SOX9 p.Pro307=
c.921G>C · rs779558292 · VCV696735
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00771%, nfe)
Conditions
1
campomelic dysplasia
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 0.63 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 12.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00771%
European (non-Finnish) · 91/1,179,884 alleles
Filtering AF
0.00639%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00592%
Overall
0.00608%
98/1,612,864 alleles · very rare
exomes 86/1,460,808 · genomes 12/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00771% | 12,966 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,615 |
| African / African-American | 0.00401% | 24,967 |
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
- SOX9
- Protein
- p.Pro307=
- Coding
- c.921G>C
- MANE Select
- NM_000346
- dbSNP
- rs779558292
- Type
- single nucleotide variant
- Location
- chr17:72123778 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.69 · 1 PDB
- Residue 307
- a UniProt-annotated variant site (in cmd1); the 'transactivation domain (tam)' region
Similar variants
- SOX9 p.Pro307Arg Conflicting classifications of pathogenicity ★ same residue
- SOX9 p.Pro307Leu Uncertain significance ★ ⚠ same residue
- SOX9 c.432-2A>T Pathogenic ★★ same condition
- SOX9 p.Ala158Val Pathogenic/Likely pathogenic ★★ same condition
- SOX9 p.Arg152Pro Pathogenic/Likely pathogenic ★★ same condition
- SOX9 p.Arg394Ter Pathogenic ★★ same condition
- SOX9 p.Gln340Ter Pathogenic/Likely pathogenic ★★ same condition
- SOX9 p.Gln357Ter Pathogenic ★★ 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/sox9-p-pro307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown