CEL p.Ser566=
c.1698C>T · rs377614653 · VCV1206445
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.888%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -2.6 |
| Overall | ||
| CADD | 1.674 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.888%
African / African-American · 661/74,476 alleles
Filtering AF
0.832%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.809%
Overall
0.0659%
1,056/1,603,216 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.888% | 113 |
| South Asian | 0.292% | 342 |
| Remaining individualsnot grpmax-eligible | 0.0722% | 1,384 |
| Admixed American | 0.0652% | 1,533 |
| Middle Eastern | 0.0165% | 6,052 |
| East Asian | 0.0112% | 8,922 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,520 |
| European (non-Finnish) | 0.00331% | 30,212 |
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.Ser566=
- Coding
- c.1698C>T
- MANE Select
- NM_001807
- dbSNP
- rs377614653
- Type
- single nucleotide variant
- Location
- chr9:133071200 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 566
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
- CEL p.Ser566Pro Uncertain significance ★ same residue
- CEL c.67-3C>A Uncertain significance ★★ same type
- CEL p.Ala295Ser Uncertain significance ★★ same type
- CEL p.Ala548Glu Uncertain significance ★★ same type
- CEL p.Ala722Val Uncertain significance ★★ same type
- CEL p.Arg116Gln Uncertain significance ★★ same type
- CEL p.Arg185Trp Uncertain significance ★★ same type
- CEL p.Arg443Trp 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/cel-p-ser566 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown