CD33 p.Pro155=
c.465C>T · rs571957160 · VCV751980
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0172%, amr)
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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0172%
Admixed American · 10/58,214 alleles
Filtering AF
0.00925%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.007%
Overall
0.0026%
40/1,538,682 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0172% | 5,821 |
| African / African-American | 0.00538% | 18,577 |
| European (non-Finnish) | 0.00225% | 44,435 |
| Remaining individualsnot grpmax-eligible | 0.00168% | 59,612 |
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.Pro155=
- Coding
- c.465C>T
- MANE Select
- NM_001772
- dbSNP
- rs571957160
- Type
- single nucleotide variant
- Location
- chr19:51225849 (GRCh38)
- Gene constraint
- LOEUF 1.072 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.30 · 11 PDB
- Residue 155
- a disulfide bond; the ig-like c2-type domain
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-pro155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown