EOMES p.Ala126=
c.378C>G · rs978035459 · VCV2653639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0298%, mid)
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 -0.28 | GERP -2, phastCons 0.9 |
| Overall | ||
| CADD | 9.371 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0298%
Middle Eastern · 1/3,360 alleles
Overall
8.06e-05%
1/1,240,862 alleles · ultra-rare
exomes 1/1,117,376 · genomes 0/123,486 · 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
- EOMES
- Protein
- p.Ala126=
- Coding
- c.378C>G
- MANE Select
- NM_001278182
- dbSNP
- rs978035459
- Type
- single nucleotide variant
- Location
- chr3:27721917 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 56.74
Similar variants
- EOMES p.Tyr231Cys Uncertain significance ★★ ⚠ same type
- EOMES p.Glu113= Likely benign ★★ same type
- EOMES p.Pro641= Benign ★★ same type
- EOMES p.Ser392= Likely benign ★★ same type
- EOMES p.Ser91Arg Likely benign ★★ same type
- EOMES p.Ala118Pro Uncertain significance ★ ⚠ same type
- EOMES p.Ala17Pro Uncertain significance ★ ⚠ same type
- EOMES p.Ala206Gly 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/eomes-p-ala126 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown