EN2 p.Ser200=
c.600G>C · rs80239010 · VCV711482
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.72%, afr)
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 -0.056 | GERP -1.6, phastCons 0.39 |
| Overall | ||
| CADD | 8.31 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.72%
African / African-American · 1,937/71,240 alleles
Filtering AF
2.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.58%
Overall
0.147%
2,271/1,545,088 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.72% | 37 |
| Admixed American | 0.28% | 357 |
| Remaining individualsnot grpmax-eligible | 0.224% | 447 |
| Middle Eastern | 0.0844% | 1,184 |
| South Asian | 0.00704% | 14,197 |
| European (non-Finnish) | 0.00337% | 29,635 |
| East Asian | 0.00251% | 39,788 |
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
- EN2
- Protein
- p.Ser200=
- Coding
- c.600G>C
- MANE Select
- NM_001427
- dbSNP
- rs80239010
- Type
- single nucleotide variant
- Location
- chr7:155458977 (GRCh38)
- Gene constraint
- LOEUF 0.775 · pLI 0.39 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.51
- Residue 200
- the 'disordered' region
Similar variants
- EN2 p.Asn68Ser Uncertain significance ★★ ⚠ same type
- EN2 p.Leu318= Benign ★★ same type
- EN2 p.Ala109Val Uncertain significance ★ ⚠ same type
- EN2 p.Ala167Ser Uncertain significance ★ ⚠ same type
- EN2 p.Ala183Thr Uncertain significance ★ ⚠ same type
- EN2 p.Ala297Thr Uncertain significance ★ ⚠ same type
- EN2 p.Ala40Glu Uncertain significance ★ ⚠ same type
- EN2 p.Ala40Gly 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/en2-p-ser200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown