CEL p.Arg532Trp
c.1594C>T · rs200231984 · VCV2659668
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.183%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.185 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 0.048, phastCons 0.007 |
| Regional constraint | o/e 0.75 | unconstrained · MANE · 651 bp · p 0.0028 · regional, not allelic |
| Overall | ||
| CADD | 20.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.183%
European (non-Finnish) · 2,154/1,179,586 alleles
Filtering AF
0.176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.174%
Overall
0.14%
2,255/1,611,122 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.183% | 548 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| African / African-American | 0.036% | 2,777 |
| Finnishnot grpmax-eligible | 0.026% | 3,852 |
| Admixed American | 0.01% | 9,993 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
| South Asian | 0.00329% | 30,357 |
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.Arg532Trp
- Coding
- c.1594C>T
- MANE Select
- NM_001807
- dbSNP
- rs200231984
- Type
- single nucleotide variant
- Location
- chr9:133071096 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
- Residue 532
- a β-strand
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-arg532trp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown