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GeneBe

ATXN10

ataxin 10, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 22:45671797-45845307

Previous symbols: [ "SCA10" ]

Links

ENSG00000130638NCBI:25814OMIM:611150HGNC:10549Uniprot:Q9UBB4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • spinocerebellar ataxia type 10 (Supportive), mode of inheritance: AD
  • spinocerebellar ataxia type 10 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Spinocerebellar ataxia 10ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic11017075; 11506407; 15127363; 16717236; 17420323; 20301354; 20818609; 21236683; 21531163

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATXN10 gene.

  • not provided (22 variants)
  • Inborn genetic diseases (9 variants)
  • Spinocerebellar ataxia type 10 (5 variants)
  • not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN10 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
3
clinvar
3
missense
10
clinvar
10
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
16
clinvar
16
Total 0 0 12 3 16

Variants in ATXN10

This is a list of pathogenic ClinVar variants found in the ATXN10 region.

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

Position Type Phenotype Significance ClinVar
22-45671813-C-T Benign (Jun 20, 2021)1228260
22-45672074-C-G Inborn genetic diseases Uncertain significance (Jan 03, 2022)2223360
22-45672076-A-G Spinocerebellar ataxia type 10 Uncertain significance (Oct 26, 2018)930239
22-45672094-C-A Inborn genetic diseases Uncertain significance (Aug 09, 2021)2224812
22-45672139-C-T Likely benign (-)1328012
22-45672142-C-T Inborn genetic diseases Uncertain significance (Sep 27, 2021)2252031
22-45672183-A-T Spinocerebellar ataxia type 10 Uncertain significance (Mar 01, 2019)930719
22-45672264-G-A Benign (Nov 10, 2018)1273409
22-45689733-C-G Inborn genetic diseases Uncertain significance (Nov 12, 2021)2260932
22-45689757-A-G ATXN10-related condition Likely benign (Jun 06, 2019)3044990
22-45693008-G-A not specified • Spinocerebellar ataxia type 10 Likely benign (Nov 01, 2022)196455
22-45693025-A-G Inborn genetic diseases Uncertain significance (Oct 11, 2021)2223637
22-45700063-T-C Benign (Jun 19, 2021)1225212
22-45700117-A-G Benign (Jun 18, 2021)1251188
22-45700294-G-T Spinocerebellar ataxia type 10 Uncertain significance (Jul 22, 2021)1298306
22-45702735-A-G Inborn genetic diseases Uncertain significance (Apr 01, 2022)1675894
22-45702848-G-A Spinocerebellar ataxia type 10 Uncertain significance (Mar 29, 2024)3065797
22-45702848-G-GT Inborn genetic diseases Uncertain significance (Sep 02, 2021)2241427
22-45718267-C-T Benign (Nov 10, 2018)1296745
22-45718364-C-T Benign (Jun 18, 2021)1232451
22-45718518-G-T Benign (Nov 10, 2018)1250676
22-45729448-T-C Inborn genetic diseases Uncertain significance (Jan 03, 2022)2268733
22-45729600-G-T Likely benign (-)1285177
22-45738744-C-T Uncertain significance (Jul 22, 2016)289272
22-45738761-G-A Inborn genetic diseases Likely benign (Sep 01, 2021)3132195

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATXN10protein_codingprotein_codingENST00000252934 11173510
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003450.9981257150331257480.000131
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3252702551.060.00001353127
Missense in Polyphen7975.7021.0436986
Synonymous0.03661001000.9950.00000537929
Loss of Function2.691024.30.4110.00000130278

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004270.000427
Ashkenazi Jewish0.000.00
East Asian0.0001630.000163
Finnish0.00004620.0000462
European (Non-Finnish)0.0001320.000132
Middle Eastern0.0001630.000163
South Asian0.0001630.000163
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Necessary for the survival of cerebellar neurons. Induces neuritogenesis by activating the Ras-MAP kinase pathway. May play a role in the maintenance of a critical intracellular glycosylation level and homeostasis. {ECO:0000250}.;
Disease
DISEASE: Note=Defects in ATXN1 may be a cause of nephronophthisis a chronic tubulo-interstitial nephropathy that leads to anemia, polyuria, polydipsia, isosthenuria and death in uremia. {ECO:0000269|PubMed:21565611}.;

Recessive Scores

pRec
0.162

Intolerance Scores

loftool
0.248
rvis_EVS
-1.02
rvis_percentile_EVS
7.94

Haploinsufficiency Scores

pHI
0.162
hipred
N
hipred_score
0.474
ghis
0.651

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.629

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Atxn10
Phenotype
skeleton 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);

Gene ontology

Biological process
nervous system development;neuron projection development;cilium assembly;protein homotrimerization
Cellular component
extracellular space;cytoplasm;cytosol;plasma membrane;membrane;dendrite;neuronal cell body;perinuclear region of cytoplasm
Molecular function
protein binding;enzyme binding;identical protein binding