ATF6 p.Val288=
c.864G>A · rs769852963 · VCV1611457
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, afr)
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 5.1 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 8.218 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,894 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00149%
24/1,613,862 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,761 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| European (non-Finnish) | 0.000847% | 117,998 |
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.Val288=
- Coding
- c.864G>A
- MANE Select
- NM_007348
- dbSNP
- rs769852963
- Type
- single nucleotide variant
- Location
- chr1:161802227 (GRCh38)
- Gene constraint
- LOEUF 0.882 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 56.09
Similar variants
- ATF6 p.Val288Glu Uncertain significance ★★ ⚠ same residue
- ATF6 p.Val288Met Uncertain significance ★ ⚠ same residue
- ATF6 c.1533+1G>C Pathogenic ★★ same type
- ATF6 c.160-1G>A Likely pathogenic ★★ same type
- ATF6 c.484+1G>A Likely pathogenic ★★ same type
- ATF6 c.484+1G>T Likely pathogenic ★★ same type
- ATF6 c.82+5G>T Pathogenic ★★ same type
- ATF6 p.Arg324Cys 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/atf6-p-val288 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown