CD55 p.Pro216=
c.648G>A · rs146687590 · VCV1562561
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.007 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -3.6 |
| Overall | ||
| CADD | 0.537 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,850 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0165%
Overall
0.0162%
262/1,612,934 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,743 |
| European (non-Finnish) | 0.0194% | 5,149 |
| East Asian | 0.0134% | 7,477 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,494 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
| Admixed American | 0.00167% | 59,984 |
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.Pro216=
- Coding
- c.648G>A
- MANE Select
- NM_000574
- dbSNP
- rs146687590
- Type
- single nucleotide variant
- Location
- chr1:207326821 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.99 · 33 PDB
- Residue 216
- a disulfide bond; the sushi 3 domain; an α-helix
Similar variants
- CD55 p.Pro216Leu Uncertain significance ★ ⚠ 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
- CD55 p.Arg357Cys 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-pro216 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown