ECEL1 p.Asp492=
c.1476C>T · rs34019519 · VCV729123
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -3.2 |
| Overall | ||
| CADD | 2.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
African / African-American · 857/74,984 alleles
Filtering AF
1.08%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.05%
Overall
0.0696%
1,122/1,611,868 alleles · low-frequency
exomes 593/1,459,586 · genomes 529/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.14% | 87 |
| Admixed American | 0.111% | 905 |
| Remaining individualsnot grpmax-eligible | 0.0929% | 1,077 |
| Middle Eastern | 0.0496% | 2,018 |
| East Asian | 0.0156% | 6,407 |
| European (non-Finnish) | 0.0109% | 9,215 |
| South Asian | 0.0033% | 30,273 |
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.Asp492=
- Coding
- c.1476C>T
- MANE Select
- NM_004826
- dbSNP
- rs34019519
- Type
- single nucleotide variant
- Location
- chr2:232483446 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62
- Residue 492
- 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-asp492 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown