EOGT p.Ser287=
c.861C>T · rs6771187 · VCV1179590
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.68%, afr)
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 -8.6 | GERP -4.3 |
| Overall | ||
| CADD | 0.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.68%
African / African-American · 3,408/72,798 alleles
Filtering AF
4.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.5%
Overall
0.25%
3,830/1,530,594 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.68% | 21 |
| Remaining individualsnot grpmax-eligible | 0.289% | 346 |
| Admixed American | 0.269% | 372 |
| Middle Eastern | 0.252% | 398 |
| South Asian | 0.024% | 4,171 |
| East Asian | 0.00737% | 13,566 |
| European (non-Finnish) | 0.00656% | 15,250 |
| Finnishnot grpmax-eligible | 0.00225% | 44,452 |
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.Ser287=
- Coding
- c.861C>T
- MANE Select
- NM_001278689
- dbSNP
- rs6771187
- Type
- single nucleotide variant
- Location
- chr3:68988988 (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-ser287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown