ECPAS p.Arg1312Trp
c.3934C>T · VCV4016085
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0494%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.278 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.25 | donor loss, 20 bp away · masked 0 · deltas |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.2, phastCons 1 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 48 kb · p 1.8e-10 · regional, not allelic |
| Overall | ||
| CADD | 33.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0494%
Middle Eastern · 3/6,078 alleles
Filtering AF
0.0134%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00716%
Overall
0.00415%
67/1,613,120 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0494% | 2,026 |
| Admixed American | 0.0133% | 7,499 |
| European (non-Finnish) | 0.00458% | 21,841 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,219 |
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.Arg1312Trp
- Coding
- c.3934C>T
- MANE Select
- NM_001364929
- Type
- single nucleotide variant
- Location
- chr9:111378600 (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-arg1312trp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown