EOMES p.Ala125=
c.375C>G · rs2473924183 · VCV3055689
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,353,874)
Conditions
1
EOMES-related disorder
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 -1.1 | GERP -2.2, phastCons 0.83 |
| Overall | ||
| CADD | 7.536 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,353,874). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- EOMES
- Protein
- p.Ala125=
- Coding
- c.375C>G
- MANE Select
- NM_001278182
- dbSNP
- rs2473924183
- Type
- single nucleotide variant
- Location
- chr3:27721920 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 56.74
Disease context
EOMES-related disorder
Similar variants
- EOMES p.Ala120= Likely benign same condition
- EOMES p.Ala123= Likely benign same condition
- EOMES p.Ala33= Likely benign same condition
- EOMES p.Pro203= Likely benign same condition
- EOMES p.Ala130del Likely benign same condition
- EOMES p.Tyr231Cys Uncertain significance ★★ ⚠ same type
- EOMES p.Glu113= Likely benign ★★ same type
- EOMES p.Pro641= Benign ★★ 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/eomes-p-ala125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown