ECPAS p.Ile285Leu
c.853A>C · rs201061247 · VCV3087004
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.076%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.165 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>C here scores Δ0.28 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.80 | unconstrained · MANE · 28 kb · p 8.8e-08 · regional, not allelic |
| Overall | ||
| CADD | 21.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.076%
European (non-Finnish) · 885/1,165,172 alleles
Filtering AF
0.0718%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0701%
Overall
0.0591%
939/1,588,498 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.076% | 1,317 |
| Middle Eastern | 0.0664% | 1,506 |
| Remaining individualsnot grpmax-eligible | 0.0292% | 3,424 |
| Admixed American | 0.0194% | 5,146 |
| African / African-American | 0.0174% | 5,747 |
| East Asian | 0.0045% | 22,222 |
| South Asian | 0.00346% | 28,932 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00343% | 29,122 |
| Finnishnot grpmax-eligible | 0.00317% | 31,540 |
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
- ECPAS
- Protein
- p.Ile285Leu
- Coding
- c.853A>C
- MANE Select
- NM_001364929
- dbSNP
- rs201061247
- Type
- single nucleotide variant
- Location
- chr9:111430624 (GRCh38)
- Gene constraint
- LOEUF 0.316 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 84.03
Similar variants
- ECPAS c.270+1G>T Uncertain significance ★ same type
- ECPAS c.-128G>A Uncertain significance ★ same type
- ECPAS c.-128G>C Uncertain significance ★ same type
- ECPAS c.-138C>T Uncertain significance ★ same type
- ECPAS c.-150C>T Uncertain significance ★ same type
- ECPAS c.-152C>T Uncertain significance ★ same type
- ECPAS c.-176C>G Uncertain significance ★ same type
- ECPAS c.-186C>T Uncertain significance ★ 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/ecpas-p-ile285leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown