SOX9 p.Arg162=
c.486C>G · rs1290444196 · VCV1983769
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.022%, sas)
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 -3.5 | GERP -4.4 |
| Overall | ||
| CADD | 11.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.022%
South Asian · 20/91,090 alleles
Filtering AF
0.0145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00173%
28/1,613,940 alleles · ultra-rare
exomes 27/1,461,822 · genomes 1/152,118 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.022% | 4,555 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| European (non-Finnish) | 0.000593% | 168,570 |
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.Arg162=
- Coding
- c.486C>G
- MANE Select
- NM_000346
- dbSNP
- rs1290444196
- Type
- single nucleotide variant
- Location
- chr17:72122773 (GRCh38)
- Gene constraint
- LOEUF 0.154 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 56.69 · 1 PDB
- Residue 162
- a DNA-binding region; a UniProt-annotated variant site (in cmd1); the 'disordered' region; an α-helix
Similar variants
- SOX9 p.Arg162Cys Uncertain significance ★ ⚠ same residue
- SRA1 p.Asp162= Benign ★ 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-arg162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown