EFEMP2 p.Pro3=
c.9C>A · VCV3506977
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000349%, nfe)
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.65 | GERP -1.7, phastCons 0.99 |
| Overall | ||
| CADD | 9.118 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000349%
European (non-Finnish) · 4/1,146,498 alleles
Filtering AF
8.2e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.5e-05%
Overall
0.000286%
4/1,398,556 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
- EFEMP2
- Protein
- p.Pro3=
- Coding
- c.9C>A
- MANE Select
- NM_016938
- Type
- single nucleotide variant
- Location
- chr11:65872346 (GRCh38)
- Gene constraint
- LOEUF 0.56 · pLI 0.62 (gnomAD)
- Structure
- AlphaFold pLDDT 82.95 · 1 PDB
Similar variants
- EFEMP2 p.Pro3Ser Uncertain significance ★ ⚠ same residue
- EFEMP2 p.Pro3Thr Uncertain significance ★ ⚠ same residue
- EFEMP2 p.Arg279Cys Likely pathogenic ★★ same condition
- EFEMP2 p.Asp203Ala 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-pro3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown