ECE1 p.Ser570=
c.1710G>A · rs149021429 · VCV716901
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.16%, 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 -20 | GERP -2.9 |
| Overall | ||
| CADD | 0.571 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.16%
African / African-American · 855/73,746 alleles
Filtering AF
1.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.07%
Overall
0.0627%
981/1,565,018 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.16% | 86 |
| Admixed American | 0.0866% | 1,155 |
| Remaining individualsnot grpmax-eligible | 0.0857% | 1,167 |
| Middle Eastern | 0.0831% | 1,203 |
| South Asian | 0.0141% | 7,086 |
| East Asian | 0.00237% | 42,256 |
| European (non-Finnish) | 0.000867% | 115,385 |
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
- ECE1
- Protein
- p.Ser570=
- Coding
- c.1710G>A
- MANE Select
- NM_001397
- dbSNP
- rs149021429
- Type
- single nucleotide variant
- Location
- chr1:21228002 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 91.16 · 1 PDB
- Residue 570
- a disulfide bond; the peptidase m13 domain; a β-strand
Similar variants
- ECE1 p.Thr312Met Uncertain significance ★★ ⚠ same type
- ECE1 c.1020+15G>A Benign ★★ same type
- ECE1 c.1164-5C>T Benign ★★ same type
- ECE1 c.1278+7C>T Benign ★★ same type
- ECE1 c.1782-4C>A Benign ★★ same type
- ECE1 c.828+8T>C Benign ★★ same type
- ECE1 p.Asn397Ser Benign ★★ same type
- ECE1 p.Asp547= Benign ★★ 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/ece1-p-ser570 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown