ATCAY p.Asp120=
c.360C>T · rs758678492 · VCV3047569
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.77 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.6 | GERP -2 |
| Overall | ||
| CADD | 9.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/59,968 alleles
Filtering AF
0.0131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0124%
Overall
0.013%
210/1,613,804 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,613 |
| Middle Eastern | 0.0165% | 6,070 |
| European (non-Finnish) | 0.0149% | 6,704 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,807 |
| East Asian | 0.00668% | 14,967 |
| African / African-American | 0.00667% | 14,989 |
| South Asian | 0.00329% | 30,362 |
| Finnishnot grpmax-eligible | 0.00156% | 64,012 |
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.Asp120=
- Coding
- c.360C>T
- MANE Select
- NM_033064
- dbSNP
- rs758678492
- Type
- single nucleotide variant
- Location
- chr19:3907735 (GRCh38)
- Gene constraint
- LOEUF 0.725 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.68
- Residue 120
- the 'required for interaction with klc1' region
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-asp120 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown