ECPAS p.Ala1313Val
c.3938C>T · rs759133299 · VCV3087058
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0468%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.274 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| 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 | 27.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0468%
East Asian · 21/44,866 alleles
Filtering AF
0.0313%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0263%
Overall
0.00298%
48/1,612,864 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0468% | 2,136 |
| African / African-American | 0.00401% | 24,955 |
| Admixed American | 0.00334% | 29,981 |
| European (non-Finnish) | 0.0017% | 58,966 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,416 |
| South Asian | 0.0011% | 90,980 |
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.Ala1313Val
- Coding
- c.3938C>T
- MANE Select
- NM_001364929
- dbSNP
- rs759133299
- Type
- single nucleotide variant
- Location
- chr9:111378596 (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-ala1313val (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown