CEL p.Thr569=
c.1707T>C · rs373542594 · VCV2673199
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.168%, mid)
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 -4.6 | GERP -2.4 |
| Overall | ||
| CADD | 0.215 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.168%
Middle Eastern · 10/5,968 alleles
Filtering AF
0.0909%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0691%
Overall
0.0251%
396/1,580,686 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.168% | 597 |
| Ashkenazi Jewishnot grpmax-eligible | 0.158% | 633 |
| Admixed American | 0.0912% | 1,097 |
| Remaining individualsnot grpmax-eligible | 0.0534% | 1,872 |
| South Asian | 0.0245% | 4,079 |
| European (non-Finnish) | 0.0183% | 5,460 |
| East Asian | 0.016% | 6,253 |
| African / African-American | 0.0131% | 7,621 |
| Finnishnot grpmax-eligible | 0.00368% | 27,189 |
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.Thr569=
- Coding
- c.1707T>C
- MANE Select
- NM_001807
- dbSNP
- rs373542594
- Type
- single nucleotide variant
- Location
- chr9:133071209 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 569
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
- CEL p.Thr569Ile Uncertain significance ★ same residue
- CEL p.Thr569Ala Likely benign ★ same residue
- CEL p.Thr569_Thr579del 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
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-thr569 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown