DEAF1 p.Pro84=
c.252C>T · rs1232046586 · VCV1568451
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00319%, sas)
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 -5.5 | GERP -1.8 |
| Overall | ||
| CADD | 3.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00319%
South Asian · 2/62,746 alleles
Filtering AF
0.000529%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000198%
Overall
0.000288%
4/1,390,784 alleles · very rare
exomes 3/1,239,306 · genomes 1/151,478 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00319% | 31,373 |
| European (non-Finnish) | 0.000186% | 536,751 |
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.Pro84=
- Coding
- c.252C>T
- MANE Select
- NM_021008
- dbSNP
- rs1232046586
- Type
- single nucleotide variant
- Location
- chr11:694796 (GRCh38)
- Gene constraint
- LOEUF 1.18 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.62 · 3 PDB
Similar variants
- DEAF1 p.Pro84Arg Uncertain significance ★★ same residue
- DEAF1 p.Pro84Leu 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
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-pro84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown