ECE1 p.Pro8=
c.24G>A · rs193017331 · VCV3032411
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.426%, afr)
Conditions
1
ECE1-related disorder
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 -1.8 | GERP -2.2 |
| Overall | ||
| CADD | 12.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.426%
African / African-American · 274/64,286 alleles
Filtering AF
0.385%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.369%
Overall
0.0238%
295/1,237,744 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.426% | 235 |
| Remaining individualsnot grpmax-eligible | 0.035% | 2,857 |
| Middle Eastern | 0.031% | 3,230 |
| Admixed American | 0.0126% | 7,919 |
| European (non-Finnish) | 0.000101% | 992,851 |
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.Pro8=
- Coding
- c.24G>A
- MANE Select
- NM_001397
- dbSNP
- rs193017331
- Type
- single nucleotide variant
- Location
- chr1:21290391 (GRCh38)
- Gene constraint
- LOEUF 0.482 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 91.16 · 1 PDB
Disease context
ECE1-related disorder
Similar variants
- ECE1 c.139-68C>G Uncertain significance same condition
- ECE1 c.1488+1G>A Uncertain significance same condition
- ECE1 p.Ala345Ser Uncertain significance ⚠ same condition
- ECE1 p.Arg618Gln Uncertain significance ⚠ same condition
- ECE1 c.139-43G>A Likely benign same condition
- ECE1 p.Gly673= Likely benign same condition
- ECE1 p.Thr354Ala Benign same condition
- ECE1 p.Thr312Met 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/ece1-p-pro8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown