ATCAY p.Ala335=
c.1005G>A · VCV3353680
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
Conditions
1
ATCAY-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -2.4 |
| Overall | ||
| CADD | 0.656 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,884 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.00223%
36/1,613,862 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,481 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,231 |
| European (non-Finnish) | 0.00229% | 43,699 |
| African / African-American | 0.00133% | 74,952 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ATCAY
- Protein
- p.Ala335=
- Coding
- c.1005G>A
- MANE Select
- NM_033064
- Type
- single nucleotide variant
- Location
- chr19:3918809 (GRCh38)
- Gene constraint
- LOEUF 0.725 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.68
- Residue 335
- the 'mediates interaction with gls' region; the 'disordered' region
Disease context
ATCAY-related disorder
Similar variants
- ATCAY c.*3332C>A Uncertain significance ★★ same type
- ATCAY p.Ala148Thr Uncertain significance ★★ ⚠ same type
- ATCAY p.Ala149Thr Uncertain significance ★★ ⚠ same type
- ATCAY p.Val124Met Uncertain significance ★★ ⚠ same type
- ATCAY c.1074-14T>C Benign ★★ same type
- ATCAY c.137-11T>C Likely benign ★★ same type
- ATCAY c.545-65T>C Benign ★★ same type
- ATCAY c.545-8C>T Benign/Likely benign ★★ same type
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-ala335 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown