ECE2 p.Ser400=
c.1200C>T · rs150617960 · VCV771357
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.6%, amr)
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 1.4 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 10.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.6%
Admixed American · 2,161/60,014 alleles
Filtering AF
3.47%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.42%
Overall
0.155%
2,510/1,614,188 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 3.6% | 28 |
| East Asian | 0.307% | 325 |
| Remaining individualsnot grpmax-eligible | 0.213% | 470 |
| African / African-American | 0.0466% | 2,144 |
| South Asian | 0.00768% | 13,013 |
| European (non-Finnish) | 0.00305% | 32,779 |
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
- ECE2
- Protein
- p.Ser400=
- Coding
- c.1200C>T
- MANE Select
- NM_001100121
- dbSNP
- rs150617960
- Type
- single nucleotide variant
- Location
- chr3:184285529 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.75
- Residue 400
- a disulfide bond; the peptidase m13 domain
Similar variants
- ECE2 p.Arg453Gln Benign ★★ same type
- ECE2 p.Val248= Benign ★★ same type
- EEF1AKMT4-ECE2 p.Val127Ala Benign ★★ ⚠ same type
- ECE2 p.Ala338Val Uncertain significance ★ ⚠ same type
- ECE2 p.Ala437Thr Uncertain significance ★ ⚠ same type
- ECE2 p.Ala575Thr Uncertain significance ★ ⚠ same type
- ECE2 p.Ala638Gly Uncertain significance ★ ⚠ same type
- ECE2 p.Ala72Val 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/ece2-p-ser400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown