ATXN3L

gene
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Also known as ATXN3L1MJDL

Summary

ATXN3L (ataxin 3 like, HGNC:24173) is a protein-coding gene on chromosome Xp22.2, encoding Ataxin-3-like protein (Q9H3M9). Deubiquitinating enzyme that cleaves both ‘Lys-48’-linked and ‘Lys-63’-linked poly-ubiquitin chains (in vitro).

This intronless gene may be a pseudogene (PMID:11450850). This gene is similar to the multi-exon gene which encodes ataxin 3 and contains a coding region which could encode a protein similar to ataxin 3. Mutations in the gene encoding ataxin 3 are associated with Machado-Joseph disease.

Source: NCBI Gene 92552 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 50 total — 1 pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_001135995

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24173
Approved symbolATXN3L
Nameataxin 3 like
LocationXp22.2
Locus typegene with protein product
StatusApproved
AliasesATXN3L1, MJDL
Ensembl geneENSG00000123594
Ensembl biotypeprotein_coding
OMIM300920
Entrez92552

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000380622

RefSeq mRNA: 2 — MANE Select: NM_001135995 NM_001135995, NM_001387036

CCDS: CCDS48080

Canonical transcript exons

ENST00000380622 — 1 exons

ExonStartEnd
ENSE000016887431331864713320053

Expression profiles

Bgee: expression breadth broad, 16 present calls, max score 78.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0019 / max 2.2548, expressed in 1 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1984560.00191

Top tissues by expression

274 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
spermCL:000001978.97gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047377.85gold quality
male germ cellCL:000001576.57gold quality
left testisUBERON:000453360.05gold quality
testisUBERON:000047359.13gold quality
right testisUBERON:000453458.85gold quality
pancreatic ductal cellCL:000207958.58silver quality
deltoidUBERON:000147652.81gold quality
ileal mucosaUBERON:000033151.07silver quality
epithelial cell of pancreasCL:000008350.95gold quality
Brodmann (1909) area 46UBERON:000648349.30gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
hair follicleUBERON:000207349.18gold quality
quadriceps femorisUBERON:000137749.10gold quality
olfactory bulbUBERON:000226448.92gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality
CA1 field of hippocampusUBERON:000388148.50gold quality
vastus lateralisUBERON:000137948.25gold quality
left ventricle myocardiumUBERON:000656648.24gold quality
orbitofrontal cortexUBERON:000416748.20gold quality
upper arm skinUBERON:000426348.06gold quality
cervix epitheliumUBERON:000480148.04gold quality
oviduct epitheliumUBERON:000480448.00gold quality
tongue squamous epitheliumUBERON:000691947.92gold quality
mucosa of urinary bladderUBERON:000125947.80gold quality
metanephric glomerulusUBERON:000473647.45gold quality
thymusUBERON:000237047.42gold quality
kidney epitheliumUBERON:000481947.39gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting ATXN3L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-144-3P99.9473.982698
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-409-3P99.5066.331192
HSA-MIR-4735-5P99.4368.491780
HSA-MIR-397899.2468.392201
HSA-MIR-302F98.4469.021776
HSA-MIR-607298.0066.47804
HSA-MIR-212-5P96.8367.43950
HSA-MIR-4433A-5P96.7965.01599
HSA-MIR-4703-3P96.6868.61545
HSA-MIR-10525-3P96.3268.04699
HSA-MIR-6891-3P95.8065.76683
HSA-MIR-4781-3P95.7865.66572

Literature-anchored findings (GeneRIF, showing 1)

  • ATXN3L has a role in the regulation of KLF5 stability in breast cancer (PMID:26079537)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioatxn3ENSDARG00000099274
mus_musculusAtxn3ENSMUSG00000021189
rattus_norvegicusAtxn3ENSRNOG00000005470
caenorhabditis_elegansWBGENE00006446

Paralogs (1): ATXN3 (ENSG00000066427)

Protein

Protein identifiers

Ataxin-3-like proteinQ9H3M9 (reviewed: Q9H3M9)

Alternative names: Machado-Joseph disease protein 1-like

All UniProt accessions (1): Q9H3M9

UniProt curated annotations — full annotation on UniProt →

Function. Deubiquitinating enzyme that cleaves both ‘Lys-48’-linked and ‘Lys-63’-linked poly-ubiquitin chains (in vitro). Acts as a deubiquitinating enzyme for the transcription factor KLF5, playing a role in the regulation of KLF5 stability.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed.

Miscellaneous. Identified only in primates. ATXN3L appeared to have arisen relatively recently, just prior to the first major division between hominids and old world monkeys.

RefSeq proteins (2): NP_001129467, NP_001373965 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003903UIM_domConserved_site
IPR006155JosephinDomain
IPR033865Ataxin-3Family

Pfam: PF02099, PF02809, PF16619

UniProt features (35 total): helix 10, strand 8, domain 3, active site 3, compositionally biased region 3, sequence variant 2, sequence conflict 2, region of interest 2, chain 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3O65X-RAY DIFFRACTION2.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H3M9-F171.850.30

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 119 (proton acceptor); 134; 14 (nucleophile)

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-5689877Josephin domain DUBs
R-HSA-392499Metabolism of proteins
R-HSA-5688426Deubiquitination
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 74 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, GOBP_NEGATIVE_REGULATION_OF_TOR_SIGNALING, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_TOR_SIGNALING, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_STRESS

GO Biological Process (6): protein quality control for misfolded or incompletely synthesized proteins (GO:0006515), protein deubiquitination (GO:0016579), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), negative regulation of TORC1 signaling (GO:1904262), positive regulation of ERAD pathway (GO:1904294), proteolysis (GO:0006508)

GO Molecular Function (4): cysteine-type deubiquitinase activity (GO:0004843), peptidase activity (GO:0008233), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787)

GO Cellular Component (2): nucleus (GO:0005634), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Deubiquitination1
Post-translational protein modification1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein catabolic process1
cysteine-type deubiquitinase activity1
protein modification by small protein removal1
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
negative regulation of TOR signaling1
TORC1 signaling1
regulation of TORC1 signaling1
ERAD pathway1
positive regulation of proteasomal protein catabolic process1
regulation of ERAD pathway1
positive regulation of response to endoplasmic reticulum stress1
protein metabolic process1
cysteine-type peptidase activity1
deubiquitinase activity1
hydrolase activity1
catalytic activity, acting on a protein1
peptidase activity1
catalytic activity1
intracellular membrane-bounded organelle1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

1226 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ATXN3LITPR1Q14643965
ATXN3LRAD23BP54727965
ATXN3LRAD23AP54725965
ATXN3LVCPP55072944
ATXN3LUBQLN1Q9UMX0921
ATXN3LHTTP42858895
ATXN3LJOSD1Q15040861
ATXN3LSTUB1Q9UNE7852
ATXN3LPRKNO60260824
ATXN3LBECN1Q14457796
ATXN3LHCRTO43612791
ATXN3LST13P50502783
ATXN3LHDAC6Q9UBN7781
ATXN3LUBE2WQ96B02781
ATXN3LATXN1P54253761

IntAct

3 interactions, top by confidence:

ABTypeScore
ATXN3LHMGA1psi-mi:“MI:0915”(physical association)0.400
ATXN3LMTA2psi-mi:“MI:0915”(physical association)0.400

BioGRID (24): UBC (Biochemical Activity), ATXN3L (Affinity Capture-Western), KLF5 (Affinity Capture-Western), KLF5 (Reconstituted Complex), KLF5 (Biochemical Activity), ATXN3L (Proximity Label-MS), ATXN3L (Proximity Label-MS), AURKA (Affinity Capture-Western), ATXN3L (Cross-Linking-MS (XL-MS)), GATAD2B (Cross-Linking-MS (XL-MS)), HDAC1 (Cross-Linking-MS (XL-MS)), HDAC2 (Cross-Linking-MS (XL-MS)), MTA1 (Cross-Linking-MS (XL-MS)), MTA2 (Cross-Linking-MS (XL-MS)), RBBP7 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0R4IXF6, A1L2G3, A2VDM8, B0W2R4, B3MIV9, B3NPV7, B4GAM2, B4HST0, B4JW98, B4KT51, B4LQ24, B4P6P6, B4QHH0, C4A0D9, D3YXJ0, D3ZHS6, E9PUQ8, F6QZ15, F6Z5C0, G3X9K3, O01991, O46382, O80866, O82486, P27448, P53204, P57080, Q03141, Q06178, Q17N72, Q1LUC3, Q24574, Q291J4, Q2HVD6, Q64398, Q6INA9, Q7K5N4, Q7Z569, Q86XP1, Q8L751

Diamond homologs: O17850, O35815, P54252, Q60XN1, Q8LQ36, Q9CVD2, Q9H3M9, Q9M391, Q9W689, Q8TAC2, Q9CR30

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

50 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance42
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2423466NC_000023.10:g.(?12885698)(13787227_?)delPathogenic

SpliceAI

104 predictions. Top by Δscore:

VariantEffectΔscore
X:13319436:CCT:Cacceptor_gain0.8700
X:13319521:C:Tacceptor_gain0.7700
X:13319695:TATTA:Tdonor_loss0.7400
X:13319697:TTA:Tdonor_loss0.7400
X:13319698:TACCT:Tdonor_loss0.7400
X:13319699:A:Cdonor_loss0.7400
X:13319700:CCT:Cdonor_loss0.7400
X:13319438:T:Cacceptor_gain0.7000
X:13319701:C:Adonor_loss0.6700
X:13319435:CC:Cacceptor_gain0.6200
X:13319521:C:CTacceptor_gain0.6100
X:13319437:C:Tacceptor_gain0.6000
X:13319590:A:Cdonor_gain0.5300
X:13319693:CTTAT:Cdonor_loss0.5000
X:13319694:TTATT:Tdonor_loss0.5000
X:13319438:T:TCacceptor_gain0.4900
X:13319438:TTG:Tacceptor_gain0.4900
X:13319434:ACCCT:Aacceptor_loss0.4800
X:13319435:CCC:Cacceptor_loss0.4800
X:13319436:CC:Cacceptor_loss0.4800
X:13319437:C:CAacceptor_loss0.4800
X:13319446:A:Tacceptor_loss0.4800
X:13319448:A:Cacceptor_loss0.4800
X:13319702:T:Cdonor_loss0.4800
X:13319451:C:CTacceptor_loss0.4700
X:13319439:T:Aacceptor_gain0.4600
X:13319452:A:Tacceptor_loss0.4600
X:13319764:CTCT:Cdonor_gain0.4600
X:13319765:TCTT:Tdonor_gain0.4600
X:13319766:CTTC:Cdonor_gain0.4600

AlphaMissense

2379 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:13319563:T:AR124S0.999
X:13319563:T:GR124S0.999
X:13319564:C:GR124T0.999
X:13319441:A:TV165D0.998
X:13319577:A:GW120R0.998
X:13319577:A:TW120R0.998
X:13319870:A:GL22P0.998
X:13319881:A:CC18W0.998
X:13319564:C:AR124I0.997
X:13319565:T:CR124G0.997
X:13319684:A:CL84W0.997
X:13319837:A:GL33S0.997
X:13319547:A:GW130R0.996
X:13319547:A:TW130R0.996
X:13319599:A:CF112L0.996
X:13319599:A:TF112L0.996
X:13319601:A:GF112L0.996
X:13319710:G:CF75L0.996
X:13319710:G:TF75L0.996
X:13319712:A:GF75L0.996
X:13319444:A:TV164D0.995
X:13319575:C:AW120C0.995
X:13319575:C:GW120C0.995
X:13319600:A:GF112S0.995
X:13319684:A:GL84S0.995
X:13319863:T:AQ24H0.995
X:13319863:T:GQ24H0.995
X:13319867:A:GL23S0.995
X:13319879:A:GL19P0.995
X:13319446:A:CF163L0.994

dbSNP variants (sampled 300 via entrez): RS1000929284 (X:13319809 T>C), RS1000960651 (X:13320199 G>A), RS1001541188 (X:13321364 A>C), RS1001614694 (X:13321794 T>C), RS1002084312 (X:13320644 A>G), RS1006803980 (X:13319991 A>G), RS1012381579 (X:13318438 C>T), RS1012689560 (X:13319097 T>G), RS1014781213 (X:13320904 T>C), RS1015679330 (X:13321260 C>T), RS1016477092 (X:13318382 G>A,T), RS1016508032 (X:13318737 C>G), RS1016816651 (X:13320001 C>A,G), RS1016847600 (X:13320422 A>G), RS1018492084 (X:13321914 A>G)

Disease associations

OMIM: gene MIM:300920 | disease phenotypes: MIM:311200, MIM:213300

GenCC curated gene-disease

Mondo (3): orofaciodigital syndrome I (MONDO:0010702), Joubert syndrome (MONDO:0018772), intellectual disability (MONDO:0001071)

Orphanet (3): Orofaciodigital syndrome type 1 (Orphanet:2750), Isolated Joubert syndrome (Orphanet:475), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

StudyTraitp-value
GCST008103_144Bipolar disorder3.000000e-06

MeSH disease descriptors (2)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
C537134Orofaciodigital syndrome type1 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4630855 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

ChemicalActions (top 5)PubMed papers
butyraldehydedecreases expression1
CGP 52608affects binding, increases reaction1
MT19c compoundincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Camptothecindecreases response to substance1
Diethylhexyl Phthalateincreases expression1
Rotenoneincreases expression1
Valproic Aciddecreases methylation1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4606005BindingInhibition of human 6His-tagged Ataxin-3L expressed in Escherichia coli assessed as cleavage of Ubiquitin-Rhodamine110-glycine to Ubiquitin and Rhodamine110-glycine using Ubiquitin-Rhodamine110-glycine as substrate by fluorescence based anaDiscovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity. — J Med Chem

Clinical trials (associated diseases)

200 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00873678Not specifiedCOMPLETEDAssessment of the Prevalence of Genes AHI1, NPHP1 and CEP290 in Joubert Syndrome
NCT01401998Not specifiedRECRUITINGARPKD Database Study
NCT04874909Not specifiedCOMPLETEDClassification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)