EAF2 p.Asp201=
c.603T>C · rs780547951 · VCV761634
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, 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 -0.87 | GERP -3.6 |
| Overall | ||
| CADD | 0.363 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,798 alleles
Filtering AF
0.0058%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00395%
Overall
0.00372%
60/1,612,910 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,466 |
| African / African-American | 0.00534% | 18,711 |
| European (non-Finnish) | 0.00399% | 25,091 |
| South Asian | 0.0022% | 45,529 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,440 |
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
- EAF2
- Protein
- p.Asp201=
- Coding
- c.603T>C
- MANE Select
- NM_019100 · reported on NM_018456
- dbSNP
- rs780547951
- Type
- single nucleotide variant
- Location
- chr3:121872655 (GRCh38)
- Structure
- AlphaFold pLDDT 75.46 · 18 PDB
- Residue 201
- an α-helix
Similar variants
- DMAP1 p.Lys201Thr Uncertain significance ★ ⚠ same residue
- EAF2 p.Asp201Asn Uncertain significance ★ ⚠ same residue
- DMAP1 p.Arg224Ter Uncertain significance ★★ same type
- DMAP1 p.Arg283His Uncertain significance ★★ ⚠ same type
- DMAP1 p.Tyr196Ser Uncertain significance ★★ ⚠ same type
- DMAP1 p.Arg226Trp Likely pathogenic ★ same type
- DMAP1 c.1344+3A>G Uncertain significance ★ same type
- DMAP1 c.394-1G>C 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/eaf2-p-asp201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown