SOX4 p.Pro337=
c.1011C>T · rs1383452385 · VCV2656279
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000102%, 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 1.6 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 15.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000102%
European (non-Finnish) · 1/976,246 alleles
Overall
8.24e-05%
1/1,212,972 alleles · very rare
exomes 0/1,063,148 · genomes 1/149,824 · joint denominator
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.Pro337=
- Coding
- c.1011C>T
- MANE Select
- NM_003107
- dbSNP
- rs1383452385
- Type
- single nucleotide variant
- Location
- chr6:21595545 (GRCh38)
- Gene constraint
- LOEUF 0.72 · pLI 0.79 (gnomAD)
- Structure
- AlphaFold pLDDT 55.71
- Residue 337
- the 'disordered' region
Similar variants
- SOX4 p.Pro337Arg 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-pro337 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown