CD55 p.Thr250=
c.750G>A · rs780475447 · VCV1109464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00879%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.033 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.058 | GERP -3.6 |
| Overall | ||
| CADD | 3.564 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00879%
South Asian · 8/91,054 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00211%
34/1,612,526 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00879% | 11,382 |
| African / African-American | 0.00401% | 24,949 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,208 |
| European (non-Finnish) | 0.0017% | 58,938 |
| Admixed American | 0.00167% | 60,002 |
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.Thr250=
- Coding
- c.750G>A
- MANE Select
- NM_000574
- dbSNP
- rs780475447
- Type
- single nucleotide variant
- Location
- chr1:207331193 (GRCh38)
- Gene constraint
- LOEUF 1.234 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.99 · 33 PDB
- Residue 250
- a disulfide bond; the sushi 4 domain; a β-strand
Similar variants
- CD55 p.Thr250Met 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-thr250 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown