SOX18 p.Phe134=
c.402C>T · VCV4755296
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.351%, eas)
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 3.7 | GERP 0.64, phastCons 1 |
| Overall | ||
| CADD | 14.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.351%
East Asian · 155/44,148 alleles
Filtering AF
0.306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.289%
Overall
0.0109%
174/1,597,002 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.351% | 285 |
| Remaining individualsnot grpmax-eligible | 0.00968% | 10,332 |
| South Asian | 0.00886% | 11,284 |
| European (non-Finnish) | 0.000425% | 235,270 |
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
- SOX18
- Protein
- p.Phe134=
- Coding
- c.402C>T
- MANE Select
- NM_018419
- Type
- single nucleotide variant
- Location
- chr20:64048919 (GRCh38)
- Gene constraint
- LOEUF 1.483 · pLI 0.22 (gnomAD)
- Structure
- AlphaFold pLDDT 63.44
- Residue 134
- a DNA-binding region
Similar variants
- SOX18 p.Gln161Ter Pathogenic/Likely pathogenic ★★ same type
- SOX18 p.Ala162Glu Uncertain significance ★★ ⚠ same type
- SOX18 p.Ala229Val Uncertain significance ★★ ⚠ same type
- SOX18 p.Ala250Thr Uncertain significance ★★ ⚠ same type
- SOX18 p.Ala30Ser Uncertain significance ★★ ⚠ same type
- SOX18 p.Arg140Leu Uncertain significance ★★ ⚠ same type
- SOX18 p.Arg271Lys Uncertain significance ★★ ⚠ same type
- SOX18 p.Asp13Asn 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/sox18-p-phe134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown