CAPS p.Arg18=
c.54C>T · VCV4218999
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.123%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.14 | GERP -3.5, phastCons 0.39 |
| Overall | ||
| CADD | 7.281 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.123%
East Asian · 55/44,872 alleles
Filtering AF
0.0967%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0873%
Overall
0.00794%
128/1,612,380 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.123% | 816 |
| African / African-American | 0.032% | 3,126 |
| Admixed American | 0.0167% | 6,001 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,245 |
| European (non-Finnish) | 0.00237% | 42,122 |
| South Asian | 0.0011% | 91,048 |
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
- CAPS
- Protein
- p.Arg18=
- Coding
- c.54C>T
- MANE Select
- NM_003716 · reported on NM_004058
- Type
- single nucleotide variant
- Location
- chr19:5914460 (GRCh38)
- Structure
- AlphaFold pLDDT 79.13 · 1 PDB
- Residue 18
- the 'disordered' region
Similar variants
- CAPS p.Arg18His Benign ★★ ⚠ same residue
- CAPS p.Leu18= Likely benign same residue
- CADPS p.Ser203= Benign ★★ same type
- CADPS p.Tyr579= Benign ★★ same type
- CAPS p.Pro88Thr Benign ★★ ⚠ same type
- CADPS c.3477+2T>G Uncertain significance ★ same type
- CADPS p.Ala1047Thr Uncertain significance ★ ⚠ same type
- CADPS p.Ala1057Val 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/caps-p-arg18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown