CD59 p.Leu52=
c.156C>T · rs533392692 · VCV1920597
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0549%, sas)
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 -0.24 | GERP 1.7 |
| Overall | ||
| CADD | 1.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0549%
South Asian · 50/90,992 alleles
Filtering AF
0.0428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0385%
Overall
0.00341%
55/1,611,320 alleles · ultra-rare
exomes 49/1,459,032 · genomes 6/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0549% | 1,820 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,807 |
| East Asian | 0.00446% | 22,433 |
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.Leu52=
- Coding
- c.156C>T
- MANE Select
- NM_000611
- dbSNP
- rs533392692
- Type
- single nucleotide variant
- Location
- chr11:33717383 (GRCh38)
- Gene constraint
- LOEUF 1.277 · pLI 0.57 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.15 · 17 PDB
- Residue 52
- the upar/ly6 domain; a β-strand
Similar variants
- 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
- CD59 p.Val18Ile 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-leu52 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown