EOGT p.Pro489=
c.1467G>A · rs188086670 · VCV2162737
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, eas)
Conditions
1
Adams-Oliver syndrome 4
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 -12 | GERP -4.1 |
| Overall | ||
| CADD | 0.856 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
East Asian · 5/44,806 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00329%
53/1,613,380 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0112% | 8,961 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| European (non-Finnish) | 0.00348% | 28,774 |
| African / African-American | 0.00133% | 75,008 |
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.Pro489=
- Coding
- c.1467G>A
- MANE Select
- NM_001278689
- dbSNP
- rs188086670
- Type
- single nucleotide variant
- Location
- chr3:68977735 (GRCh38)
- Gene constraint
- LOEUF 1.121 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.71
Similar variants
- EOGT p.Pro489Leu Uncertain significance ★★ ⚠ same residue
- EOGT c.1335-1G>A Pathogenic/Likely pathogenic ★★ same condition
- EOGT c.311+1G>T Pathogenic/Likely pathogenic ★★ same condition
- EOGT c.621-2A>T Pathogenic/Likely pathogenic ★★ same condition
- EOGT p.Arg372Trp Uncertain significance ★★ ⚠ same condition
- EOGT p.Arg377Trp Uncertain significance ★★ ⚠ same condition
- EOGT p.Arg452His Uncertain significance ★★ ⚠ same condition
- EOGT p.Arg470Trp Uncertain significance ★★ ⚠ same condition
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-pro489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown