CEL p.Ser599Ala
c.1795T>G · rs1461795570 · VCV3141894
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0287%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.077 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.96 | GERP -1.4 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic |
| Overall | ||
| CADD | 8.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0287%
Admixed American · 8/27,908 alleles
Filtering AF
0.0143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.00689%
39/565,808 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0287% | 3,489 |
| African / African-American | 0.0183% | 5,473 |
| Remaining individualsnot grpmax-eligible | 0.0143% | 7,014 |
| European (non-Finnish) | 0.00564% | 17,720 |
| East Asian | 0.00294% | 34,024 |
| South Asian | 0.00193% | 51,792 |
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.Ser599Ala
- Coding
- c.1795T>G
- MANE Select
- NM_001807
- dbSNP
- rs1461795570
- Type
- single nucleotide variant
- Location
- chr9:133071297 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 599
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
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- CEL p.Arg185Trp Uncertain significance ★★ same condition
- CEL p.Arg443Trp Uncertain significance ★★ same condition
- CEL p.Gln460Arg Uncertain significance ★★ same condition
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- 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-ser599ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown