CD55 p.Leu15=
c.45C>T · VCV3680669
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000787%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.016 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -1.8 |
| Overall | ||
| CADD | 6.278 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000787%
European (non-Finnish) · 9/1,143,402 alleles
Filtering AF
0.00037%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000268%
Overall
0.000589%
9/1,528,264 alleles · very rare
exomes 9/1,375,966 · genomes 0/152,298 · joint denominator
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
- CD55
- Protein
- p.Leu15=
- Coding
- c.45C>T
- MANE Select
- NM_000574
- Type
- single nucleotide variant
- Location
- chr1:207321810 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.99 · 33 PDB
Similar variants
- CD55 p.Leu15Phe Uncertain significance ★ ⚠ same residue
- CD55 p.Leu15fs Pathogenic same residue
- CD55 c.286+1G>A Likely pathogenic ★★ same type
- CD55 c.286+2T>G Likely pathogenic ★★ same type
- CD55 p.Glu50Ter Pathogenic/Likely pathogenic ★★ same type
- CD55 p.Trp213Ter Pathogenic/Likely pathogenic ★★ same type
- CD55 c.1081+1G>C Uncertain significance ★★ same type
- CD55 p.Arg221Ser 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/cd55-p-leu15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown