ATF3 p.Asn137=
c.411C>T · VCV3959697
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.236%, eas)
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 -11 | GERP -4.4 |
| Overall | ||
| CADD | 1.385 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.236%
East Asian · 106/44,882 alleles
Filtering AF
0.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.186%
Overall
0.00861%
139/1,614,086 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.236% | 423 |
| South Asian | 0.00769% | 13,011 |
| African / African-American | 0.00267% | 37,498 |
| European (non-Finnish) | 0.00186% | 53,638 |
| Admixed American | 0.00167% | 60,016 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
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
- ATF3
- Protein
- p.Asn137=
- Coding
- c.411C>T
- MANE Select
- NM_001674
- Type
- single nucleotide variant
- Location
- chr1:212619420 (GRCh38)
- Gene constraint
- LOEUF 0.879 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 77.45
- Residue 137
- the bzip domain; the 'leucine-zipper' region
Similar variants
- ATF3 p.Ser12Pro Uncertain significance ★★ ⚠ same type
- ATF3 p.Ala82Val Uncertain significance ★ ⚠ same type
- ATF3 p.Asn168Ile Uncertain significance ★ ⚠ same type
- ATF3 p.Asp69Asn Uncertain significance ★ ⚠ same type
- ATF3 p.Gln115Glu Uncertain significance ★ ⚠ same type
- ATF3 p.Glu32Lys Uncertain significance ★ ⚠ same type
- ATF3 p.Glu80Lys Uncertain significance ★ ⚠ same type
- ATF3 p.Ile171Thr Uncertain significance ★ ⚠ 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/atf3-p-asn137 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown