CD59 p.Leu14=
c.42C>T · rs372568051 · VCV2889002
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, 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 -0.31 | GERP -2.6 |
| Overall | ||
| CADD | 2.466 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,068 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000496%
8/1,613,790 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,767 |
| African / African-American | 0.00267% | 37,466 |
| Finnishnot grpmax-eligible | 0.00156% | 64,032 |
| European (non-Finnish) | 8.48e-05% | 1,179,796 |
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.Leu14=
- Coding
- c.42C>T
- MANE Select
- NM_000611
- dbSNP
- rs372568051
- Type
- single nucleotide variant
- Location
- chr11:33722404 (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.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-leu14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown