SOX9 p.Pro346=
c.1038G>A · VCV4685859
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00706%, sas)
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 -0.13 | GERP -2.7 |
| Overall | ||
| CADD | 6.383 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00706%
South Asian · 5/70,828 alleles
Filtering AF
0.00276%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00143%
21/1,464,272 alleles · very rare
exomes 20/1,313,134 · genomes 1/151,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00706% | 14,166 |
| European (non-Finnish) | 0.00144% | 69,410 |
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.Pro346=
- Coding
- c.1038G>A
- MANE Select
- NM_000346
- Type
- single nucleotide variant
- Location
- chr17:72123895 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.69 · 1 PDB
- Residue 346
- a UniProt-annotated variant site (in cmd1); the 'disordered' region
Similar variants
- SOX9 p.Pro346Ser Uncertain significance ★ ⚠ same residue
- SOX9 p.Pro346dup Benign/Likely benign ★★ same residue
- SOX9 p.Pro346fs Likely pathogenic ★ 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
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-pro346 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown