EOMES p.Ala39=
c.117G>A · rs372426145 · VCV593475
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0663%, 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 -1.7 | GERP -2.6 |
| Overall | ||
| CADD | 6.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0663%
Middle Eastern · 4/6,032 alleles
Filtering AF
0.0226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.0017%
27/1,592,274 alleles · ultra-rare
exomes 18/1,440,042 · genomes 9/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0663% | 1,508 |
| African / African-American | 0.0147% | 6,794 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,863 |
| Admixed American | 0.00178% | 56,132 |
| European (non-Finnish) | 0.000769% | 130,084 |
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.Ala39=
- Coding
- c.117G>A
- MANE Select
- NM_001278182
- dbSNP
- rs372426145
- Type
- single nucleotide variant
- Location
- chr3:27722178 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 56.74
- Residue 39
- the 'disordered' region
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-ala39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown