CEL p.Leu11Phe
c.31C>T · VCV4225125
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0118%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.09 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.46 | GERP -1.8, phastCons 1 |
| Regional constraint | o/e 0.12 | constrained · MANE · 60 bp · p 7.3e-06 · regional, not allelic |
| Overall | ||
| CADD | 17.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0118%
Admixed American · 6/51,020 alleles
Filtering AF
0.00511%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00346%
Overall
0.000968%
15/1,548,882 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0118% | 8,503 |
| European (non-Finnish) | 0.000786% | 127,289 |
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.Leu11Phe
- Coding
- c.31C>T
- MANE Select
- NM_001807
- Type
- single nucleotide variant
- Location
- chr9:133062033 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
Similar variants
- CEL p.Ala295Ser Uncertain significance ★★ same condition
- CEL p.Ala548Glu Uncertain significance ★★ same condition
- CEL p.Arg185Trp Uncertain significance ★★ same condition
- CEL p.Arg443Trp Uncertain significance ★★ same condition
- CEL p.Gln460Arg Uncertain significance ★★ same condition
- CEL p.Glu710Lys Uncertain significance ★★ same condition
- CEL p.Gly147Ser Uncertain significance ★★ same condition
- CEL p.His68Leu Uncertain significance ★★ same condition
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-leu11phe (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown