EFEMP2 p.Asn313=
c.939C>T · rs754497556 · VCV1209891
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000678%, 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 4.6 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 9.304 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000678%
European (non-Finnish) · 8/1,180,028 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000547%
8/1,461,534 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.Asn313=
- Coding
- c.939C>T
- MANE Select
- NM_016938
- dbSNP
- rs754497556
- Type
- single nucleotide variant
- Location
- chr11:65868330 (GRCh38)
- Gene constraint
- LOEUF 0.56 · pLI 0.62 (gnomAD)
- Structure
- AlphaFold pLDDT 82.95 · 1 PDB
- Residue 313
- the egf-like 6; calcium-binding domain
Similar variants
- EFEMP2 p.Asn313Asp Uncertain significance ★ same residue
- EFEMP2 p.Asn313Ile Likely pathogenic ★ ⚠ 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-asn313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown