ECEL1 p.Ser725=
c.2175G>A · rs199696717 · VCV778049
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.249%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.51 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -5.9 |
| Overall | ||
| CADD | 16.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.249%
African / African-American · 187/75,036 alleles
Filtering AF
0.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.209%
Overall
0.0169%
272/1,613,864 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.249% | 401 |
| Middle Eastern | 0.0662% | 1,511 |
| Admixed American | 0.04% | 2,501 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| South Asian | 0.0132% | 7,590 |
| European (non-Finnish) | 0.00246% | 40,688 |
| East Asian | 0.00223% | 44,870 |
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.Ser725=
- Coding
- c.2175G>A
- MANE Select
- NM_004826
- dbSNP
- rs199696717
- Type
- single nucleotide variant
- Location
- chr2:232480452 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62
- Residue 725
- 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-ser725 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown