SOX11 p.Pro72=
c.216G>A · rs781471503 · VCV1997362
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -0.44 | GERP -3.9, phastCons 0.007 |
| Overall | ||
| CADD | 11.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,810 alleles
Filtering AF
0.00074%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000186%
3/1,613,110 alleles · very rare
exomes 3/1,461,786 · genomes 0/151,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,405 |
| European (non-Finnish) | 8.48e-05% | 1,179,647 |
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.Pro72=
- Coding
- c.216G>A
- MANE Select
- NM_003108
- dbSNP
- rs781471503
- Type
- single nucleotide variant
- Location
- chr2:5692937 (GRCh38)
- Gene constraint
- LOEUF 1.148 · pLI 0.09 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44 · 4 PDB
- Residue 72
- a DNA-binding region; a UniProt-annotated variant site (in iddmoh)
Similar variants
- 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
- SOX11 p.Arg51Gln Pathogenic/Likely pathogenic ★★ same type
- SOX11 p.Arg51Gly Likely pathogenic ★★ same type
- SOX11 p.Arg64Cys 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-pro72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown