CD59 p.Pro128=
c.384C>A · rs549099946 · VCV1943798
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.99 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.92 | GERP -0.47, phastCons 0.5 |
| Overall | ||
| CADD | 6.911 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,832 alleles
Filtering AF
0.00884%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.000559%
9/1,611,266 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,604 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,398 |
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
- CD59
- Protein
- p.Pro128=
- Coding
- c.384C>A
- MANE Select
- NM_000611
- dbSNP
- rs549099946
- Type
- single nucleotide variant
- Location
- chr11:33710129 (GRCh38)
- Gene constraint
- LOEUF 1.277 · pLI 0.57 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.15 · 17 PDB
Similar variants
- CD59 p.Pro128Ser Uncertain significance ★ ⚠ same residue
- CD59 p.Cys89Tyr Pathogenic ★★ same type
- CD59 p.Met1Thr Likely pathogenic ★★ same type
- CD59 p.Ala50Val Uncertain significance ★★ ⚠ same type
- CD59 p.Arg78Cys Uncertain significance ★★ ⚠ same type
- CD59 p.Asn33Thr Uncertain significance ★★ ⚠ same type
- CD59 p.Asp92Asn Uncertain significance ★★ ⚠ same type
- CD59 p.Thr105Pro 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/cd59-p-pro128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown