ATF4 p.Arg193=
c.579G>A · rs146204295 · VCV717867
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.191%, 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 0.53 | GERP -1.1, phastCons 0.97 |
| Overall | ||
| CADD | 2.633 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.191%
African / African-American · 143/74,998 alleles
Filtering AF
0.165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.155%
Overall
0.0116%
187/1,613,898 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.191% | 524 |
| Middle Eastern | 0.0495% | 2,019 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| Admixed American | 0.01% | 10,003 |
| South Asian | 0.00439% | 22,766 |
| European (non-Finnish) | 0.00119% | 84,275 |
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.Arg193=
- Coding
- c.579G>A
- MANE Select
- NM_182810
- dbSNP
- rs146204295
- Type
- single nucleotide variant
- Location
- chr22:39522125 (GRCh38)
- Gene constraint
- LOEUF 0.718 · pLI 0.38 (gnomAD)
- Structure
- AlphaFold pLDDT 62.95 · 2 PDB
Similar variants
- 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
- ATF4 p.Tyr200= 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-arg193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown