ATF4 p.Ser80=
c.240C>T · rs115111682 · VCV791218
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.569%, 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 -1 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 7.886 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.569%
African / African-American · 427/75,028 alleles
Filtering AF
0.525%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.507%
Overall
0.0292%
472/1,613,936 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.569% | 176 |
| Middle Eastern | 0.066% | 1,516 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,125 |
| Admixed American | 0.0267% | 3,752 |
| European (non-Finnish) | 0.000424% | 235,973 |
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
- ATF4
- Protein
- p.Ser80=
- Coding
- c.240C>T
- MANE Select
- NM_182810
- dbSNP
- rs115111682
- Type
- single nucleotide variant
- Location
- chr22:39521786 (GRCh38)
- Gene constraint
- LOEUF 0.718 · pLI 0.38 (gnomAD)
- Structure
- AlphaFold pLDDT 62.95 · 2 PDB
Similar variants
- ATF4 p.Ser80Phe Uncertain significance ★ ⚠ same residue
- ATF4 p.Ala324Val Benign ★★ same type
- ATF4 p.Asn131= Benign ★★ same type
- ATF4 p.Glu322Asp Benign ★★ ⚠ same type
- ATF4 p.Glu3Lys Benign ★★ ⚠ same type
- ATF4 p.Ile208Met Likely benign ★★ ⚠ same type
- ATF4 p.Pro258Ala Benign ★★ same type
- ATF4 p.Thr137Ser 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/atf4-p-ser80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown