Human Gene ATRX (ENST00000373344.10) Description and Page Index
  Description: Homo sapiens ATRX chromatin remodeler (ATRX), transcript variant 1, mRNA. (from RefSeq NM_000489)
RefSeq Summary (NM_000489): 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 X-linked syndromes exhibiting cognitive disabilities as well as 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, Jul 2017].
Gencode Transcript: ENST00000373344.10
Gencode Gene: ENSG00000085224.22
Transcript (Including UTRs)
   Position: hg38 chrX:77,504,878-77,786,216 Size: 281,339 Total Exon Count: 35 Strand: -
Coding Region
   Position: hg38 chrX:77,508,351-77,786,001 Size: 277,651 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesGeneReviewsMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chrX:77,504,878-77,786,216)mRNA (may differ from genome)Protein (2492 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Transcriptional regulator ATRX; EC=; AltName: Full=ATP-dependent helicase ATRX; AltName: Full=X-linked helicase II; AltName: Full=X-linked nuclear protein; Short=XNP; AltName: Full=Znf-HX;
FUNCTION: Could be a global transcriptional regulator. Modifies gene expression by affecting chromatin. May be involved in brain development and facial morphogenesis.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Probably binds EZH2. Binds annexin V in a calcium and phosphatidylcholine/phosphatidylserine-dependent manner (By similarity). Interacts directly with CBX5 via the PxVxL motif.
INTERACTION: Q9UER7:DAXX; NbExp=3; IntAct=EBI-396461, EBI-77321;
SUBCELLULAR LOCATION: Nucleus. Note=Associated with pericentromeric heterochromatin during interphase and mitosis, probably by interacting with HP1.
DOMAIN: Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the chromoshadow domain.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in ATRX are the cause of alpha-thalassemia mental retardation syndrome X-linked (ATRX) [MIM:301040]. ATR-X is an X- linked disorder comprising severe psychomotor retardation, facial dysmorphism, urogenital abnormalities, and alpha-thalassemia. An essential phenotypic trait are hemoglobin H erythrocyte inclusions.
DISEASE: Defects in ATRX are the cause of mental retardation syndromic X-linked with hypotonic facies syndrome type 1 (MRXSHF1) [MIM:309580]; also called Carpenter-Waziri syndrome (CWS), Juberg- Marsidi syndrome (JMS), Smith-Fineman-Myers syndrome type 1 (SFM1). Clinical features include severe mental retardation, dysmorphic facies, and a highly skewed X-inactivation pattern in carrier women. Other more variable features include hypogonadism, deafness, renal anomalies, and mild skeletal defects.
DISEASE: Defects in ATRX are a cause of alpha-thalassemia myelodysplasia syndrome (ATMDS) [MIM:300448]. In this disorder, alpha-thalassemia occurs as an acquired abnormality in association with a multilineage myelodysplasia.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 1 ADD domain.
SIMILARITY: Contains 1 GATA-type zinc finger.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SIMILARITY: Contains 1 PHD-type zinc finger.
SEQUENCE CAUTION: Sequence=AAA20872.1; Type=Miscellaneous discrepancy; Note=Many frameshifts and conflits; Sequence=AAC50069.1; Type=Frameshift; Positions=Several; Sequence=BAD92165.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
WEB RESOURCE: Name=GeneReviews; URL="";

-  MalaCards Disease Associations
  MalaCards Gene Search: ATRX
Diseases sorted by gene-association score: mental retardation-hypotonic facies syndrome, x-linked* (1671), alpha-thalassemia/mental retardation syndrome* (1628), alpha-thalassemia myelodysplasia syndrome, somatic* (1250), alpha thalassemia-x-linked intellectual disability syndrome* (528), intellectual disability* (113), thalassemia (90), alacrima, achalasia, and mental retardation syndrome* (83), gastric neuroendocrine tumor* (18), thalassemias, alpha- (15), adult astrocytic tumour (15), nodular ganglioneuroblastoma (10), syndromic intellectual disability (8), choroid plexus cancer (7), hemoglobin h disease, nondeletional (6), specific developmental disorder (6), mental retardation, x-linked syndromic, lubs type (4), multiple enchondromatosis, maffucci type (4), myelodysplastic syndrome (3), rett syndrome (2), microcephaly (2), autosomal genetic disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.01 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 312.55 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -76.20215-0.354 Picture PostScript Text
3' UTR -767.103473-0.221 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR025766 - ADD
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N
IPR011011 - Znf_FYVE_PHD
IPR001841 - Znf_RING

Pfam Domains:
PF00271 - Helicase conserved C-terminal domain
PF00176 - SNF2 family N-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help



To conserve bandwidth, only the images from the first 3 structures are shown.
3QL9 - X-ray MuPIT 3QLA - X-ray MuPIT 3QLC - X-ray MuPIT
3QLN - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P46100
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl WormBase 
Protein SequenceProtein Sequence  Protein Sequence 
AlignmentAlignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0003682 chromatin binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0015616 DNA translocase activity
GO:0016787 hydrolase activity
GO:0035064 methylated histone binding
GO:0042393 histone binding
GO:0046872 metal ion binding
GO:0070087 chromo shadow domain binding

Biological Process:
GO:0000212 meiotic spindle organization
GO:0006281 DNA repair
GO:0006306 DNA methylation
GO:0006310 DNA recombination
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006336 DNA replication-independent nucleosome assembly
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006974 cellular response to DNA damage stimulus
GO:0007283 spermatogenesis
GO:0010571 positive regulation of nuclear cell cycle DNA replication
GO:0030330 DNA damage response, signal transduction by p53 class mediator
GO:0030900 forebrain development
GO:0031297 replication fork processing
GO:0032206 positive regulation of telomere maintenance
GO:0032508 DNA duplex unwinding
GO:0035128 post-embryonic forelimb morphogenesis
GO:0035264 multicellular organism growth
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060009 Sertoli cell development
GO:0070192 chromosome organization involved in meiotic cell cycle
GO:0070198 protein localization to chromosome, telomeric region
GO:0072520 seminiferous tubule development
GO:0072711 cellular response to hydroxyurea
GO:1900112 regulation of histone H3-K9 trimethylation
GO:1901581 negative regulation of telomeric RNA transcription from RNA pol II promoter
GO:1901582 positive regulation of telomeric RNA transcription from RNA pol II promoter
GO:1904908 negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric

Cellular Component:
GO:0000228 nuclear chromosome
GO:0000780 condensed nuclear chromosome, centromeric region
GO:0000781 chromosome, telomeric region
GO:0000784 nuclear chromosome, telomeric region
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005720 nuclear heterochromatin
GO:0005721 pericentric heterochromatin
GO:0016604 nuclear body
GO:0016605 PML body
GO:0031618 nuclear pericentric heterochromatin
GO:0031933 telomeric heterochromatin
GO:0070603 SWI/SNF superfamily-type complex
GO:1990707 nuclear subtelomeric heterochromatin

-  Descriptions from all associated GenBank mRNAs
  BC002521 - Homo sapiens alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae), mRNA (cDNA clone IMAGE:3139907), complete cds.
LF385346 - JP 2014500723-A/192849: Polycomb-Associated Non-Coding RNAs.
MA620923 - JP 2018138019-A/192849: Polycomb-Associated Non-Coding RNAs.
U72936 - Homo sapiens putative DNA dependent ATPase and helicase (ATRX) mRNA, alternatively spliced product 1, complete cds.
U72937 - Homo sapiens putative DNA dependent ATPase and helicase (ATRX) mRNA, alternatively spliced product 2, complete cds.
U72938 - Homo sapiens putative DNA dependent ATPase and helicase (ATRX) mRNA, alternatively spliced product 3, complete cds.
BX647222 - Homo sapiens mRNA; cDNA DKFZp686K1888 (from clone DKFZp686K1888).
U09820 - Human helicase II (RAD54L) mRNA, complete cds.
AK295107 - Homo sapiens cDNA FLJ56865 complete cds, highly similar to Transcriptional regulator ATRX (EC 3.6.1.-).
AK296959 - Homo sapiens cDNA FLJ56848 complete cds, highly similar to Transcriptional regulator ATRX (EC 3.6.1.-).
AB102641 - Homo sapiens ATRX mRNA, complete cds.
BC156296 - Synthetic construct Homo sapiens clone IMAGE:100061776, MGC:190097 alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) (ATRX) mRNA, encodes complete protein.
AB208928 - Homo sapiens mRNA for transcriptional regulator ATRX isoform 2 variant protein.
AK308419 - Homo sapiens cDNA, FLJ98367.
AK307791 - Homo sapiens cDNA, FLJ97739.
BT007188 - Homo sapiens alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae) mRNA, complete cds.
JD509429 - Sequence 490453 from Patent EP1572962.
JD224847 - Sequence 205871 from Patent EP1572962.
JD198893 - Sequence 179917 from Patent EP1572962.
JD022391 - Sequence 3415 from Patent EP1572962.
JD295562 - Sequence 276586 from Patent EP1572962.
JD316191 - Sequence 297215 from Patent EP1572962.
JD263176 - Sequence 244200 from Patent EP1572962.
JD087322 - Sequence 68346 from Patent EP1572962.
JD496151 - Sequence 477175 from Patent EP1572962.
JD066638 - Sequence 47662 from Patent EP1572962.
JD267129 - Sequence 248153 from Patent EP1572962.
JD095563 - Sequence 76587 from Patent EP1572962.
JD238004 - Sequence 219028 from Patent EP1572962.
JD263103 - Sequence 244127 from Patent EP1572962.
JD042842 - Sequence 23866 from Patent EP1572962.
JD299576 - Sequence 280600 from Patent EP1572962.
JD424561 - Sequence 405585 from Patent EP1572962.
AK297183 - Homo sapiens cDNA FLJ56873 complete cds, highly similar to Transcriptional regulator ATRX (EC 3.6.1.-).
JD510747 - Sequence 491771 from Patent EP1572962.
JD301591 - Sequence 282615 from Patent EP1572962.
JD291380 - Sequence 272404 from Patent EP1572962.
JD053362 - Sequence 34386 from Patent EP1572962.
JD083704 - Sequence 64728 from Patent EP1572962.
JD343672 - Sequence 324696 from Patent EP1572962.
JD545866 - Sequence 526890 from Patent EP1572962.
JD048934 - Sequence 29958 from Patent EP1572962.
JD166464 - Sequence 147488 from Patent EP1572962.
JD177818 - Sequence 158842 from Patent EP1572962.
JD068190 - Sequence 49214 from Patent EP1572962.
AB209545 - Homo sapiens mRNA for transcriptional regulator ATRX isoform 1 variant protein.
AK293241 - Homo sapiens cDNA FLJ56867 complete cds, highly similar to Transcriptional regulator ATRX (EC 3.6.1.-).
L33812 - Human (clone HF4551-D3) DXS56-PGK1 1 Mb region mRNA.
JD201924 - Sequence 182948 from Patent EP1572962.
JD038244 - Sequence 19268 from Patent EP1572962.
JD419851 - Sequence 400875 from Patent EP1572962.
JD534265 - Sequence 515289 from Patent EP1572962.
LF211627 - JP 2014500723-A/19130: Polycomb-Associated Non-Coding RNAs.
MA447204 - JP 2018138019-A/19130: Polycomb-Associated Non-Coding RNAs.
LF382080 - JP 2014500723-A/189583: Polycomb-Associated Non-Coding RNAs.
MA617657 - JP 2018138019-A/189583: Polycomb-Associated Non-Coding RNAs.
JD454158 - Sequence 435182 from Patent EP1572962.
JD432954 - Sequence 413978 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ATRX_HUMAN, D3DTE2, NM_000489, P46100, P51068, Q15886, Q59FB5, Q59H31, Q5H9A2, Q5JWI4, Q7Z2J1, Q9H0Z1, Q9NTS3, RAD54L, uc004ecp.1, uc004ecp.2, uc004ecp.3, uc004ecp.4, uc004ecp.5, uc004ecp.6, XH2
UCSC ID: uc004ecp.6
RefSeq Accession: NM_000489
Protein: P46100 (aka ATRX_HUMAN)
CCDS: CCDS14434.1, CCDS14435.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ATRX:
xlmr (Alpha-Thalassemia X-Linked Intellectual Disability Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.