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

Gene ID: 546, updated on 19-Jul-2014
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
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]
See ATRX in Epigenomics, MapViewer
Location:
Xq21.1
Exon count :
37
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 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)

ISCA Genome Curation Page
Haploinsufficency

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

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

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 
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
 
methylated histone binding IDA
Inferred from Direct Assay
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
ATP catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
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
 
cellular response to hydroxyurea ISS
Inferred from Sequence or Structural Similarity
more info
 
chromatin remodeling IDA
Inferred from Direct Assay
more info
 
forebrain development 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
 
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
 
regulation of transcription, DNA-templated TAS
Traceable Author Statement
more info
PubMed 
replication fork processing ISS
Inferred from Sequence or Structural Similarity
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 
cytoplasm IDA
Inferred from Direct Assay
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nuclear heterochromatin TAS
Traceable Author Statement
more info
PubMed 
nucleolus 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
transcriptional regulator ATRX
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_000480.3
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 

    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 proteins identical to 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
    cd11726
    Location:161289
    Blast Score: 575
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15881750
    Blast Score: 188
    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: 237
    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: 788
    SNF2_N; SNF2 family N-terminal domain
  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
    cd11726
    Location:124251
    Blast Score: 575
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15501712
    Blast Score: 188
    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: 237
    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: 788
    SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000023.11 

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

mRNA and Protein(s)

  1. XM_005262157.2XP_005262214.2  

    Conserved Domains (4) summary
    cd11726
    Location:124250
    Blast Score: 573
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15201682
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  2. XM_006724666.1XP_006724729.1  

    Conserved Domains (4) summary
    cd11726
    Location:124250
    Blast Score: 574
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15491711
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  3. XM_005262153.2XP_005262210.2  

    Conserved Domains (4) summary
    cd11726
    Location:162288
    Blast Score: 574
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15871749
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  4. XM_005262154.2XP_005262211.2  

    Conserved Domains (4) summary
    cd11726
    Location:161289
    Blast Score: 575
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15591721
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  5. XM_005262155.2XP_005262212.2  

    Conserved Domains (4) summary
    cd11726
    Location:122250
    Blast Score: 574
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15491711
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  6. XM_005262156.2XP_005262213.2  

    Conserved Domains (4) summary
    cd11726
    Location:106234
    Blast Score: 574
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15331695
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  7. XM_006724667.1XP_006724730.1  

    Conserved Domains (4) summary
    cd11726
    Location:69196
    Blast Score: 573
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:14951657
    Blast Score: 188
    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
    Blast Score: 237
    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
    Blast Score: 788
    SNF2_N; SNF2 family N-terminal domain
  8. XM_006724668.1XP_006724731.1  

    Conserved Domains (3) summary
    cd11726
    Location:161289
    Blast Score: 557
    ADDz_ATRX; ADDz domain of ATRX (alpha-thalassemia/mental retardation, X-linked)
    cd00046
    Location:15881750
    Blast Score: 188
    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
    Blast Score: 724
    SNF2_N; SNF2 family N-terminal domain

Alternate HuRef

Genomic

  1. AC_000155.1 

    Range
    70349443..70629065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 

    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.

Supplemental Content

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