Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 55.6%, afr) — too common for a highly-penetrant pathogenic allele
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 2 | GERP -0.14, phastCons 1 |
| Overall | ||
| CADD | 12.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
55.6%
African / African-American · 41,576/74,774 alleles
Filtering AF
55.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 55%
Overall
14.1%
227,938/1,613,254 alleles · common
exomes 191,242/1,461,416 · genomes 36,696/151,838 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 55.6% | 2 |
| East Asian | 20.2% | 5 |
| Remaining individualsnot grpmax-eligible | 16.4% | 6 |
| Middle Eastern | 16.1% | 6 |
| South Asian | 14.4% | 7 |
| Ashkenazi Jewishnot grpmax-eligible | 13.8% | 7 |
| European (non-Finnish) | 11.5% | 9 |
| Admixed American | 10.6% | 9 |
| Finnishnot grpmax-eligible | 10% | 10 |
| Amishnot grpmax-eligible | 5.3% | 19 |
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
- DEAF1
- Protein
- p.Gln529=
- Coding
- c.1587A>G
- MANE Select
- NM_021008
- dbSNP
- rs10615
- Type
- single nucleotide variant
- Location
- chr11:653968 (GRCh38)
- Gene constraint
- LOEUF 1.18 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.62 · 3 PDB
- Residue 529
- an α-helix
Similar variants
- DEAF1 c.998-2A>G Likely pathogenic ★★ same type
- DEAF1 p.Arg224Pro Pathogenic/Likely pathogenic ★★ same type
- DEAF1 p.Arg224Trp Pathogenic/Likely pathogenic ★★ same type
- DEAF1 p.Arg226Trp Pathogenic/Likely pathogenic ★★ same type
- DEAF1 p.Arg246Thr Pathogenic/Likely pathogenic ★★ same type
- DEAF1 p.Arg261Ter Pathogenic/Likely pathogenic ★★ same type
- DEAF1 p.Arg351Ter Likely pathogenic ★★ same type
- DEAF1 p.Arg484Ter Pathogenic/Likely 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/deaf1-p-gln529 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown