EFEMP1 p.Asp53=
c.159C>T · rs17047322 · VCV1166128
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0401%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.6 | GERP -5.2 |
| Overall | ||
| CADD | 7.491 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0401%
East Asian · 18/44,884 alleles
Filtering AF
0.0259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.0031%
50/1,614,162 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0401% | 2,494 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,254 |
| African / African-American | 0.00267% | 37,511 |
| European (non-Finnish) | 0.00212% | 47,201 |
| Admixed American | 0.00167% | 60,024 |
| South Asian | 0.0011% | 91,080 |
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
- EFEMP1
- Protein
- p.Asp53=
- Coding
- c.159C>T
- MANE Select
- NM_001039348
- dbSNP
- rs17047322
- Type
- single nucleotide variant
- Location
- chr2:55918023 (GRCh38)
- Gene constraint
- LOEUF 0.373 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.67
- Residue 53
- the egf-like 1; atypical domain
Similar variants
- EFEMP1 p.Asp53fs Pathogenic ★ same residue
- EFEMP1 p.Arg345Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- EFEMP1 p.Ala104Thr Uncertain significance ★★ ⚠ same type
- EFEMP1 p.Ala126Pro Uncertain significance ★★ ⚠ same type
- EFEMP1 p.Ala126Thr Uncertain significance ★★ ⚠ same type
- EFEMP1 p.Ala447Ser Uncertain significance ★★ ⚠ same type
- EFEMP1 p.Ala447Thr Uncertain significance ★★ ⚠ same type
- EFEMP1 p.Arg148His Uncertain significance ★★ ⚠ same type
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/efemp1-p-asp53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown