DEAF1 p.Ser54=
c.162G>C · rs141389829 · VCV772998
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, 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 -1.4 | GERP -1.6 |
| Overall | ||
| CADD | 10.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
Middle Eastern · 53/4,642 alleles
Filtering AF
0.897%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.809%
Overall
0.138%
2,068/1,499,790 alleles · low-frequency
exomes 1,842/1,348,268 · genomes 226/151,522 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.14% | 88 |
| South Asian | 0.385% | 259 |
| Admixed American | 0.238% | 421 |
| Remaining individualsnot grpmax-eligible | 0.156% | 640 |
| European (non-Finnish) | 0.129% | 777 |
| African / African-American | 0.0417% | 2,397 |
| Ashkenazi Jewishnot grpmax-eligible | 0.034% | 2,942 |
| Finnishnot grpmax-eligible | 0.0107% | 9,347 |
| East Asian | 0.00563% | 17,777 |
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.Ser54=
- Coding
- c.162G>C
- MANE Select
- NM_021008
- dbSNP
- rs141389829
- Type
- single nucleotide variant
- Location
- chr11:694886 (GRCh38)
- Gene constraint
- LOEUF 1.18 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.62 · 3 PDB
- Residue 54
- the 'disordered' region
Similar variants
- DEAF1 p.Ser54Trp 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-ser54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown