CEL p.Val582Met
c.1744G>A · VCV3489956
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0221%, sas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.128 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.16 | GERP -1.9 |
| Regional constraint | o/e 1.11 | unconstrained · MANE · 642 bp · p 0.096 · regional, not allelic |
| Overall | ||
| CADD | 1.608 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0221%
South Asian · 19/85,834 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.012%
Overall
0.0019%
30/1,577,564 alleles · ultra-rare
exomes 26/1,430,030 · genomes 4/147,534 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0221% | 4,518 |
| African / African-American | 0.00686% | 14,583 |
| European (non-Finnish) | 0.000513% | 195,037 |
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.Val582Met
- Coding
- c.1744G>A
- MANE Select
- NM_001807
- Type
- single nucleotide variant
- Location
- chr9:133071246 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 582
- the 'disordered' region; the '17 x 11 aa tandem repeats, glycodomain, o-linked (mucin type)' region
Similar variants
- CEL p.Val582Ala Uncertain significance ★ 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-val582met (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown