VAX1 p.Pro236=
c.708A>T · VCV3668213
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0113%, nfe)
Conditions
1
microphthalmia, syndromic 11
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 -0.23 | GERP -3 |
| Overall | ||
| CADD | 2.746 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0113%
European (non-Finnish) · 105/929,512 alleles
Filtering AF
0.00951%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00889%
Overall
0.00931%
106/1,138,154 alleles · ultra-rare
exomes 91/991,600 · genomes 15/146,554 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0113% | 8,852 |
| African / African-American | 0.00165% | 60,532 |
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
- VAX1
- Protein
- p.Pro236=
- Coding
- c.708A>T
- MANE Select
- NM_001112704
- Type
- single nucleotide variant
- Location
- chr10:117134305 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI 0.66 (gnomAD)
- Structure
- AlphaFold pLDDT 65.77
- Residue 236
- the 'disordered' region
Similar variants
- VAX1 p.Ala227Val Uncertain significance ★★ ⚠ same condition
- VAX1 p.Lys27Thr Uncertain significance ★★ ⚠ same condition
- VAX1 p.Met295Val Uncertain significance ★★ ⚠ same condition
- VAX1 p.Ser213Thr Uncertain significance ★★ ⚠ same condition
- VAX1 p.Ala230Thr Likely benign ★★ ⚠ same condition
- VAX1 p.Ala42= Benign/Likely benign ★★ same condition
- VAX1 p.Leu217= Benign/Likely benign ★★ same condition
- VAX1 p.Ala285Ser Uncertain significance ★ ⚠ same condition
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/vax1-p-pro236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown