ECPAS p.Thr789Ala
c.2365A>G · rs763333602 · VCV3087031
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.109 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP 1.8, phastCons 1 |
| Regional constraint | o/e 1.27 | unconstrained · MANE · 2,029 bp · p 0.00086 · regional, not allelic |
| Overall | ||
| CADD | 21.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/75,034 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000186%
3/1,613,838 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,517 |
| East Asian | 0.00223% | 44,884 |
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.Thr789Ala
- Coding
- c.2365A>G
- MANE Select
- NM_001364929
- dbSNP
- rs763333602
- Type
- single nucleotide variant
- Location
- chr9:111410992 (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-thr789ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown