Gene Gene information from NCBI Gene database.
Entrez ID 546
Gene name ATRX chromatin remodeler
Gene symbol ATRX
Synonyms (NCBI Gene)
JMSMRX52RAD54RAD54LXH2XNPZNF-HX
Chromosome X
Chromosome location Xq21.1
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
SNPs SNP information provided by dbSNP.
79
SNP ID Visualize variation Clinical significance Consequence
rs45439799 T>C,G Likely-benign, pathogenic, benign Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant
rs122445093 T>C Pathogenic Coding sequence variant, non coding transcript variant, missense variant
rs122445094 A>G Pathogenic Coding sequence variant, non coding transcript variant, missense variant
rs122445095 C>A,T Pathogenic Coding sequence variant, non coding transcript variant, synonymous variant, missense variant
rs122445096 T>A,C Pathogenic, likely-pathogenic Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant
miRNA miRNA information provided by mirtarbase database.
483
miRTarBase ID miRNA Experiments Reference
MIRT005165 hsa-miR-30a-5p pSILAC 18668040
MIRT005165 hsa-miR-30a-5p Proteomics;Other 18668040
MIRT030808 hsa-miR-21-5p Microarray 18591254
MIRT050897 hsa-miR-17-5p CLASH 23622248
MIRT043383 hsa-miR-331-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
79
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0000212 Process Meiotic spindle organization IEA
GO:0000228 Component Nuclear chromosome IEA
GO:0000779 Component Condensed chromosome, centromeric region IEA
GO:0000781 Component Chromosome, telomeric region IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300032 886 ENSG00000085224
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P46100
Protein name Transcriptional regulator ATRX (EC 3.6.4.12) (ATP-dependent helicase ATRX) (X-linked helicase II) (X-linked nuclear protein) (XNP) (Znf-HX)
Protein function Involved in transcriptional regulation and chromatin remodeling. Facilitates DNA replication in multiple cellular environments and is required for efficient replication of a subset of genomic loci. Binds to DNA tandem repeat sequences in both te
PDB 2JM1 , 2LBM , 2LD1 , 3QL9 , 3QLA , 3QLC , 3QLN , 4W5A , 5GRQ , 5Y18 , 5Y6O , 6G0O
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF17981 ADD_ATRX 158 213 Cysteine Rich ADD domain Domain
PF00176 SNF2_N 1536 1889 SNF2 family N-terminal domain Family
PF00271 Helicase_C 2018 2155 Helicase conserved C-terminal domain Family
Tissue specificity TISSUE SPECIFICITY: Ubiquitous.
Sequence
MTAEPMSESKLNTLVQKLHDFLAHSSEESEETSSPPRLAMNQNTDKISGSGSNSDMMENS
KEEGTSSSEKSKSSGSSRSKRKPSIVTKYVESDDEKPLDDETVNEDASNENSENDITMQS
LPKGTVIVQPEPVLNEDKDDFKGPEFRSRSKMKTENLKKRGEDGLHGIVSCTACGQQVNH
FQKDSIYRHPSLQVLICKNCFKYYMSDDISRDS
DGMDEQCRWCAEGGNLICCDFCHNAFC
KKCILRNLGRKELSTIMDENNQWYCYICHPEPLLDLVTACNSVFENLEQLLQQNKKKIKV
DSEKSNKVYEHTSRFSPKKTSSNCNGEEKKLDDSCSGSVTYSYSALIVPKEMIKKAKKLI
ETTANMNSSYVKFLKQATDNSEISSATKLRQLKAFKSVLADIKKAHLALEEDLNSEFRAM
DAVNKEKNTKEHKVIDAKFETKARKGEKPCALEKKDISKSEAKLSRKQVDSEHMHQNVPT
EEQRTNKSTGGEHKKSDRKEEPQYEPANTSEDLDMDIVSVPSSVPEDIFENLETAMEVQS
SVDHQGDGSSGTEQEVESSSVKLNISSKDNRGGIKSKTTAKVTKELYVKLTPVSLSNSPI
KGADCQEVPQDKDGYKSCGLNPKLEKCGLGQENSDNEHLVENEVSLLLEESDLRRSPRVK
TTPLRRPTETNPVTSNSDEECNETVKEKQKLSVPVRKKDKRNSSDSAIDNPKPNKLPKSK
QSETVDQNSDSDEMLAILKEVSRMSHSSSSDTDINEIHTNHKTLYDLKTQAGKDDKGKRK
RKSSTSGSDFDTKKGKSAKSSIISKKKRQTQSESSNYDSELEKEIKSMSKIGAARTTKKR
IPNTKDFDSSEDEKHSKKGMDNQGHKNLKTSQEGSSDDAERKQERETFSSAEGTVDKDTT
IMELRDRLPKKQQASASTDGVDKLSGKEQSFTSLEVRKVAETKEKSKHLKTKTCKKVQDG
LSDIAEKFLKKDQSDETSEDDKKQSKKGTEEKKKPSDFKKKVIKMEQQYESSSDGTEKLP
EREEICHFPKGIKQIKNGTTDGEKKSKKIRDKTSKKKDELSDYAEKSTGKGDSCDSSEDK
KSKNGAYGREKKRCKLLGKSSRKRQDCSSSDTEKYSMKEDGCNSSDKRLKRIELRERRNL
SSKRNTKEIQSGSSSSDAEESSEDNKKKKQRTSSKKKAVIVKEKKRNSLRTSTKRKQADI
TSSSSSDIEDDDQNSIGEGSSDEQKIKPVTENLVLSSHTGFCQSSGDEALSKSVPVTVDD
DDDDNDPENRIAKKMLLEEIKANLSSDEDGSSDDEPEEGKKRTGKQNEENPGDEEAKNQV
NSESDSDSEESKKPRYRHRLLRHKLTVSDGESGEEKKTKPKEHKEVKGRNRRKVSSEDSE
DSDFQESGVSEEVSESEDEQRPRTRSAKKAELEENQRSYKQKKKRRRIKVQEDSSSENKS
NSEEEEEEKEEEEEEEEEEEEEEEDENDDSKSPGKGRKKIRKILKDDKLRTETQNALKEE
EERRKRIAEREREREKLREVIEIEDASPTKCPITTKLVLDEDEETKEPLVQVHRNMVIKL
KPHQVDGVQFMWDCCCESVKKTKKSPGSGCILAHCMGLGKTLQVVSFLHTVLLCDKLDFS
TALVVCPLNTALNWMNEFEKWQEGLKDDEKLEVSELATVKRPQERSYMLQRWQEDGGVMI
IGYEMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNEASAVSKAMNSIRS
RRRIILTGTPLQNNLIEYHCMVNFIKENLLGSIKEFRNRFINPIQNGQCADSTMVDVRVM
KKRAHILYEMLAGCVQRKDYTALTKFLPPKHEYVLAVRMTSIQCKLYQYYLDHLTGVGNN
SEGGRGKAGAKLFQDFQMLSRIWTHPWCL
QLDYISKENKGYFDEDSMDEFIASDSDETSM
SLSSDDYTKKKKKGKKGKKDSSSSGSGSDNDVEVIKVWNSRSRGGGEGNVDETGNNPSVS
LKLEESKATSSSNPSSPAPDWYKDFVTDADAEVLEHSGKMVLLFEILRMAEEIGDKVLVF
SQSLISLDLIEDFLELASREKTEDKDKPLIYKGEGKWLRNIDYYRLDGSTTAQSRKKWAE
EFNDETNVRGRLFIISTKAGSLGINLVAANRVIIFDASWNPSYDIQSIFRVYRFG
QTKPV
YVYRFLAQGTMEDKIYDRQVTKQSLSFRVVDQQQVERHFTMNELTELYTFEPDLLDDPNS
EKKKKRDTPMLPKDTILAELLQIHKEHIVGYHEHDSLLDHKEEEELTEEERKAAWAEYEA
EKKGLTMRFNIPTGTNLPPVSFNSQTPYIPFNLGALSAMSNQQLEDLINQGREKVVEATN
SVTAVRIQPLEDIISAVWKENMNLSEAQVQALALSRQASQELDVKRREAIYNDVLTKQQM
LISCVQRILMNRRLQQQYNQQQQQQMTYQQATLGHLMMPKPPNLIMNPSNYQQIDMRGMY
QPVAGGMQPPPLQRAPPPMRSKNPGPSQGKSM
Sequence length 2492
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Cell cycle  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
59
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of the nervous system Likely pathogenic; Pathogenic rs2148019913 RCV001814494
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Acquired hemoglobin H disease Likely pathogenic; Pathogenic rs1057521987, rs122445105, rs587776756, rs122445107, rs122445108 RCV005040305
RCV000763634
RCV000012506
RCV000012507
RCV004795394
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Adrenal cortex carcinoma Pathogenic rs2148020083 RCV004813190
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Alpha thalassemia-X-linked intellectual disability syndrome Likely pathogenic; Pathogenic rs2067371776, rs2148657465, rs1557140492, rs2148685852, rs1057521987, rs2148019913, rs2148020083, rs2148260943, rs2148591494, rs2147761759, rs2148656473, rs891068548, rs2148259374, rs2520173058, rs2148623651
View all (48 more)
RCV001598686
RCV001379146
RCV001387072
RCV001384857
RCV001882566
View all (60 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Alpha thalassemia X-linked intellectual disability (ATRX) syndrome Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Astrocytoma, anaplastic Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATR-X SYNDROME CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atypical teratoid rhabdoid tumor Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Abdominal Cryptorchidism Cryptorchidism CTD_human_DG 19291773
★☆☆☆☆
Found in Text Mining only
Absent mastoid Absent mastoid HPO_DG
★☆☆☆☆
Found in Text Mining only
Acquired Kyphoscoliosis Acquired Kyphoscoliosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Acrocephalopolysyndactyly type 2 Carpenter syndrome BEFREE 11449489
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 27590521
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 17957225, 30745338
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 31374064, 31611308
★☆☆☆☆
Found in Text Mining only
Adenoid Cystic Carcinoma Adenocarcinoma CTD_human_DG 23685749
★☆☆☆☆
Found in Text Mining only
Adrenal Gland Pheochromocytoma Adrenal Gland Pheochromocytoma BEFREE 25608029, 26839173, 27209355
★☆☆☆☆
Found in Text Mining only