ECEL1 p.Leu164=
c.492G>A · rs200359962 · VCV729794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.215%, 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 0.45 | GERP -2.2, phastCons 0.99 |
| Overall | ||
| CADD | 9.572 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.215%
African / African-American · 158/73,434 alleles
Filtering AF
0.188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.177%
Overall
0.0112%
177/1,576,024 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.215% | 465 |
| Middle Eastern | 0.0357% | 2,802 |
| Admixed American | 0.0181% | 5,524 |
| Remaining individualsnot grpmax-eligible | 0.00819% | 12,215 |
| European (non-Finnish) | 0.000171% | 583,308 |
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.Leu164=
- Coding
- c.492G>A
- MANE Select
- NM_004826
- dbSNP
- rs200359962
- Type
- single nucleotide variant
- Location
- chr2:232486162 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62
- Residue 164
- 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-leu164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown