SOX9 p.Ser322=
c.966C>T · VCV4936821
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,609,326)
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 5.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 14.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,609,326). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SOX9
- Protein
- p.Ser322=
- Coding
- c.966C>T
- MANE Select
- NM_000346
- Type
- single nucleotide variant
- Location
- chr17:72123823 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.69 · 1 PDB
- Residue 322
- a UniProt-annotated variant site (in cmd1)
Similar variants
- SOX9 p.Ser322Asn Uncertain significance ★★ ⚠ same residue
- SOX9 c.432-2A>T Pathogenic ★★ same type
- SOX9 p.Ala158Val Pathogenic/Likely pathogenic ★★ same type
- SOX9 p.Arg152Pro Pathogenic/Likely pathogenic ★★ same type
- SOX9 p.Arg394Ter Pathogenic ★★ same type
- SOX9 p.Gln340Ter Pathogenic/Likely pathogenic ★★ same type
- SOX9 p.Gln357Ter Pathogenic ★★ same type
- SOX9 p.Glu148Ter 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/sox9-p-ser322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown