CEL p.Glu389Lys
c.1165G>A · rs1226275795 · VCV1310689
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00492%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.039 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.32 | GERP -0.72 |
| Regional constraint | o/e 0.01 | constrained · MANE · 1,632 bp · p 4.1e-17 · regional, not allelic |
| Overall | ||
| CADD | 11.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00492%
East Asian · 2/40,668 alleles
Filtering AF
0.000815%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000305%
Overall
0.00099%
10/1,009,850 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00492% | 20,334 |
| African / African-American | 0.00461% | 21,688 |
| Remaining individualsnot grpmax-eligible | 0.00235% | 42,588 |
| Admixed American | 0.00185% | 54,136 |
| South Asian | 0.00135% | 73,870 |
| European (non-Finnish) | 0.00045% | 222,064 |
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
- CEL
- Protein
- p.Glu389Lys
- Coding
- c.1165G>A
- MANE Select
- NM_001807
- dbSNP
- rs1226275795
- Type
- single nucleotide variant
- Location
- chr9:133069138 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 389
- an α-helix
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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/cel-p-glu389lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown