Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.906%, afr)
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 -0.72 | GERP -5 |
| Overall | ||
| CADD | 0.262 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.906%
African / African-American · 680/75,028 alleles
Filtering AF
0.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.827%
Overall
0.0535%
864/1,614,032 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.906% | 110 |
| Admixed American | 0.0933% | 1,072 |
| Middle Eastern | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,841 |
| European (non-Finnish) | 0.00814% | 12,292 |
| Finnishnot grpmax-eligible | 0.00469% | 21,321 |
| South Asian | 0.00439% | 22,768 |
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
- CD180
- Protein
- p.Thr222=
- Coding
- c.666G>A
- MANE Select
- NM_005582
- dbSNP
- rs2230521
- Type
- single nucleotide variant
- Location
- chr5:67184177 (GRCh38)
- Gene constraint
- LOEUF 1.886 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.27 · 1 PDB
Similar variants
- CD180 p.Leu398= Benign ★★ same type
- CD180 p.Ser584= Benign ★★ same type
- CD180 p.Thr430Ala Benign ★★ same type
- CD180 p.Ala415Ser Uncertain significance ★ ⚠ same type
- CD180 p.Ala466Ser Uncertain significance ★ ⚠ same type
- CD180 p.Ala649Thr Uncertain significance ★ ⚠ same type
- CD180 p.Arg173Trp Uncertain significance ★ ⚠ same type
- CD180 p.Arg472Trp 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/cd180-p-thr222 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown