ATF6 p.His660=
c.1980C>T · rs746085909 · VCV1657098
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
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 -9.5 | GERP -4.1 |
| Overall | ||
| CADD | 0.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,978 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00161%
26/1,613,526 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,996 |
| African / African-American | 0.00267% | 37,430 |
| European (non-Finnish) | 0.00144% | 69,401 |
| South Asian | 0.0011% | 91,004 |
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.His660=
- Coding
- c.1980C>T
- MANE Select
- NM_007348
- dbSNP
- rs746085909
- Type
- single nucleotide variant
- Location
- chr1:161958621 (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 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
- ATF6 p.Arg376Ter Pathogenic ★★ same type
- ATF6 p.Gln237Ter 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-his660 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown