SOX4 p.Arg342=
c.1026C>A · rs1356091191 · VCV2656281
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.021%, eas)
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 0.69 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 15.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.021%
East Asian · 6/28,618 alleles
Filtering AF
0.0091%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00622%
Overall
0.000749%
9/1,202,168 alleles · ultra-rare
exomes 7/1,052,794 · genomes 2/149,374 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.021% | 4,770 |
| European (non-Finnish) | 0.000309% | 323,672 |
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.Arg342=
- Coding
- c.1026C>A
- MANE Select
- NM_003107
- dbSNP
- rs1356091191
- Type
- single nucleotide variant
- Location
- chr6:21595560 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI 0.79 (gnomAD)
- Structure
- AlphaFold pLDDT 55.71
- Residue 342
- 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-arg342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown