EFEMP2 p.Ile259Val
c.774_775inv · VCV1090452
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
Conditions
1
cutis laxa, autosomal recessive, type 1B
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 1.8 | GERP 0.74, phastCons 0.92 |
| Regional constraint | o/e 0.83 | unconstrained · MANE · 5,433 bp · p 3.8e-05 · regional, not allelic |
Variant & gene context
- Gene
- EFEMP2
- Protein
- p.Ile259Val
- Coding
- c.774_775inv
- MANE Select
- NM_016938
- Type
- Inversion
- Location
- chr11:65868582 (GRCh38)
- Gene constraint
- LOEUF 0.56 · pLI 0.62 (gnomAD)
- Structure
- AlphaFold pLDDT 82.95 · 1 PDB
- Residue 259
- a UniProt-annotated variant site (in); the egf-like 5; calcium-binding domain
Disease context
cutis laxa, autosomal recessive, type 1B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal recessive cutis laxa type 1 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- EFEMP2 p.Ile259Ala Uncertain significance ★ same residue
- EFEMP2 p.Arg279Cys Likely pathogenic ★★ same condition
- EFEMP2 p.Asp203Ala Pathogenic/Likely pathogenic ★★ same condition
- EFEMP2 p.Cys287fs Pathogenic/Likely pathogenic ★★ same condition
- EFEMP2 p.Glu126Lys Pathogenic/Likely pathogenic ★★ same condition
- EFEMP2 p.Glu161Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- EFEMP2 p.Glu167Ter Pathogenic ★★ same condition
- EFEMP2 c.161-6C>G 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/efemp2-p-ile259val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown