CD19 p.Tyr439=
c.1317C>T · rs560880134 · VCV1611114
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
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 -0.14 | phastCons 0.74 |
| Overall | ||
| CADD | 9.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.0208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.018%
Overall
0.00446%
72/1,614,136 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| South Asian | 0.0296% | 3,374 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| East Asian | 0.00669% | 14,958 |
| European (non-Finnish) | 0.00271% | 36,875 |
| African / African-American | 0.00267% | 37,514 |
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.Tyr439=
- Coding
- c.1317C>T
- MANE Select
- NM_001770
- dbSNP
- rs560880134
- Type
- single nucleotide variant
- Location
- chr16:28937468 (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 439
- a modified residue (phosphotyrosine); the 'disordered' region
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-tyr439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown