CEL p.Pro583Thr
c.1747C>A · rs1172388702 · VCV2395331
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0204%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.121 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -1.4 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic |
| Overall | ||
| CADD | 14.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0204%
African / African-American · 15/73,356 alleles
Filtering AF
0.0125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.00108%
17/1,574,466 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0204% | 4,890 |
| European (non-Finnish) | 0.000171% | 584,126 |
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.Pro583Thr
- Coding
- c.1747C>A
- MANE Select
- NM_001807
- dbSNP
- rs1172388702
- Type
- single nucleotide variant
- Location
- chr9:133071249 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 583
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
- CEL p.Pro583= Likely benign ★ same residue
- CEL p.Ala295Ser Uncertain significance ★★ same condition
- CEL p.Ala548Glu Uncertain significance ★★ same condition
- CEL p.Arg185Trp Uncertain significance ★★ same condition
- CEL p.Arg443Trp Uncertain significance ★★ same condition
- CEL p.Gln460Arg Uncertain significance ★★ same condition
- CEL p.Glu710Lys Uncertain significance ★★ same condition
- CEL p.Gly147Ser 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-pro583thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown