CD55 p.Cys98=
c.294C>T · rs28371603 · VCV1164473
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.905%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.095 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.61 | GERP -0.21, phastCons 0.4 |
| Overall | ||
| CADD | 11.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.905%
African / African-American · 658/72,668 alleles
Filtering AF
0.848%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.825%
Overall
0.0784%
1,215/1,549,034 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.905% | 110 |
| Middle Eastern | 0.221% | 452 |
| Ashkenazi Jewishnot grpmax-eligible | 0.171% | 586 |
| Admixed American | 0.147% | 678 |
| Remaining individualsnot grpmax-eligible | 0.146% | 686 |
| East Asian | 0.0486% | 2,057 |
| European (non-Finnish) | 0.0257% | 3,888 |
| South Asian | 0.024% | 4,160 |
| Finnishnot grpmax-eligible | 0.00159% | 62,834 |
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.Cys98=
- Coding
- c.294C>T
- MANE Select
- NM_000574
- dbSNP
- rs28371603
- Type
- single nucleotide variant
- Location
- chr1:207324566 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.99 · 33 PDB
- Residue 98
- a disulfide bond; the sushi 2 domain
Similar variants
- 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
- CD55 p.Arg357His 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-cys98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown