CD19 p.Pro164=
c.492T>A · VCV4779063
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, 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 0.26 | |
| Overall | ||
| CADD | 4.183 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,982 alleles
Overall
0.000137%
2/1,461,250 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 59,982 |
| European (non-Finnish) | 8.48e-05% | 1,179,549 |
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
- CD19
- Protein
- p.Pro164=
- Coding
- c.492T>A
- MANE Select
- NM_001770
- Type
- single nucleotide variant
- Location
- chr16:28933047 (GRCh38)
- Gene constraint
- LOEUF 0.627 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.99 · 4 PDB
- Residue 164
- a disulfide bond; a β-strand
Similar variants
- CD19 c.835+3A>G Uncertain significance ★★ same type
- CD19 p.Ala191Thr Uncertain significance ★★ ⚠ same type
- CD19 p.Arg123Trp Uncertain significance ★★ ⚠ same type
- CD19 p.Arg163His Uncertain significance ★★ ⚠ same type
- CD19 p.Arg234Cys Uncertain significance ★★ ⚠ same type
- CD19 p.Arg263His Uncertain significance ★★ ⚠ same type
- CD19 p.Arg321Lys Uncertain significance ★★ ⚠ same type
- CD19 p.Arg490Gln 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/cd19-p-pro164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown