EOGT p.Phe435=
c.1305C>T · rs527394057 · VCV732068
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.22%, sas)
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 3.9 | GERP 0.3, phastCons 1 |
| Overall | ||
| CADD | 11.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.22%
South Asian · 2,931/91,048 alleles
Filtering AF
3.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.08%
Overall
0.191%
3,085/1,613,902 alleles · low-frequency
exomes 2,922/1,461,606 · genomes 163/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.22% | 31 |
| Remaining individualsnot grpmax-eligible | 0.218% | 460 |
| Middle Eastern | 0.132% | 757 |
| East Asian | 0.00223% | 44,844 |
| Admixed American | 0.00167% | 60,008 |
| African / African-American | 0.00133% | 75,044 |
| European (non-Finnish) | 0.000593% | 168,552 |
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.Phe435=
- Coding
- c.1305C>T
- MANE Select
- NM_001278689
- dbSNP
- rs527394057
- Type
- single nucleotide variant
- Location
- chr3:68979697 (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 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
- EOGT p.Asp252Asn 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-phe435 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown