ECPAS p.Lys404Gln
c.1210A>C · VCV3274431
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0745%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.172 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 0.80 | unconstrained · MANE · 28 kb · p 8.8e-08 · regional, not allelic |
| Overall | ||
| CADD | 24.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0745%
East Asian · 33/44,276 alleles
Filtering AF
0.0545%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0477%
Overall
0.0031%
49/1,581,530 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0745% | 1,342 |
| South Asian | 0.0118% | 8,447 |
| Remaining individualsnot grpmax-eligible | 0.00818% | 12,232 |
| European (non-Finnish) | 8.58e-05% | 1,165,504 |
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.Lys404Gln
- Coding
- c.1210A>C
- MANE Select
- NM_001364929
- Type
- single nucleotide variant
- Location
- chr9:111425423 (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-lys404gln (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown