CEL p.Arg3Cys
c.7C>T · rs201383133 · VCV218596
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.08%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.365 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP 1.7, phastCons 0.86 |
| Regional constraint | o/e 0.12 | constrained · MANE · 60 bp · p 7.3e-06 · regional, not allelic |
| Overall | ||
| CADD | 24.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.08%
African / African-American · 1,513/72,746 alleles
Filtering AF
1.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.96%
Overall
0.204%
3,166/1,549,678 alleles · low-frequency
exomes 2,241/1,397,752 · genomes 925/151,926 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.08% | 48 |
| Middle Eastern | 1.09% | 91 |
| Admixed American | 0.387% | 259 |
| Remaining individualsnot grpmax-eligible | 0.359% | 279 |
| Ashkenazi Jewishnot grpmax-eligible | 0.185% | 540 |
| European (non-Finnish) | 0.0962% | 1,040 |
| South Asian | 0.0226% | 4,422 |
| East Asian | 0.00245% | 40,854 |
| Finnishnot grpmax-eligible | 0.00168% | 59,552 |
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.Arg3Cys
- Coding
- c.7C>T
- MANE Select
- NM_001807
- dbSNP
- rs201383133
- Type
- single nucleotide variant
- Location
- chr9:133062009 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 7 PDB
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-arg3cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown