SOX5 p.Ser693=
c.2079G>A · rs138876515 · VCV720607
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.833%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -5 |
| Overall | ||
| CADD | 0.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.833%
African / African-American · 625/75,012 alleles
Filtering AF
0.779%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.758%
Overall
0.0485%
782/1,614,032 alleles · rare
exomes 391/1,461,812 · genomes 391/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.833% | 120 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Middle Eastern | 0.0825% | 1,212 |
| Admixed American | 0.0667% | 1,500 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0372% | 2,691 |
| South Asian | 0.00659% | 15,177 |
| European (non-Finnish) | 0.00347% | 28,781 |
| East Asian | 0.00223% | 44,864 |
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
- SOX5
- Protein
- p.Ser693=
- Coding
- c.2079G>A
- MANE Select
- NM_006940
- dbSNP
- rs138876515
- Type
- single nucleotide variant
- Location
- chr12:23534432 (GRCh38)
- Gene constraint
- LOEUF 0.204 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.95
Similar variants
- SOX5 p.Ser693Leu Uncertain significance ⚠ same residue
- SOX5 c.1164+2T>G Pathogenic ★★ same type
- SOX5 p.Arg118Ter Pathogenic ★★ same type
- SOX5 p.Arg213Ter Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg471Ter Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg493Ter Pathogenic ★★ same type
- SOX5 p.Arg558Cys Pathogenic/Likely pathogenic ★★ same type
- SOX5 p.Arg558His 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/sox5-p-ser693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown