ECEL1 p.Leu682=
c.2046G>A · VCV4822767
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0609%, 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 -1.7 | GERP -9 |
| Overall | ||
| CADD | 3.104 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0609%
Admixed American · 32/52,582 alleles
Filtering AF
0.0443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0386%
Overall
0.00205%
32/1,560,992 alleles · ultra-rare
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
- ECEL1
- Protein
- p.Leu682=
- Coding
- c.2046G>A
- MANE Select
- NM_004826
- Type
- single nucleotide variant
- Location
- chr2:232481100 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62
- Residue 682
- a disulfide bond; the peptidase m13 domain
Similar variants
- ECEL1 c.1685+1G>A Pathogenic ★★ same type
- ECEL1 c.2151+2T>C Likely pathogenic ★★ same type
- ECEL1 c.966+1G>A Pathogenic ★★ same type
- ECEL1 p.Ala675Thr Pathogenic ★★ same type
- ECEL1 p.Arg333Ter Pathogenic ★★ same type
- ECEL1 p.Arg395Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- ECEL1 p.Arg418Cys Likely pathogenic ★★ same type
- ECEL1 p.Gln435Ter Pathogenic/Likely pathogenic ★★ 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/ecel1-p-leu682 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown