SOX11 p.Pro263=
c.789G>A · rs746501349 · VCV747619
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.56e-05%, nfe)
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 -2.7, phastCons 0.98 |
| Overall | ||
| CADD | 12.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.56e-05%
European (non-Finnish) · 1/1,168,456 alleles
Overall
6.35e-05%
1/1,575,980 alleles · very rare
exomes 1/1,423,738 · genomes 0/152,242 · joint denominator
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
- SOX11
- Protein
- p.Pro263=
- Coding
- c.789G>A
- MANE Select
- NM_003108
- dbSNP
- rs746501349
- Type
- single nucleotide variant
- Location
- chr2:5693510 (GRCh38)
- Gene constraint
- LOEUF 1.148 · pLI 0.09 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44 · 4 PDB
- Residue 263
- a UniProt-annotated variant site (in iddmoh); the 'disordered' region
Similar variants
- SOX11 p.Pro263Gln Uncertain significance ★ ⚠ same residue
- SOX11 p.Pro263Ser Uncertain significance ★ ⚠ same residue
- SOX11 p.Pro263Thr Uncertain significance ★ ⚠ same residue
- SOX11 p.Ala102Glu Pathogenic/Likely pathogenic ★★ same type
- SOX11 p.Ala102Val Pathogenic/Likely pathogenic ★★ same type
- SOX11 p.Arg100Pro Pathogenic/Likely pathogenic ★★ same type
- SOX11 p.Arg106Pro Pathogenic/Likely pathogenic ★★ same type
- SOX11 p.Arg119Trp 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/sox11-p-pro263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown