CD22 p.Cys39=
c.117C>T · rs750364404 · VCV2649717
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.51 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.52 | GERP -3.1 |
| Overall | ||
| CADD | 10.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,880 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000547%
8/1,461,852 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,880 |
| Finnishnot grpmax-eligible | 0.00156% | 64,024 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.000424% | 235,995 |
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
- CD22
- Protein
- p.Cys39=
- Coding
- c.117C>T
- MANE Select
- NM_001771
- dbSNP
- rs750364404
- Type
- single nucleotide variant
- Location
- chr19:35332629 (GRCh38)
- Gene constraint
- LOEUF 0.639 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.33 · 7 PDB
- Residue 39
- a disulfide bond; the ig-like v-type domain
Similar variants
- CD22 p.Ala391Thr Benign ★★ same type
- CD22 p.Cys265= Benign ★★ same type
- CD22 p.Gly551Arg Benign ★★ same type
- CD22 p.Gly727Ser Likely benign ★★ same type
- CD22 p.Pro681= Benign ★★ same type
- CD22 p.Ala17Val Uncertain significance ★ ⚠ same type
- CD22 p.Ala498Ser Uncertain significance ★ ⚠ same type
- CD22 p.Ala656Thr 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/cd22-p-cys39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown