EOGT p.Tyr280=
c.840C>T · rs17048266 · VCV1281297
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 11.8%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.40 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -4.3 |
| Overall | ||
| CADD | 0.383 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.8%
African / African-American · 8,520/72,404 alleles
Filtering AF
11.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.5%
Overall
0.652%
9,919/1,520,990 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.8% | 8 |
| Remaining individualsnot grpmax-eligible | 0.991% | 101 |
| Admixed American | 0.907% | 110 |
| Middle Eastern | 0.791% | 126 |
| South Asian | 0.0508% | 1,970 |
| European (non-Finnish) | 0.0238% | 4,194 |
| East Asian | 0.00246% | 40,594 |
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
- EOGT
- Protein
- p.Tyr280=
- Coding
- c.840C>T
- MANE Select
- NM_001278689
- dbSNP
- rs17048266
- Type
- single nucleotide variant
- Location
- chr3:68989009 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71
Similar variants
- EOGT c.1335-1G>A Pathogenic/Likely pathogenic ★★ same type
- EOGT c.311+1G>T Pathogenic/Likely pathogenic ★★ same type
- EOGT c.621-2A>T Pathogenic/Likely pathogenic ★★ same type
- EOGT p.Arg149His Uncertain significance ★★ ⚠ same type
- EOGT p.Arg372Trp Uncertain significance ★★ ⚠ same type
- EOGT p.Arg377Trp Uncertain significance ★★ ⚠ same type
- EOGT p.Arg452His Uncertain significance ★★ ⚠ same type
- EOGT p.Arg470Trp 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/eogt-p-tyr280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown