CEL p.Ser687Ala
c.2059T>G · VCV3910776
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.153%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.14 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP 0.033 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic |
| Overall | ||
| CADD | 16.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.153%
African / African-American · 57/37,310 alleles
Filtering AF
0.121%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.11%
Overall
0.0213%
144/675,574 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.153% | 655 |
| South Asian | 0.0744% | 1,344 |
| Remaining individualsnot grpmax-eligible | 0.0221% | 4,532 |
| Finnishnot grpmax-eligible | 0.0164% | 6,089 |
| Admixed American | 0.016% | 6,235 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0152% | 6,565 |
| European (non-Finnish) | 0.00534% | 18,721 |
| East Asian | 0.00443% | 22,560 |
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.Ser687Ala
- Coding
- c.2059T>G
- MANE Select
- NM_001807
- Type
- single nucleotide variant
- Location
- chr9:133071561 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 687
- 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-ser687ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown