ENG p.Ile263del
c.787_789del · rs1830579035 · VCV862246
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
Conditions
2
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP 1.6, phastCons 0.92 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,686 alleles · very rare
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
- ENG
- Protein
- p.Ile263del
- Coding
- c.787_789del
- MANE Select
- NM_001114753
- dbSNP
- rs1830579035
- Type
- Deletion
- Location
- chr9:127825258 (GRCh38)
- Gene constraint
- LOEUF 0.374 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.84 · 3 PDB
- Residue 263
- a β-strand; a disulfide bond; a UniProt-annotated variant site (in hht1); the 'required for interaction with gdf2' region; the 'or1, c-terminal part' region
Similar variants
- ENG p.Ile263= Likely benign ★★ same residue
- ENG c.1687delG Pathogenic ★★ same condition
- ENG p.Ala55fs Pathogenic ★★ same condition
- ENG p.Arg232_Thr233del Likely pathogenic ★★ same condition
- ENG p.Arg399fs Pathogenic/Likely pathogenic ★★ same condition
- ENG p.Asn163fs Pathogenic/Likely pathogenic ★★ same condition
- ENG p.Asn423fs Pathogenic ★★ same condition
- ENG p.Asp578fs Pathogenic/Likely pathogenic ★★ 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/eng-p-ile263del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown