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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:Q9UBB4AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

  • spinocerebellar ataxia type 10 (Supportive), 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 (24 variants)
  • Inborn genetic diseases (9 variants)
  • Spinocerebellar ataxia type 10 (7 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 4 4
missense 11 11
nonsense 1 1
start loss 0
frameshift 1 1
inframe indel 0
splice variant 2 2
non coding 1 1 16 18
Total 1 0 15 5 16

Variants in ATXN10

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

Position Type Phenotype Significance ClinVar
22-45671813-C-T Benign (Jun 20, 2021)link
22-45672074-C-G Inborn genetic diseases Uncertain significance (Jan 03, 2022)link
22-45672076-A-G Spinocerebellar ataxia type 10 Uncertain significance (Oct 26, 2018)link
22-45672094-C-A Inborn genetic diseases Uncertain significance (Aug 09, 2021)link
22-45672139-C-T Likely benign (-)link
22-45672142-C-T Inborn genetic diseases Uncertain significance (Sep 27, 2021)link
22-45672183-A-T Spinocerebellar ataxia type 10 Uncertain significance (Mar 01, 2019)link
22-45672264-G-A Benign (Nov 10, 2018)link
22-45689733-C-G Inborn genetic diseases Uncertain significance (Nov 12, 2021)link
22-45693008-G-A not specified • Spinocerebellar ataxia type 10 Likely benign (Apr 25, 2022)link
22-45693025-A-G Inborn genetic diseases Uncertain significance (Oct 11, 2021)link
22-45700063-T-C Benign (Jun 19, 2021)link
22-45700117-A-G Benign (Jun 18, 2021)link
22-45700294-G-T Spinocerebellar ataxia type 10 Uncertain significance (Jul 22, 2021)link
22-45702735-A-G Inborn genetic diseases Uncertain significance (Apr 01, 2022)link
22-45702848-G-GT Inborn genetic diseases Uncertain significance (Sep 02, 2021)link
22-45718267-C-T Benign (Nov 10, 2018)link
22-45718364-C-T Benign (Jun 18, 2021)link
22-45718518-G-T Benign (Nov 10, 2018)link
22-45729448-T-C Inborn genetic diseases Uncertain significance (Jan 03, 2022)link
22-45729600-G-T Likely benign (-)link
22-45738744-C-T Uncertain significance (Jul 22, 2016)link
22-45738783-A-AT Uncertain significance (Oct 10, 2016)link
22-45738814-C-T Likely benign (Jan 01, 2021)link
22-45739053-G-A Benign (Nov 10, 2018)link

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