• Gene id: 546

Gene Summary

• Gene Symbol: ATRX   Gene   UCSC   Ensembl
• Aliases: JMS, MRX52, RAD54, RAD54L, XH2, XNP, ZNF-HX
• Gene name: ATRX chromatin remodeler
• Alternate names: transcriptional regulator ATRX, ATP-dependent helicase ATRX, X-linked helicase II, X-linked nuclear protein, alpha thalassemia/mental retardation syndrome X-linked (RAD54 homolog, S. cerevisiae),
• Gene location: Xq21.1 (9140394: 9163418)     Exons: 8     NC_000019.10
• Gene summary(Entrez): 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
• OMIM: 300032

SNPs

rs13206743

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000006.12   g.52152310T>C
NC_000006.11   g.52017108T>C|SEQ=[T/C]|GENE=LINCMD1

rs3000811

Strand:    Allele origin:   Allele change:   Mutation type: snv

NC_000001.11   g.227400755G>A
NC_000001.11   g.227400755G>C
NC_000001.10   g.227588456G>A
NC_000001.10   g.227588456G>C|SEQ=[G/A/C]|GENE=LINC01641

Protein Summary

• Protein general information: P46100  
  • Name: Transcriptional regulator ATRX (EC 3.6.4.12) (ATP dependent helicase ATRX) (X linked helicase II) (X linked nuclear protein) (XNP) (Znf HX)
  • Length: 2492  
  • Mass: 282586
  • Tissue specificity: Ubiquitous.
• Sequence:

  MTAEPMSESKLNTLVQKLHDFLAHSSEESEETSSPPRLAMNQNTDKISGSGSNSDMMENSKEEGTSSSEKSKSSG
  SSRSKRKPSIVTKYVESDDEKPLDDETVNEDASNENSENDITMQSLPKGTVIVQPEPVLNEDKDDFKGPEFRSRS
  KMKTENLKKRGEDGLHGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAE
  GGNLICCDFCHNAFCKKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQLLQQNKKKIKV
  DSEKSNKVYEHTSRFSPKKTSSNCNGEEKKLDDSCSGSVTYSYSALIVPKEMIKKAKKLIETTANMNSSYVKFLK
  QATDNSEISSATKLRQLKAFKSVLADIKKAHLALEEDLNSEFRAMDAVNKEKNTKEHKVIDAKFETKARKGEKPC
  ALEKKDISKSEAKLSRKQVDSEHMHQNVPTEEQRTNKSTGGEHKKSDRKEEPQYEPANTSEDLDMDIVSVPSSVP
  EDIFENLETAMEVQSSVDHQGDGSSGTEQEVESSSVKLNISSKDNRGGIKSKTTAKVTKELYVKLTPVSLSNSPI
  KGADCQEVPQDKDGYKSCGLNPKLEKCGLGQENSDNEHLVENEVSLLLEESDLRRSPRVKTTPLRRPTETNPVTS
  NSDEECNETVKEKQKLSVPVRKKDKRNSSDSAIDNPKPNKLPKSKQSETVDQNSDSDEMLAILKEVSRMSHSSSS
  DTDINEIHTNHKTLYDLKTQAGKDDKGKRKRKSSTSGSDFDTKKGKSAKSSIISKKKRQTQSESSNYDSELEKEI
  KSMSKIGAARTTKKRIPNTKDFDSSEDEKHSKKGMDNQGHKNLKTSQEGSSDDAERKQERETFSSAEGTVDKDTT
  IMELRDRLPKKQQASASTDGVDKLSGKEQSFTSLEVRKVAETKEKSKHLKTKTCKKVQDGLSDIAEKFLKKDQSD
  ETSEDDKKQSKKGTEEKKKPSDFKKKVIKMEQQYESSSDGTEKLPEREEICHFPKGIKQIKNGTTDGEKKSKKIR
  DKTSKKKDELSDYAEKSTGKGDSCDSSEDKKSKNGAYGREKKRCKLLGKSSRKRQDCSSSDTEKYSMKEDGCNSS
  DKRLKRIELRERRNLSSKRNTKEIQSGSSSSDAEESSEDNKKKKQRTSSKKKAVIVKEKKRNSLRTSTKRKQADI
  TSSSSSDIEDDDQNSIGEGSSDEQKIKPVTENLVLSSHTGFCQSSGDEALSKSVPVTVDDDDDDNDPENRIAKKM
  LLEEIKANLSSDEDGSSDDEPEEGKKRTGKQNEENPGDEEAKNQVNSESDSDSEESKKPRYRHRLLRHKLTVSDG
  ESGEEKKTKPKEHKEVKGRNRRKVSSEDSEDSDFQESGVSEEVSESEDEQRPRTRSAKKAELEENQRSYKQKKKR
  RRIKVQEDSSSENKSNSEEEEEEKEEEEEEEEEEEEEEEDENDDSKSPGKGRKKIRKILKDDKLRTETQNALKEE
  EERRKRIAEREREREKLREVIEIEDASPTKCPITTKLVLDEDEETKEPLVQVHRNMVIKLKPHQVDGVQFMWDCC
  CESVKKTKKSPGSGCILAHCMGLGKTLQVVSFLHTVLLCDKLDFSTALVVCPLNTALNWMNEFEKWQEGLKDDEK
  LEVSELATVKRPQERSYMLQRWQEDGGVMIIGYEMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILK
  NEASAVSKAMNSIRSRRRIILTGTPLQNNLIEYHCMVNFIKENLLGSIKEFRNRFINPIQNGQCADSTMVDVRVM
  KKRAHILYEMLAGCVQRKDYTALTKFLPPKHEYVLAVRMTSIQCKLYQYYLDHLTGVGNNSEGGRGKAGAKLFQD
  FQMLSRIWTHPWCLQLDYISKENKGYFDEDSMDEFIASDSDETSMSLSSDDYTKKKKKGKKGKKDSSSSGSGSDN
  DVEVIKVWNSRSRGGGEGNVDETGNNPSVSLKLEESKATSSSNPSSPAPDWYKDFVTDADAEVLEHSGKMVLLFE
  ILRMAEEIGDKVLVFSQSLISLDLIEDFLELASREKTEDKDKPLIYKGEGKWLRNIDYYRLDGSTTAQSRKKWAE
  EFNDETNVRGRLFIISTKAGSLGINLVAANRVIIFDASWNPSYDIQSIFRVYRFGQTKPVYVYRFLAQGTMEDKI
  YDRQVTKQSLSFRVVDQQQVERHFTMNELTELYTFEPDLLDDPNSEKKKKRDTPMLPKDTILAELLQIHKEHIVG
  YHEHDSLLDHKEEEELTEEERKAAWAEYEAEKKGLTMRFNIPTGTNLPPVSFNSQTPYIPFNLGALSAMSNQQLE
  DLINQGREKVVEATNSVTAVRIQPLEDIISAVWKENMNLSEAQVQALALSRQASQELDVKRREAIYNDVLTKQQM
  LISCVQRILMNRRLQQQYNQQQQQQMTYQQATLGHLMMPKPPNLIMNPSNYQQIDMRGMYQPVAGGMQPPPLQRA
  PPPMRSKNPGPSQGKSM

• Structural information:
  • Protein Domains: (159..29-)
    (/note="ADD-)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00865-)
    (1581..176-)
    (/note="Helicase-ATP-binding)
    (/evidence="ECO:0000255|PROSITE-ProRule:PRU00541-)
    (2025..220-)
    (/note="Helicase-C-terminal)
    (/evidence="ECO:0000255-)
  • Interpro: IPR025766  IPR041430  IPR014001  IPR001650  IPR027417   IPR038718  IPR000330  IPR011011  IPR013083  
  • Prosite: PS51533 PS51192 PS51194
  • PDB: 2JM1 2LBM 2LD1 3QL9 3QLA 3QLC 3QLN 4W5A 5GRQ 5Y18 5Y6O 6G0O
  • PDBsum: 2JM1 2LBM 2LD1 3QL9 3QLA 3QLC 3QLN 4W5A 5GRQ 5Y18 5Y6O 6G0O
  • DIP: 31532
  • STRING: ENSP00000362441
• Other Databases: GeneCards:  ATRX  Malacards:  ATRX

Gene ontology

GO accession	Term name	Evidence code	Go category
GO:0042393	histone binding	IDA	molecular function
GO:0035064	methylated histone binding	IDA	molecular function
GO:0006334	nucleosome assembly	IDA	biological process
GO:0015616	DNA translocase activity	IDA	molecular function
GO:0006338	chromatin remodeling	IDA	biological process
GO:0003682	chromatin binding	IDA	molecular function
GO:1901581	negative regulation of telomeric RNA transcription from RNA pol II promoter	ISS	biological process
GO:0032206	positive regulation of telomere maintenance	ISS	biological process
GO:0031297	replication fork processing	ISS	biological process
GO:0010571	positive regulation of nuclear cell cycle DNA replication	ISS	biological process
GO:0072711	cellular response to hydroxyurea	ISS	biological process
GO:0045944	positive regulation of transcription by RNA polymerase II	IMP	biological process
GO:0030330	DNA damage response, signal transduction by p53 class mediator	ISS	biological process
GO:0006336	DNA replication-independent nucleosome assembly	IMP	biological process
GO:0005515	protein binding	IPI	molecular function
GO:1900112	regulation of histone H3-K9 trimethylation	IMP	biological process
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005524	ATP binding	IEA	molecular function
GO:0006281	DNA repair	IEA	biological process
GO:0000781	chromosome, telomeric region	IEA	cellular component
GO:0046872	metal ion binding	IEA	molecular function
GO:0016787	hydrolase activity	IEA	molecular function
GO:0006325	chromatin organization	IEA	biological process
GO:0004386	helicase activity	IEA	molecular function
GO:0005634	nucleus	IEA	cellular component
GO:0005524	ATP binding	IEA	molecular function
GO:0000166	nucleotide binding	IEA	molecular function
GO:0005694	chromosome	IEA	cellular component
GO:0003677	DNA binding	IEA	molecular function
GO:0006974	cellular response to DNA damage stimulus	IEA	biological process
GO:0005634	nucleus	TAS	cellular component
GO:0006355	regulation of transcription, DNA-templated	TAS	biological process
GO:0005720	nuclear heterochromatin	TAS	cellular component
GO:0006306	DNA methylation	TAS	biological process
GO:0003678	DNA helicase activity	IEA	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:0005515	protein binding	IPI	molecular function
GO:1901581	negative regulation of telomeric RNA transcription from RNA pol II promoter	IEA	biological process
GO:0072520	seminiferous tubule development	IEA	biological process
GO:0070192	chromosome organization involved in meiotic cell cycle	IEA	biological process
GO:0060009	Sertoli cell development	IEA	biological process
GO:0042393	histone binding	IEA	molecular function
GO:0035128	post-embryonic forelimb morphogenesis	IEA	biological process
GO:0032206	positive regulation of telomere maintenance	IEA	biological process
GO:0031297	replication fork processing	IEA	biological process
GO:0010571	positive regulation of nuclear cell cycle DNA replication	IEA	biological process
GO:0007283	spermatogenesis	IEA	biological process
GO:0005721	pericentric heterochromatin	IEA	cellular component
GO:0003682	chromatin binding	IEA	molecular function
GO:0000792	heterochromatin	IEA	cellular component
GO:0072711	cellular response to hydroxyurea	IEA	biological process
GO:0070198	protein localization to chromosome, telomeric region	IEA	biological process
GO:0045944	positive regulation of transcription by RNA polymerase II	IEA	biological process
GO:0035264	multicellular organism growth	IEA	biological process
GO:0031618	nuclear pericentric heterochromatin	IEA	cellular component
GO:0030900	forebrain development	IEA	biological process
GO:0030330	DNA damage response, signal transduction by p53 class mediator	IEA	biological process
GO:0016605	PML body	IEA	cellular component
GO:0005634	nucleus	IEA	cellular component
GO:0000784	nuclear chromosome, telomeric region	IEA	cellular component
GO:0000780	condensed nuclear chromosome, centromeric region	IEA	cellular component
GO:0000228	nuclear chromosome	IEA	cellular component
GO:0000212	meiotic spindle organization	IEA	biological process
GO:1990707	nuclear subtelomeric heterochromatin	IDA	cellular component
GO:0016605	PML body	ISS	cellular component
GO:0000784	nuclear chromosome, telomeric region	ISS	colocalizes with
GO:0005721	pericentric heterochromatin	ISS	cellular component
GO:1901582	positive regulation of telomeric RNA transcription from RNA pol II promoter	IMP	biological process
GO:0000784	nuclear chromosome, telomeric region	ISS	cellular component
GO:0070198	protein localization to chromosome, telomeric region	ISS	biological process
GO:1904908	negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric	IMP	biological process
GO:0070087	chromo shadow domain binding	IPI	molecular function
GO:0000781	chromosome, telomeric region	IEA	cellular component
GO:0016605	PML body	IEA	cellular component
GO:0005634	nucleus	IEA	cellular component
GO:0005654	nucleoplasm	IDA	cellular component
GO:0016604	nuclear body	IDA	cellular component
GO:0000781	chromosome, telomeric region	ISS	cellular component
GO:0032508	DNA duplex unwinding	IEA	biological process
GO:0042393	histone binding	IDA	molecular function

Diseases

Associated diseases	References
Thalassemia	KEGG:H00228
Pancreatic neuroendocrine tumor	KEGG:H00045
ATR-X syndrome	KEGG:H01752
Thalassemia	KEGG:H00228
Pancreatic neuroendocrine tumor	KEGG:H00045
ATR-X syndrome	KEGG:H01752
Alpha thalassemia-X-linked intellectual disability syndrome	PMID:24327140
Sarcoma	PMID:26428317
Melanoma	PMID:24468746
Glioblastoma multiforme	PMID:27478330
Astrocytoma	PMID:24810474
Malignant glioma	PMID:23104868
Cryptorchidism	MIK: 28606200
Spermatogenic defects	MIK: 31037746
Teratozoospermia	MIK: 17327269

PubMed references

PMID	Condition	Mutation	Ethnicity	Population details	Infertility_type	Associated_genes
17327269	Teratozoospermia			13 (5 controls, 8 cases)	Male infertility	GSE6967 analyzed by GEO2R (cutoff 1.5 fold)
28606200	Cryptorchidism			Monozgotic twins (1 control, I cwith cryptorchidism)	Male infertility	MeDIP-Seq
31037746	Spermatogenic defects			16 (1 control, 15 cases)	Male infertility	GSE6023 analyzed using GEO2R