ECEL1 p.Val17=
c.51C>A · rs191331240 · VCV128955
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.977%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.41 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.59 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 16.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.977%
European (non-Finnish) · 11,091/1,135,080 alleles
Filtering AF
0.962%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.956%
Overall
0.821%
12,338/1,502,442 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.977% | 102 |
| Ashkenazi Jewishnot grpmax-eligible | 0.817% | 122 |
| Remaining individualsnot grpmax-eligible | 0.726% | 138 |
| Amishnot grpmax-eligible | 0.659% | 152 |
| Middle Eastern | 0.48% | 208 |
| Admixed American | 0.335% | 299 |
| Finnishnot grpmax-eligible | 0.261% | 384 |
| South Asian | 0.218% | 458 |
| African / African-American | 0.19% | 525 |
| East Asian | 0.00276% | 36,192 |
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.Val17=
- Coding
- c.51C>A
- MANE Select
- NM_004826
- dbSNP
- rs191331240
- Type
- single nucleotide variant
- Location
- chr2:232486603 (GRCh38)
- Gene constraint
- LOEUF 1.099 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62
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-val17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown