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GeneBe

ATXN1

ataxin 1

Basic information

Region (hg38): 6:16299111-16761491

Previous symbols: [ "SCA1" ]

Links

ENSG00000124788NCBI:6310OMIM:601556HGNC:10548Uniprot:P54253AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • spinocerebellar ataxia type 1 (Moderate), mode of inheritance: AD
  • spinocerebellar ataxia type 1 (Supportive), mode of inheritance: AD
  • spinocerebellar ataxia type 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spinocerebellar ataxia 1ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic8275090; 8358429; 7951322; 8198139; 8037204; 8615077; 10424816; 11973625; 14967775; 16133185; 15747371; 18262566; 18685131; 20301363

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATXN1 gene.

  • Inborn genetic diseases (32 variants)
  • not provided (20 variants)
  • not specified (11 variants)
  • Spinocerebellar ataxia type 1 (8 variants)
  • Tip-toe gait (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
3
clinvar
3
clinvar
7
missense
35
clinvar
3
clinvar
3
clinvar
41
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
1
inframe indel
2
clinvar
2
clinvar
3
clinvar
7
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 41 8 10

Variants in ATXN1

This is a list of pathogenic ClinVar variants found in the ATXN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
6-16306340-C-T Inborn genetic diseases • ATXN1-related condition Conflicting classifications of pathogenicity (Aug 11, 2022)2227645
6-16306357-A-G Inborn genetic diseases Uncertain significance (Oct 04, 2022)2316517
6-16306360-C-A Inborn genetic diseases Uncertain significance (Dec 27, 2022)2339662
6-16306438-C-T Inborn genetic diseases Uncertain significance (Jul 12, 2022)2301162
6-16306520-G-A not specified Likely benign (-)128499
6-16306563-G-A Likely benign (Jul 01, 2023)2656247
6-16306607-C-T Inborn genetic diseases Uncertain significance (Mar 16, 2022)2278810
6-16306627-G-A Spinocerebellar ataxia type 1 • not specified Likely benign (Oct 30, 2017)522259
6-16306634-C-T Inborn genetic diseases Conflicting classifications of pathogenicity (Mar 29, 2022)809880
6-16306700-CG-C Uncertain significance (Apr 18, 2022)1711919
6-16306746-T-C ATXN1-related condition Benign (Aug 14, 2019)3037222
6-16326380-C-A Benign (Jun 25, 2021)1304636
6-16326440-G-A ATXN1-related condition Likely benign (May 09, 2019)3042386
6-16326468-C-T Inborn genetic diseases Uncertain significance (Mar 21, 2023)2541532
6-16326507-C-A Spinocerebellar ataxia type 1 Uncertain significance (Aug 13, 2019)932128
6-16326616-C-T Benign (Jul 01, 2022)2656248
6-16326617-G-A Inborn genetic diseases Uncertain significance (Nov 08, 2022)2230043
6-16326633-C-T Uncertain significance (Jul 01, 2016)809881
6-16326660-G-A Uncertain significance (Aug 07, 2017)451257
6-16326676-T-C ATXN1-related condition Likely benign (Apr 01, 2022)3032421
6-16326736-G-A Likely benign (Mar 01, 2022)1676010
6-16326748-C-G Tip-toe gait Uncertain significance (Dec 08, 2020)1048085
6-16326808-C-T ATXN1-related condition Likely benign (Mar 25, 2019)3057574
6-16326809-G-A Spinocerebellar ataxia type 1 Uncertain significance (Nov 07, 2023)2688657
6-16326906-G-T Uncertain significance (Aug 14, 2023)2578409

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATXN1protein_codingprotein_codingENST00000244769 2462380
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9750.025012567424281257260.000207
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.254345140.8450.00003535214
Missense in Polyphen105172.150.609941741
Synonymous-1.982902501.160.00002111750
Loss of Function4.03324.60.1220.00000117259

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001540.00107
Ashkenazi Jewish0.0004080.000198
East Asian0.0006810.000272
Finnish0.0002920.000231
European (Non-Finnish)0.0002870.000114
Middle Eastern0.0006810.000272
South Asian0.0008550.000392
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Chromatin-binding factor that repress Notch signaling in the absence of Notch intracellular domain by acting as a CBF1 corepressor. Binds to the HEY promoter and might assist, along with NCOR2, RBPJ-mediated repression. Binds RNA in vitro. May be involved in RNA metabolism (PubMed:21475249). In concert with CIC and ATXN1L, involved in brain development (By similarity). {ECO:0000250|UniProtKB:P54254, ECO:0000269|PubMed:21475249}.;
Disease
DISEASE: Spinocerebellar ataxia 1 (SCA1) [MIM:164400]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to cerebellum degeneration with variable involvement of the brainstem and spinal cord. SCA1 belongs to the autosomal dominant cerebellar ataxias type I (ADCA I) which are characterized by cerebellar ataxia in combination with additional clinical features like optic atrophy, ophthalmoplegia, bulbar and extrapyramidal signs, peripheral neuropathy and dementia. SCA1 is caused by expansion of a CAG repeat in the coding region of ATXN1. Longer expansions result in earlier onset and more severe clinical manifestations of the disease. {ECO:0000269|PubMed:7647801, ECO:0000269|PubMed:7951322, ECO:0000269|PubMed:8634720}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease is caused by expansion of the polyglutamine tract to about 40-83 repeats, causing accumulation in neurons and exerting toxicity. {ECO:0000269|PubMed:7647801, ECO:0000269|PubMed:8634720}.;

Recessive Scores

pRec
0.429

Intolerance Scores

loftool
0.0948
rvis_EVS
-0.52
rvis_percentile_EVS
20.94

Haploinsufficiency Scores

pHI
0.973
hipred
Y
hipred_score
0.825
ghis
0.509

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.934

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Atxn1
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; skeleton phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;RNA processing;brain development;learning;memory;social behavior;negative regulation of transcription, DNA-templated;lung alveolus development;nuclear export
Cellular component
nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;nuclear matrix;nuclear inclusion body
Molecular function
DNA binding;protein binding;protein C-terminus binding;poly(U) RNA binding;poly(G) binding;identical protein binding;protein self-association