ATXN2

Chr 12ADMulti

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]

Primary Disease Associations & Inheritance

{Amyotrophic lateral sclerosis, susceptibility to, 13}MIM #183090
AD
{Parkinson disease, late-onset, susceptibility to}MIM #168600
ADMulti
Spinocerebellar ataxia 2MIM #183090
AD
222
ClinVar variants
11
Pathogenic / LP
0.85
pLI score
1
Active trials
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
11 Pathogenic / Likely Pathogenic· 161 VUS of 222 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

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

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

Missense Constraint?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.
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?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.0.20 (0.130.33)
00.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.74 (0.680.80)
00.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.94
01.21.6
LoF obs/exp: 11 / 54.8Missense obs/exp: 466 / 632.0Syn Z: 0.68

ClinVar Variant Classifications

222 submitted variants in ClinVar

Classification Summary

Pathogenic9
Likely Pathogenic2
VUS161
Likely Benign30
Benign15
Conflicting5
9
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
0
9
0
9
Likely Pathogenic
1
0
1
0
2
VUS
1
103
56
1
161
Likely Benign
5
7
11
7
30
Benign
0
2
10
3
15
Conflicting
5
Total71128711222

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

View in ClinVar →

Protein Context — Lollipop Plot

ATXN2 · 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

ATAXIN 2; ATXN2
MIM #601517 · *

{Amyotrophic lateral sclerosis, susceptibility to, 13}

MIM #183090

Molecular basis of disorder known

Autosomal dominant

{Parkinson disease, late-onset, susceptibility to}

MIM #168600

Molecular basis of disorder known

Autosomal dominantMultifactorial

Spinocerebellar ataxia 2

MIM #183090

Molecular basis of disorder known

Autosomal dominant
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GeneReview available — ATXN2
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence