CEL p.Thr579Ala
c.1735A>G · rs35169970 · VCV1208803
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.296%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.107 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.13 | GERP -2 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic |
| Overall | ||
| CADD | 0.057 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.296%
South Asian · 242/81,796 alleles
Filtering AF
0.265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.253%
Overall
0.0267%
405/1,515,522 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.296% | 338 |
| Middle Eastern | 0.0693% | 1,442 |
| African / African-American | 0.0521% | 1,921 |
| East Asian | 0.0319% | 3,134 |
| Remaining individualsnot grpmax-eligible | 0.0303% | 3,297 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0216% | 4,634 |
| European (non-Finnish) | 0.00746% | 13,408 |
| Admixed American | 0.00737% | 13,560 |
| Finnishnot grpmax-eligible | 0.00435% | 22,996 |
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.Thr579Ala
- Coding
- c.1735A>G
- MANE Select
- NM_001807
- dbSNP
- rs35169970
- Type
- single nucleotide variant
- Location
- chr9:133071237 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 579
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
- 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
- CEL p.Asn37Ser 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-thr579ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown