGNC
    Primary source
    HGNC:886
    Locus tag
    RP5-875J14.1
    See related
    Ensembl:ENSG00000085224; HPRD:02069; MIM:300032; 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; RAD54; MRXHF1; RAD54L; ZNF-HX; MGC2094
    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. The mutations of 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. 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. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

    Genomic context

    Location :
    Xq21.1
    Sequence :
    Chromosome: X; NC_000023.10 (76760356..77041719, complement)
    See ATRX in Epigenomics, MapViewer

    Chromosome X - NC_000023.10Genomic Context describing neighboring genes Neighboring gene SPRY domain containing 7 pseudogene Neighboring gene fibroblast growth factor 16 Neighboring gene uncharacterized LOC100506800 Neighboring gene magnesium transporter 1 Neighboring gene cytochrome c oxidase subunit VIIb

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    Phenotypes

    Alpha-thalassemia myelodysplasia syndrome, somatic

    Chudley-Lowry syndrome

    Sutherland-Haan syndrome-like

    Summary from GeneReviews: Go to GeneReviews

    Disease Characteristics
    Alpha-thalassemia X-linked intellectual disability (ATRX) syndrome is characterized by distinctive craniofacial features, genital anomalies, severe developmental delays, hypotonia, intellectual disability, and mild-to-moderate anemia secondary to alpha-thalassemia. Craniofacial abnormalities include small head circumference, telecanthus or ocular hypertelorism, small nose, tented upper lip, and prominent or everted lower lip with coarsening of the facial features over time. Although all affected individuals have a normal 46,XY karyotype, genital anomalies range from hypospadias and undescended testicles to severe hypospadias and ambiguous genitalia, to normal-appearing female genitalia. Global developmental delays are evident in infancy and some affected individuals never walk independently or develop significant speech.
    Diagnosis Testing
    The diagnosis of ATRX syndrome is established in individuals with somatic abnormalities, intellectual disability, hypotonia, abnormal hemoglobin H production, and a family history consistent with X-linked inheritance. Molecular genetic testing of ATRX, the only gene associated with ATRX syndrome, is clinically available.
    Genetic Counseling
    ATRX syndrome is inherited in an X-linked manner. The mother of a proband may be a carrier or the affected individual may have a de novo gene mutation. Carrier women have a 50% chance in each pregnancy of transmitting the ATRX mutation; offspring with a 46,XY karyotype who inherit the ATRX mutation will be affected; offspring with a 46,XX karyotype who inherit the mutation are unaffected female carriers. Affected individuals do not reproduce. Carrier testing for at-risk females and prenatal testing for pregnancies at increased risk are possible if the disease-causing mutation in the family is known.
    References

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    P46100 P54259 ATN1    HPRD  PubMed  
    P46100 Q9UER7 DAXX    HPRD  PubMed  
    P46100 Q15910 EZH2    HPRD  PubMed  
    P46100 KIAA1128 FAM190B    HPRD  PubMed  
    P46100 Q13547 HDAC1    HPRD  PubMed  
    P46100 P56524 HDAC4    HPRD  PubMed  
    P46100 Q9P2H0 KIAA1377    HPRD  PubMed  
    P46100 Q9Y383 LUC7L2    HPRD  PubMed  
    P46100 Q96PY6 NEK1    HPRD  PubMed  
    P46100 P21246 PTN    HPRD  PubMed  
    P46100 P29074 PTPN4    HPRD  PubMed  
    P46100 Q06609 RAD51    HPRD  PubMed  
    BioGRID:107028 BioGRID:107252 CALM1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107028 BioGRID:117030 CBX5    BioGRID  PubMed Affinity Capture-Western; Co-localization; Protein-peptide 
    BioGRID:107028 BioGRID:107985 DAXX    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western; Co-fractionation; Co-purification; Reconstituted Complex 
    BioGRID:107028 BioGRID:108290 EIF4A2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107028 BioGRID:108446 EZH2    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:107028 BioGRID:119968 FAM190B    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:109272 H3F3A    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western 
    BioGRID:107028 BioGRID:109273 H3F3B    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:107028 BioGRID:115106 HDAC4    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:113946 HIST1H3A    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107028 BioGRID:121617 KIAA1377    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:119646 LUC7L2    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:32804 MMS4    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107028 BioGRID:32447 MUS81    BioGRID  PubMed Reconstituted Complex 
    BioGRID:107028 BioGRID:248038 Mecp2    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:111731 PTN    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:111741 PTPN4    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:111825 RAD51    BioGRID  PubMed Reconstituted Complex; Two-hybrid 
    BioGRID:107028 BioGRID:113871 SMC1A    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:107028 BioGRID:112497 SUMO2    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107028 BioGRID:112707 SVIL    BioGRID  PubMed Two-hybrid 
    BioGRID:107028 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:107028 BioGRID:113323 WRN    BioGRID  PubMed Far Western 
    BioGRID:107028 BioGRID:114626 ZBED1    BioGRID  PubMed Affinity Capture-Western; Reconstituted Complex 

    General gene information

    Markers

    Homology

    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 
    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 
    hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    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 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
     
    forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription, DNA-dependent TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    nuclear chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    nuclear heterochromatin TAS
    Traceable Author Statement
    more info
    PubMed 
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    transcriptional regulator ATRX
    Names
    transcriptional regulator ATRX
    RAD54 homolog
    X-linked helicase II
    Zinc finger helicase
    helicase 2, X-linked
    X-linked nuclear protein
    ATP-dependent helicase ATRX
    DNA dependent ATPase and helicase
    alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae)
    NP_000480.2
    NP_612114.1

    NCBI Reference Sequences (RefSeq)

    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_008838.1 RefSeqGene

      Range
      5001..286364
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000489.3NP_000480.2  transcriptional regulator ATRX isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA484729, AA732359, AI733378, BE927791, BM714186, BQ189245, BX647222, CB114986, DA759777, DR422800, U72937
      Consensus CDS
      CCDS14434.1
      UniProtKB/Swiss-Prot
      P46100
      Related
      ENSP00000362441, OTTHUMP00000024265, ENST00000373344, OTTHUMT00000058860
      Conserved Domains (3) summary
      cd00046
      Location:15881750
      Blast Score: 165
      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
      Blast Score: 209
      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
      Blast Score: 808
      SNF2_N; SNF2 family N-terminal domain
    2. NM_138270.2NP_612114.1  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)
      AA484729, AA732359, AI733378, BE927791, BM714186, BQ189245, BX647222, CB114986, DA759777, DR422800, U72938
      Consensus CDS
      CCDS14435.1
      UniProtKB/Swiss-Prot
      P46100
      Related
      ENSP00000378967, OTTHUMP00000024266, ENST00000395603, OTTHUMT00000058861
      Conserved Domains (3) summary
      cd00046
      Location:15501712
      Blast Score: 165
      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
      Blast Score: 209
      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
      Blast Score: 808
      SNF2_N; SNF2 family N-terminal domain

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000023.10 Reference GRCh37.p5 Primary Assembly

      Range
      76760356..77041719, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000155.1 Alternate HuRef

      Range
      70349443..70629029, complement
      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.

    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AB101681.1 BAC80270.1
    genomic AB101682.1 BAC80271.1
    genomic AB101683.1 BAC80272.1
    genomic AB101684.1 BAC80273.1
    genomic AB101685.1 BAC80274.1
    genomic AB101686.1 BAC80275.1
    genomic AB101687.1 BAC80276.1
    genomic AB101688.1 BAC80277.1
    genomic AB101689.1 BAC80278.1
    genomic AB101690.1 BAC80279.1
    genomic AB101691.1 BAC80280.1
    genomic AB101692.1 BAC80281.1
    genomic AB101693.1 BAC80282.1
    genomic AB101694.1 BAC80283.1
    genomic AB101695.1 BAC80284.1
    genomic AB101696.1 BAC80285.1
    genomic AB101697.1 BAC80286.1
    genomic AB101698.1 BAC80287.1
    genomic AB101699.1 BAC80288.1
    genomic AB101700.1 BAC80289.1
    genomic AL109753.9 CAI43115.1
      CAI43116.1
      CAI43117.1
    genomic AL121874.12 CAB90351.2
      CAI40710.1
    genomic AL121874.12 CAB90351.2
      CAI40710.1
    genomic CH471104.2 EAW98611.1
      EAW98612.1
      EAW98613.1
      EAW98614.1
      EAW98615.1
    genomic L34363.1 AAA20872.1
    genomic U72935.1 AAB40698.1
      AAB40699.1
      AAB40700.1
    genomic U75653.1 AAC51655.1
    genomic U97103.1 AAC51657.1
    genomic X83753.1 CAA58711.1
    genomic Z84487.2 CAI42674.1
      CAI42675.1
      CAI42677.1
    mRNA AA484729.1 None
    mRNA AA732359.1 None
    mRNA AB102641.1 BAC81110.1
    mRNA AB208928.1 BAD92165.1
    mRNA AB209545.1 BAD92782.1
    mRNA AI733378.1 None
    mRNA AK293241.1 BAH11474.1
    mRNA AK295107.1 BAG58140.1
    mRNA AK296959.1 BAG59503.1
    mRNA AK297183.1 BAG59673.1
    mRNA AK307791.1 None
    mRNA AK308419.1 None
    mRNA BC002521.2 AAH02521.1
    mRNA BE927791.1 None
    mRNA BM714186.1 None
    mRNA BQ189245.1 None
    mRNA BT007188.1 AAP35852.1
    mRNA BX647222.1 None
    mRNA CB114986.1 None
    mRNA DA759777.1 None
    mRNA DR422800.1 None
    mRNA L33812.1 None
    mRNA U09820.1 AAC50069.1
    mRNA U72936.2 AAB49969.1
    mRNA U72937.2 AAB49970.2
    mRNA U72938.2 AAB49971.2
    other-genetic BC156296.1 AAI56297.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    P46100.5 GenPept UniProtKB/Swiss-Prot:P46100
    Q86U63 GenPept UniProtKB/TrEMBL:Q86U63

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