DEAF1 p.Ala467=
c.1401G>A · rs35303725 · VCV585771
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 6.5%, sas) — 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 -13 | GERP -2.9 |
| Overall | ||
| CADD | 0.093 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.5%
South Asian · 5,922/91,088 alleles
Filtering AF
6.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.31%
Overall
1.89%
30,440/1,614,138 alleles · common
exomes 28,244/1,461,812 · genomes 2,196/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 6.5% | 15 |
| Middle Eastern | 5.05% | 20 |
| Ashkenazi Jewishnot grpmax-eligible | 3.97% | 25 |
| Remaining individualsnot grpmax-eligible | 2.32% | 43 |
| European (non-Finnish) | 1.68% | 60 |
| Admixed American | 1.45% | 69 |
| East Asian | 0.911% | 110 |
| African / African-American | 0.42% | 238 |
| Finnishnot grpmax-eligible | 0.27% | 370 |
| Amishnot grpmax-eligible | 0.219% | 456 |
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.Ala467=
- Coding
- c.1401G>A
- MANE Select
- NM_021008
- dbSNP
- rs35303725
- Type
- single nucleotide variant
- Location
- chr11:674638 (GRCh38)
- Gene constraint
- LOEUF 1.18 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.62 · 3 PDB
- Residue 467
- the 'interaction with lmo4' region
Similar variants
- DEAF1 p.Ala467Val Uncertain significance ★★ ⚠ same residue
- 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
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-ala467 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown