SOX4 p.Pro193=
c.579G>C · rs1445393759 · VCV3025613
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, afr)
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 -0.59 | GERP -4, phastCons 0.99 |
| Overall | ||
| CADD | 3.055 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
African / African-American · 5/65,030 alleles
Filtering AF
0.00295%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00193%
Overall
0.00189%
26/1,378,152 alleles · very rare
exomes 20/1,226,432 · genomes 6/151,720 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00769% | 13,006 |
| Remaining individualsnot grpmax-eligible | 0.00761% | 13,134 |
| South Asian | 0.00523% | 19,139 |
| East Asian | 0.00296% | 33,744 |
| European (non-Finnish) | 0.00121% | 82,624 |
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
- SOX4
- Protein
- p.Pro193=
- Coding
- c.579G>C
- MANE Select
- NM_003107
- dbSNP
- rs1445393759
- Type
- single nucleotide variant
- Location
- chr6:21595113 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI 0.79 (gnomAD)
- Structure
- AlphaFold pLDDT 55.71
- Residue 193
- the 'disordered' region
Similar variants
- SOX4 p.Gln241Ter Likely pathogenic ★★ same type
- SOX4 p.Ser347Ter Pathogenic/Likely pathogenic ★★ same type
- SOX4 p.Ala145Thr Uncertain significance ★★ ⚠ same type
- SOX4 p.Ala231Thr Uncertain significance ★★ ⚠ same type
- SOX4 p.Ala234Pro Uncertain significance ★★ ⚠ same type
- SOX4 p.Ala253Val Uncertain significance ★★ ⚠ same type
- SOX4 p.Arg110Pro Uncertain significance ★★ ⚠ same type
- SOX4 p.Gly226Ser Uncertain significance ★★ ⚠ 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/sox4-p-pro193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown