ATXN10

Chr 22AD

ataxin 10

Also known as: ATX10, E46L, HUMEEP, SCA10

NCBI Gene: 25814ENSG00000130638UniProt: Q9UBB4

This gene encodes a protein that may function in neuron survival, neuron differentiation, and neuritogenesis. These roles may be carried out via activation of the mitogen-activated protein kinase cascade. Expansion of an ATTCT repeat from 9-32 copies to 800-4500 copies in an intronic region of this locus has been associated with spinocerebellar ataxia, type 10. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jul 2016]

Primary Disease Associations & Inheritance

Spinocerebellar ataxia 10MIM #603516
AD
148
ClinVar variants
81
Pathogenic / LP
0.00
pLI score
1
Active trials
Clinical Summary— ATXN10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
81 Pathogenic / Likely Pathogenic· 21 VUS of 148 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.70LOEUF
pLI 0.000
Z-score 2.69
OE 0.41 (0.25–0.70)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.33Z-score
OE missense 1.06 (0.96–1.17)
270 obs / 255.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.41 (0.25–0.70)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.06 (0.96–1.17)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.00
0≤1.21.6
LoF obs/exp: 10 / 24.3Missense obs/exp: 270 / 255.4Syn Z: 0.04

ClinVar Variant Classifications

148 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic80
Likely Pathogenic1
VUS21
Likely Benign9
Benign19
80
Pathogenic
1
Likely Pathogenic
21
VUS
9
Likely Benign
19
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
80
0
80
Likely Pathogenic
0
0
1
0
1
VUS
3
11
7
0
21
Likely Benign
0
2
1
6
9
Benign
0
0
19
0
19
Total3131086130

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ATXN10 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
ATAXIN 10; ATXN10
MIM #611150 · *

Spinocerebellar ataxia 10

MIM #603516

Molecular basis of disorder known

Autosomal dominant
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Spinocerebellar Ataxia Type 10 (SCA 10) in Brazil.
Teive HAG et al.·Cerebellum
2025Review
Association of Non-Coding Repeat Expansions with Parkinson's Disease Risk: Evidence from a UK Biobank-Based Whole-Genome Sequencing Study.
Hu Z et al.·Mov Disord
2026
The role of ataxin 10 in the pathogenesis of spinocerebellar ataxia type 10.
Wakamiya M et al.·Neurology
2006
The impact of interrupted ATXN10 expansions on clinical findings of spinocerebellar ataxia type 10.
Hasan A et al.·J Neurol
2025
Frequency of spinocerebellar ataxia mutations in patients with multiple system atrophy.
Wernick AI et al.·Clin Auton Res
2021Cohort
ATXN10 Gene Expansions in Mexican Patients with Ataxia Without Epilepsy.
Jara-Prado A et al.·Cerebellum
2025Cohort
Spinocerebellar Ataxia Type 10 with Atypical Clinical Manifestation in Han Chinese.
Mao C et al.·Cerebellum
2023
[Molecular and genetic analysis of spinocerebellar ataxia type 10 (SCA10)].
Matsuura T·Rinsho Shinkeigaku
2008Review
Extensive cerebellar and thalamic degeneration in spinocerebellar ataxia type 10.
Hernandez-Castillo CR et al.·Parkinsonism Relat Disord
2019
Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.
Borghini L et al.·Sci Rep
2019
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Rare DisordersUndiagnosed DisordersDisorders of Unknown Prevalence

Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford

RECRUITING
NCT01793168Sanford HealthStarted 2010-07

External Resources

Links to major genomics databases and tools