ATF6 p.Ala278=
c.834G>A · rs202091973 · VCV3054409
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
ATF6-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 -0.31 | GERP -3.5 |
| Overall | ||
| CADD | 6.516 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000496%
8/1,614,024 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Admixed American | 0.005% | 19,989 |
| European (non-Finnish) | 0.000339% | 295,000 |
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
- ATF6
- Protein
- p.Ala278=
- Coding
- c.834G>A
- MANE Select
- NM_007348
- dbSNP
- rs202091973
- Type
- single nucleotide variant
- Location
- chr1:161802197 (GRCh38)
- Gene constraint
- LOEUF 0.882 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 56.09
Disease context
ATF6-related disorder
Similar variants
- ATF6 p.Ala278Val Benign ★★ same residue
- ATF6 c.1533+1G>C Pathogenic ★★ same condition
- ATF6 c.160-1G>A Likely pathogenic ★★ same condition
- ATF6 c.484+1G>A Likely pathogenic ★★ same condition
- ATF6 p.Arg324Cys Pathogenic ★★ same condition
- ATF6 p.Gln217Ter Likely pathogenic ★ same condition
- ATF6 p.Gln224Ter Likely pathogenic ★ same condition
- ATF6 p.Ser277Ter Likely pathogenic ★ 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/atf6-p-ala278 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown