DEAF1 p.Ile403=
c.1209C>T · rs540108800 · VCV444241
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -7.4 | GERP -2.9 |
| Overall | ||
| CADD | 2.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.0031%
50/1,614,082 alleles · ultra-rare
exomes 41/1,461,860 · genomes 9/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00934% | 10,706 |
| South Asian | 0.00659% | 15,181 |
| Admixed American | 0.00333% | 30,005 |
| European (non-Finnish) | 0.00271% | 36,876 |
| East Asian | 0.00223% | 44,900 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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.Ile403=
- Coding
- c.1209C>T
- MANE Select
- NM_021008
- dbSNP
- rs540108800
- Type
- single nucleotide variant
- Location
- chr11:678740 (GRCh38)
- Gene constraint
- LOEUF 1.18 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.62 · 3 PDB
- Residue 403
- the 'interaction with lmo4' region
Similar variants
- DEAF1 p.Ile403Met Likely benign ★ same residue
- DEAF1 p.Ile403Val Likely benign ★ 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
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-ile403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown