DIAPH3 p.Leu229Pro
c.686T>C · rs201688909 · VCV1215569
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8621 | likely pathogenic · top 8% in DIAPH3 |
|---|---|---|
| REVEL | 0.844 | moderately pathogenic-leaning |
| SaProt | LLR -15.44 | damaging |
| ⇒ AlphaMissense, REVEL and SaProt all call this damaging. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 497 kb · p 0.83 · regional, not allelic |
| Overall | ||
| CADD | 28.1 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Amishnot grpmax-eligible | 0.11% | 910 |
| European (non-Finnish)grpmax | 0.0164% | 6,113 |
| Admixed American | 0.00834% | 11,996 |
| African / African-American | 0.00668% | 14,980 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,613 |
Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- DIAPH3
- Protein
- p.Leu229Pro
- Coding
- c.686T>C
- MANE Select
- NM_001042517
- dbSNP
- rs201688909
- Type
- single nucleotide variant
- Location
- chr13:60016086 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.33 · 2 PDB
- Residue 229
- the gbd/fh3 domain
Similar variants
- DIAPH3 p.Leu229Val Uncertain significance ★ ⚠ same residue
- DIAPH3 p.Leu229= Likely benign ★ same residue
- DIAPH3 p.Ala500Val Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Ala546Thr Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1027His Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1048Cys Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1048Gly Uncertain significance ★★ ⚠ same type
- DIAPH3 p.Arg1089Pro Uncertain significance ★★ ⚠ 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/diaph3-p-leu229pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown