ATL1 p.Gly404=
c.1212G>A · rs1468685951 · VCV2644231
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -0.048 | GERP -3.4, phastCons 0.26 |
| Overall | ||
| CADD | 7.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,874 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000205%
3/1,461,892 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,437 |
| European (non-Finnish) | 8.47e-05% | 1,180,032 |
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
- ATL1
- Protein
- p.Gly404=
- Coding
- c.1212G>A
- MANE Select
- NM_015915
- dbSNP
- rs1468685951
- Type
- single nucleotide variant
- Location
- chr14:50628123 (GRCh38)
- Gene constraint
- LOEUF 0.57 · pLI 0.36 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 14 PDB
- Residue 404
- an α-helix; the '3hb (three-helix bundle) domain' region
Similar variants
- ATL1 p.Arg217Gln Pathogenic/Likely pathogenic ★★ same type
- ATL1 p.Arg239Cys Pathogenic/Likely pathogenic ★★ same type
- ATL1 p.Arg239His Likely pathogenic ★★ same type
- ATL1 p.Arg403Pro Likely pathogenic ★★ same type
- ATL1 p.Arg415Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- ATL1 p.Arg416Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- ATL1 p.Arg495Trp Pathogenic/Likely pathogenic ★★ same type
- ATL1 p.Arg501Ter Pathogenic ★★ 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/atl1-p-gly404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown