EGF p.Pro402=
c.1206A>G · rs1447416838 · VCV2152207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 1 | GERP -2.7, phastCons 0.63 |
| Overall | ||
| CADD | 5.628 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,882 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000434%
7/1,613,748 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,882 |
| European (non-Finnish) | 0.000509% | 196,634 |
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
- EGF
- Protein
- p.Pro402=
- Coding
- c.1206A>G
- MANE Select
- NM_001963
- dbSNP
- rs1447416838
- Type
- single nucleotide variant
- Location
- chr4:109961879 (GRCh38)
- Gene constraint
- LOEUF 0.741 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.66 · 13 PDB
- Residue 402
- the egf-like 3 domain; a disulfide bond
Similar variants
- EGF c.2221+4C>T Uncertain significance ★★ same type
- EGF c.2858-11G>T Uncertain significance ★★ same type
- EGF c.-60C>T Uncertain significance ★★ same type
- EGF p.Ala1025Ser Uncertain significance ★★ ⚠ same type
- EGF p.Ala1037Val Uncertain significance ★★ ⚠ same type
- EGF p.Ala45Val Uncertain significance ★★ ⚠ same type
- EGF p.Ala862Thr Uncertain significance ★★ ⚠ same type
- EGF p.Arg213Gln 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/egf-p-pro402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown