ATCAY

Chr 19AR

ATCAY kinesin light chain interacting caytaxin

Also known as: BNIP-H, CLAC

NCBI Gene: 85300ENSG00000167654UniProt: Q86WG3

This gene encodes a neuron-restricted protein that contains a CRAL-TRIO motif common to proteins that bind small lipophilic molecules. Mutations in this gene are associated with cerebellar ataxia, Cayman type. [provided by RefSeq, Jul 2008]

Primary Disease Associations & Inheritance

Ataxia, cerebellar, Cayman typeMIM #601238
AR
Ataxia, cerebellar, Cayman typeMIM #601238
AR
UniProtCerebellar ataxia, cayman type
253
ClinVar variants
25
Pathogenic / LP
0.62
pLI score
1
Active trials
Clinical Summary— ATCAY
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.62) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
25 Pathogenic / Likely Pathogenic· 156 VUS of 253 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
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.
0.45LOEUF
pLI 0.621
Z-score 3.38
OE 0.20 (0.10–0.45)
Moderately constrained

More LoF-intolerant than ~75% 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.
1.61Z-score
OE missense 0.72 (0.64–0.81)
185 obs / 257.8 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.0.20 (0.10–0.45)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.72 (0.64–0.81)
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.1.05
0≤1.21.6
LoF obs/exp: 4 / 20.5Missense obs/exp: 185 / 257.8Syn Z: -0.41

ClinVar Variant Classifications

253 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic2
VUS156
Likely Benign33
Benign30
Conflicting7
23
Pathogenic
2
Likely Pathogenic
156
VUS
33
Likely Benign
30
Benign
7
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
2
20
0
23
Likely Pathogenic
0
0
2
0
2
VUS
0
67
83
6
156
Likely Benign
0
0
20
13
33
Benign
0
0
29
1
30
Conflicting
—7
Total16915420251

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

View in ClinVar →

Protein Context — Lollipop Plot

ATCAY · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

2 OMIM entries

OMIM
CAYTAXIN; ATCAY
MIM #608179 · *

Ataxia, cerebellar, Cayman type

MIM #601238

Molecular basis of disorder known

Autosomal recessive

Ataxia, cerebellar, Cayman type

MIM #601238

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Novel homozygous frameshift variant in the ATCAY gene in an Iranian patient with Cayman cerebellar ataxia; expanding the neuroimaging and clinical features: a case report.
Siavashani ES et al.·BMC Med Genomics
2023Case report
Expression of Caytaxin protein in Cayman Ataxia mouse models correlates with phenotype severity.
Sikora KM et al.·PLoS One
2012Functional
Novel homozygous variants in ATCAY, MCOLN1, and SACS in complex neurological disorders.
Manzoor H et al.·Parkinsonism Relat Disord
2018
A novel signature model based on mitochondrial-related genes for predicting survival of colon adenocarcinoma.
Gao H et al.·BMC Med Inform Decis Mak
2022Functional
Alzheimer's disease: an integrative bioinformatics and machine learning analysis reveals glutamine metabolism-associated gene biomarkers.
Xing N et al.·BMC Pharmacol Toxicol
2025
Multipotent genetic suppression of retrotransposon-induced mutations by Nxf1 through fine-tuning of alternative splicing.
Concepcion D et al.·PLoS Genet
2009
Clinical comparison of overlapping deletions of 19p13.3.
Risheg H et al.·Am J Med Genet A
2013Case report
Expanding the clinical spectrum of 19p13.3 microduplication syndrome: a case report highlighting nephrotic syndrome and literature review.
Sun W et al.·BMC Pediatr
2025Review
Identification of novel molecular markers for prognosis estimation of acute myeloid leukemia: over-expression of PDCD7, FIS1 and Ang2 may indicate poor prognosis in pretreatment patients with acute myeloid leukemia.
Tian Y et al.·PLoS One
2014Cohort
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