CD33 p.Pro189=
c.567C>G · rs374361331 · VCV789671
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0561%, 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 -7.4 | GERP -0.27 |
| Overall | ||
| CADD | 7.878 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0561%
African / African-American · 42/74,904 alleles
Filtering AF
0.0425%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0379%
Overall
0.00372%
60/1,614,002 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0561% | 1,783 |
| Admixed American | 0.0167% | 5,999 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000169% | 590,012 |
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
- CD33
- Protein
- p.Pro189=
- Coding
- c.567C>G
- MANE Select
- NM_001772
- dbSNP
- rs374361331
- Type
- single nucleotide variant
- Location
- chr19:51225951 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.30 · 11 PDB
- Residue 189
- a disulfide bond; the ig-like c2-type domain; a β-strand
Similar variants
- CD33 p.Asp51Asn Uncertain significance ★★ ⚠ same type
- CD33 c.924+295A>G Benign ★★ same type
- CD33 c.924+296C>T Benign ★★ same type
- CD33 c.924+2T>C Benign ★★ same type
- CD33 c.924+469G>C Benign ★★ same type
- CD33 c.*201G>C Benign ★★ same type
- CD33 p.Ala14Val Benign ★★ ⚠ same type
- CD33 p.Ala65Pro Benign ★★ ⚠ 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/cd33-p-pro189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown