ATXN1L

Chr 16

ataxin 1 like

Also known as: BOAT, BOAT1

NCBI Gene: 342371 ENSG00000224470 UniProt: P0C7T5

Predicted to enable RNA binding activity and chromatin binding activity. Predicted to be involved in several processes, including learning or memory; negative regulation of transcription by RNA polymerase II; and social behavior. Predicted to act upstream of or within extracellular matrix organization; lung alveolus development; and positive regulation of hematopoietic stem cell proliferation. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Active trials

Pathogenic / LP

151

ClinVar variants

Pubs (1 yr)

1.1

Missense Z

0.30

LOEUF· LoF intolerant

Clinical Summary— ATXN1L

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

28 Pathogenic / Likely Pathogenic· 121 VUS of 151 total submissions

Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

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.

0.30LOEUF

pLI 0.979

Z-score 3.80

OE 0.10 (0.04–0.30)

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.

1.08Z-score

OE missense 0.84 (0.77–0.93)

323 obs / 382.5 exp

Tolerant

Mild missense constraint

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.0.10 (0.04–0.30)

0≤0.351.4

Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.84 (0.77–0.93)

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.0.86

0≤1.21.6

LoF obs/exp: 2 / 20.6Missense obs/exp: 323 / 382.5Syn Z: 1.43

0.3097th %ile

GOF

0.2497th %ile

LOF

0.78top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.30

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