SOX9 p.Pro501=
c.1503C>T · rs139015010 · VCV324920
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.056%, 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 -10 | GERP -3.8 |
| Overall | ||
| CADD | 3.658 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.056%
European (non-Finnish) · 661/1,179,940 alleles
Filtering AF
0.0525%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.051%
Overall
0.045%
720/1,600,610 alleles · ultra-rare
exomes 674/1,448,358 · genomes 46/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.056% | 1,785 |
| Admixed American | 0.0483% | 2,070 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,672 |
| African / African-American | 0.0173% | 5,770 |
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.Pro501=
- Coding
- c.1503C>T
- MANE Select
- NM_000346
- dbSNP
- rs139015010
- Type
- single nucleotide variant
- Location
- chr17:72124360 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.69 · 1 PDB
- Residue 501
- a UniProt-annotated variant site (in cmd1); the 'transactivation domain (tac)' region; the 'disordered' region
Similar variants
- 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
- SOX9 p.Glu148Ter Pathogenic ★★ same condition
- SOX9 p.Pro170Ala Likely 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-pro501 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown