ATXN2

Chr 12

ataxin 2

Also known as: ATX2, SCA2, TNRC13

This gene belongs to a group of genes that is associated with microsatellite-expansion diseases, a class of neurological and neuromuscular disorders caused by expansion of short stretches of repetitive DNA. The protein encoded by this gene has two globular domains near the N-terminus, one of which contains a clathrin-mediated trans-Golgi signal and an endoplasmic reticulum exit signal. The encoded cytoplasmic protein localizes to the endoplasmic reticulum and plasma membrane, is involved in endocytosis, and modulates mTOR signals, modifying ribosomal translation and mitochondrial function. The N-terminal region of the protein contains a polyglutamine tract of 14-31 residues that can be expanded in the pathogenic state to 32-200 residues. Intermediate length expansions of this tract increase susceptibility to amyotrophic lateral sclerosis, while long expansions of this tract result in spinocerebellar ataxia-2, an autosomal-dominantly inherited, neurodegenerative disorder. Genome-wide association studies indicate that loss-of-function mutations in this gene may be associated with susceptibility to type I diabetes, obesity and hypertension. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

GeneReviewsResearchGenerating clinical summary…
MultiplemechanismLOEUF 0.33
Clinical SummaryATXN2
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Gene-Disease Validity (ClinGen)
spinocerebellar ataxia type 2 · ADDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.85) — some intolerance to loss-of-function variants.
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ClinVar Variants
3 unique Pathogenic / Likely Pathogenic· 161 VUS of 240 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
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GeneReview available — ATXN2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.33LOEUF
pLI 0.853
Z-score 5.48
OE 0.20 (0.130.33)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.35Z-score
OE missense 0.74 (0.680.80)
466 obs / 632.0 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.20 (0.130.33)
00.351.4
Missense OE?0.74 (0.680.80)
00.61.4
Synonymous OE?0.94
01.21.6
LoF obs/exp: 11 / 54.8Missense obs/exp: 466 / 632.0Syn Z: 0.68

This gene — mechanism propensity

DN
0.2997th %ile
GOF
0.2597th %ile
LOF
0.83top 5%

This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to loss-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

LOFprediction above median · LOEUF 0.33
GOF1 literature citation

Literature Evidence

GOFSpinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the ATXN2 gene.1

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

References

  1. 1.PMID 28525545

ClinVar Variant Classifications

240 submitted variants in ClinVar

Classification Summary

Pathogenic1
Likely Pathogenic2
VUS161
Likely Benign30
Benign15
Conflicting5
1
Pathogenic
2
Likely Pathogenic
161
VUS
30
Likely Benign
15
Benign
5
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
1
0
0
1
Likely Pathogenic
1
1
0
0
2
VUS
1
107
52
1
161
Likely Benign
5
10
8
7
30
Benign
0
5
7
3
15
Conflicting
5
Total71246711214

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

View in ClinVar →

8 pathogenic / likely-pathogenic (of 11) ClinVar copy-number / structural variants overlap ATXN2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

ATXN2 · protein map & ClinVar variants

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