SOX4 p.Pro124=
c.372C>G · VCV3905180
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0089%, nfe)
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 0.98 | GERP 0.25, phastCons 1 |
| Overall | ||
| CADD | 13.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0089%
European (non-Finnish) · 105/1,179,744 alleles
Filtering AF
0.00749%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.007%
Overall
0.00713%
115/1,612,982 alleles · very rare
exomes 109/1,460,790 · genomes 6/152,192 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0089% | 11,236 |
| Finnishnot grpmax-eligible | 0.00628% | 15,915 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,820 |
| Admixed American | 0.00334% | 29,964 |
| African / African-American | 0.00133% | 74,924 |
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.Pro124=
- Coding
- c.372C>G
- MANE Select
- NM_003107
- Type
- single nucleotide variant
- Location
- chr6:21594906 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI 0.79 (gnomAD)
- Structure
- AlphaFold pLDDT 55.71
- Residue 124
- a DNA-binding region
Similar variants
- SOX4 p.Pro124Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown