Gene Gene information from NCBI Gene database.
Entrez ID 23064
Gene name Senataxin
Gene symbol SETX
Synonyms (NCBI Gene)
ALS4AOA2SCAN2SCAR1STEXSen1bA479K20.2
Chromosome 9
Chromosome location 9q34.13
Summary This gene encodes a protein named for its homology to the Sen1p protein of fungi which has RNA helicase activity encoded by a domain at the C-terminal end of the protein. The protein encoded by this gene contains a DNA/RNA helicase domain at its C-termina
SNPs SNP information provided by dbSNP.
63
SNP ID Visualize variation Clinical significance Consequence
rs28940290 G>A Pathogenic Missense variant, downstream transcript variant, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs28941475 G>A Likely-pathogenic, pathogenic, uncertain-significance Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs29001584 A>G Pathogenic, uncertain-significance Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs29001665 G>A Pathogenic Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs113831637 G>C Conflicting-interpretations-of-pathogenicity, likely-benign Non coding transcript variant, genic upstream transcript variant, coding sequence variant, upstream transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
660
miRTarBase ID miRNA Experiments Reference
MIRT016893 hsa-miR-335-5p Microarray 18185580
MIRT040922 hsa-miR-18a-3p CLASH 23622248
MIRT462332 hsa-miR-541-5p PAR-CLIP 23592263
MIRT462331 hsa-miR-586 PAR-CLIP 23592263
MIRT462330 hsa-miR-125a-3p PAR-CLIP 23592263
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
53
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0000228 Component Nuclear chromosome IDA 24105744
GO:0000781 Component Chromosome, telomeric region IEA
GO:0001147 Function Transcription termination site sequence-specific DNA binding IBA
GO:0001147 Function Transcription termination site sequence-specific DNA binding IDA 21700224
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608465 445 ENSG00000107290
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q7Z333
Protein name Probable helicase senataxin (EC 3.6.4.-) (Amyotrophic lateral sclerosis 4 protein) (SEN1 homolog) (Senataxin)
Protein function Probable RNA/DNA helicase involved in diverse aspects of RNA metabolism and genomic integrity. Plays a role in transcription regulation by its ability to modulate RNA Polymerase II (Pol II) binding to chromatin and through its interaction with p
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13086 AAA_11 1933 2218 AAA domain Domain
PF13087 AAA_12 2225 2426 AAA domain Domain
Tissue specificity TISSUE SPECIFICITY: Highly expressed in skeletal muscle. Expressed in heart, fibroblast, placenta and liver. Weakly expressed in brain and lung. Expressed in the cortex of the kidney (highly expressed in tubular epithelial cells but low expression in the
Sequence
MSTCCWCTPGGASTIDFLKRYASNTPSGEFQTADEDLCYCLECVAEYHKARDELPFLHEV
LWELETLRLINHFEKSMKAEIGDDDELYIVDNNGEMPLFDITGQDFENKLRVPLLEILKY
PYLLLHERVNELCVEALCRMEQANCSFQVFDKHPGIYLFLVHPNEMVRRWAILTARNLGK
VDRDDYYDLQEVLLCLFKVIELGLLESPDIYTSSVLEKGKLILLPSHMYDTTNYKSYWLG
ICMLLTILEEQAMDSLLLGSDKQNDFMQSILHTMEREADDDSVDPFWPALHCFMVILDRL
GSKVWGQLMDPIVAFQTIINNASYNREIRHIRNSSVRTKLEPESYLDDMVTCSQIVYNYN
PEKTKKDSGWRTAICPDYCPNMYEEMETLASVLQSDIGQDMRVHNSTFLWFIPFVQSLMD
LKDLGVAYIAQVVNHLYSEVKEVLNQTDAVCDKVTEFFLLILVSVIELHRNKKCLHLLWV
SSQQWVEAVVKCAKLPTTAFTRSSEKSSGNCSKGTAMISSLSLHSMPSNSVQLAYVQLIR
SLLKEGYQLGQQSLCKRFWDKLNLFLRGNLSLGWQLTSQETHELQSCLKQIIRNIKFKAP
PCNTFVDLTSACKISPASYNKEESEQMGKTSRKDMHCLEASSPTFSKEPMKVQDSVLIKA
DNTIEGDNNEQNYIKDVKLEDHLLAGSCLKQSSKNIFTERAEDQIKISTRKQKSVKEISS
YTPKDCTSRNGPERGCDRGIIVSTRLLTDSSTDALEKVSTSNEDFSLKDDALAKTSKRKT
KVQKDEICAKLSHVIKKQHRKSTLVDNTINLDENLTVSNIESFYSRKDTGVQKGDGFIHN
LSLDPSGVLDDKNGEQKSQNNVLPKEKQLKNEELVIFSFHENNCKIQEFHVDGKELIPFT
EMTNASEKKSSPFKDLMTVPESRDEEMSNSTSVIYSNLTREQAPDISPKSDTLTDSQIDR
DLHKLSLLAQASVITFPSDSPQNSSQLQRKVKEDKRCFTANQNNVGDTSRGQVIIISDSD
DDDDERILSLEKLTKQDKICLEREHPEQHVSTVNSKEEKNPVKEEKTETLFQFEESDSQC
FEFESSSEVFSVWQDHPDDNNSVQDGEKKCLAPIANTTNGQGCTDYVSEVVKKGAEGIEE
HTRPRSISVEEFCEIEVKKPKRKRSEKPMAEDPVRPSSSVRNEGQSDTNKRDLVGNDFKS
IDRRTSTPNSRIQRATTVSQKKSSKLCTCTEPIRKVPVSKTPKKTHSDAKKGQNRSSNYL
SCRTTPAIVPPKKFRQCPEPTSTAEKLGLKKGPRKAYELSQRSLDYVAQLRDHGKTVGVV
DTRKKTKLISPQNLSVRNNKKLLTSQELQMQRQIRPKSQKNRRRLSDCESTDVKRAGSHT
AQNSDIFVPESDRSDYNCTGGTEVLANSNRKQLIKCMPSEPETIKAKHGSPATDDACPLN
QCDSVVLNGTVPTNEVIVSTSEDPLGGGDPTARHIEMAALKEGEPDSSSDAEEDNLFLTQ
NDPEDMDLCSQMENDNYKLIELIHGKDTVEVEEDSVSRPQLESLSGTKCKYKDCLETTKN
QGEYCPKHSEVKAADEDVFRKPGLPPPASKPLRPTTKIFSSKSTSRIAGLSKSLETSSAL
SPSLKNKSKGIQSILKVPQPVPLIAQKPVGEMKNSCNVLHPQSPNNSNRQGCKVPFGESK
YFPSSSPVNILLSSQSVSDTFVKEVLKWKYEMFLNFGQCGPPASLCQSISRPVPVRFHNY
GDYFNVFFPLMVLNTFETVAQEWLNSPNRENFYQLQVRKFPADYIKYWEFAVYLEECELA
KQLYPKENDLVFLAPERINEEKKDTERNDIQDLHEYHSGYVHKFRRTSVMRNGKTECYLS
IQTQENFPANLNELVNCIVISSLVTTQRKLKAMSLLGSRNQLARAVLNPNPMDFCTKDLL
TTTSERIIAYLRDFNEDQKKAIETAYAMVKHSPSVAKICLIHGPPGTGKSKTIVGLLYRL
LTENQRKGHSDENSNAKIKQNRVLVCAPSNAAVDELMKKIILEFKEKCKDKKNPLGNCGD
INLVRLGPEKSINSEVLKFSLDSQVNHRMKKELPSHVQAMHKRKEFLDYQLDELSRQRAL
CRGGREIQRQELDENISKVSKERQELASKIKEVQGRPQKTQSIIILESHIICCTLSTSGG
LLLESAFRGQGGVPFSCVIVDEAGQSCEIETLTPLIHRCNKLILVGDPKQLPPTVISM
KA
QEYGYDQSMMARFCRLLEENVEHNMISRLPILQLTVQYRMHPDICLFPSNYVYNRNLKTN
RQTEAIRCSSDWPFQPYLVFDVGDGSERRDNDSYINVQEIKLVMEIIKLIKDKRKDVSFR
NIGIITHYKAQKTMIQKDLDKEFDRKGPAEVDTVDAFQGRQKDCVIVTCVRANSIQGSIG
FLASLQRLNVTITRAKYSLFILGHLR
TLMENQHWNQLIQDAQKRGAIIKTCDKNYRHDAV
KILKLKPVLQRSLTHPPTIAPEGSRPQGGLPSSKLDSGFAKTSVAASLYHTPSDSKEITL
TVTSKDPERPPVHDQLQDPRLLKRMGIEVKGGIFLWDPQPSSPQHPGATPPTGEPGFPVV
HQDLSHIQQPAAVVAALSSHKPPVRGEPPAASPEASTCQSKCDDPEEELCHRREARAFSE
GEQEKCGSETHHTRRNSRWDKRTLEQEDSSSKKRKLL
Sequence length 2677
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG 
  Amyotrophic lateral sclerosis  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
60
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
Abnormal central motor function Likely pathogenic; Pathogenic rs750959420 RCV001814179
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic lateral sclerosis Likely pathogenic; Pathogenic rs750959420 RCV001260555
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic lateral sclerosis type 4 Likely pathogenic; Pathogenic rs2131463657, rs2131463325, rs2131461009, rs2131440608, rs1038776365, rs2131463306, rs1391764195, rs29001584, rs28941475, rs121434378, rs2539140886, rs1554804809, rs768349691, rs757883779, rs1846980272
View all (16 more)
RCV001809082
RCV001829275
RCV001872206
RCV002014627
RCV001983771
View all (26 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia Likely pathogenic rs1847100683 RCV001255856
★★★★☆
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
Acute myeloid leukemia Benign; Conflicting classifications of pathogenicity ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AMYOTROPHIC LATERAL SCLEROSIS 4, JUVENILE CTD, Disgenet, HPO
CTD, Disgenet, HPO
CTD, Disgenet, HPO
★★☆☆☆
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
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 30419062
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 10430837, 19058054, 19840884, 21190393, 21576111, 23129421, 24105744, 24244371, 24760770, 25822250, 26700805, 27197982, 27771483, 28245518, 28413711
View all (5 more)
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis LHGDN 15106121
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic Lateral Sclerosis Amyotrophic lateral sclerosis Pubtator 23755159, 23881933, 28413711, 29416069, 32686621, 33661429, 33709219, 36271102, 37208601, 9497266 Associate
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis HPO_DG
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis GENOMICS_ENGLAND_DG
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic Lateral Sclerosis 2 Juvenile Amyotrophic lateral sclerosis Pubtator 30052327 Associate
★☆☆☆☆
Found in Text Mining only
AMYOTROPHIC LATERAL SCLEROSIS 2, JUVENILE (disorder) Amyotrophic lateral sclerosis BEFREE 10430837, 16717225
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis 4 Juvenile Amyotrophic lateral sclerosis Pubtator 23141540, 24105744, 24244371, 27718307, 29395064, 29416069, 31957062, 32686621, 35045161 Associate
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis 4, Juvenile Amyotrophic lateral sclerosis UNIPROT_DG 14770181, 15106121, 21190393, 24105744, 24244371
★★☆☆☆
Found in Text Mining + Unknown/Other Associations