Is ATCAY p.Asp201fs (c.602_608del) pathogenic?

ATCAY p.Asp201fs (c.602608del) is classified Pathogenic in ATCAY (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-11-03). Absent from gnomAD; Associated with Cayman type cerebellar ataxia.

What condition is associated with ATCAY p.Asp201fs (c.602_608del)?

ATCAY p.Asp201fs (c.602_608del) is associated with Cayman type cerebellar ataxia (ClinVar).

How common is ATCAY p.Asp201fs (c.602_608del) in the general population?

ATCAY p.Asp201fs (c.602_608del) is absent from gnomAD (gnomAD).

How is Cerebellar ataxia, Cayman type inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ATCAY p.Asp201fs

c.602_608del · rs2145248615 · VCV1319958

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Cayman type cerebellar ataxia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 6 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.4	GERP 2.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ATCAY
Protein: p.Asp201fs
Coding: c.602_608del
MANE Select: NM_033064
dbSNP: rs2145248615
Type: Deletion
Location: chr19:3908322 (GRCh38)
Gene constraint: LOEUF 0.725 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 70.68
Residue 201: the cral-trio domain; the 'mediates interaction with gls' region

Full ATCAY gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cayman type cerebellar ataxia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Cerebellar ataxia, Cayman type (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ATCAY c.*3332C>A Uncertain significance ★★ same condition
ATCAY p.Ala148Thr Uncertain significance ★★ ⚠ same condition
ATCAY p.Val124Met Uncertain significance ★★ ⚠ same condition
ATCAY c.1074-14T>C Benign ★★ same condition
ATCAY c.137-11T>C Likely benign ★★ same condition
ATCAY c.545-65T>C Benign ★★ same condition
ATCAY c.545-8C>T Benign/Likely benign ★★ same condition
ATCAY c.647+10C>T Benign/Likely benign ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/atcay-p-asp201fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown