CD19 p.Asp538Asn
c.1612G>A · rs542387169 · VCV871886
Computational evidence
| Protein change | ||
| AlphaMissense | 0.1214 | likely benign |
|---|---|---|
| REVEL | 0.043 | moderately benign-leaning |
| SaProt | LLR -7.30 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.4 | phastCons 1 |
| Regional constraint | o/e 0.87 | unconstrained · MANE · 6,959 bp · p 0.00041 · regional, not allelic |
| Overall | ||
| CADD | 21.4 | PHRED · no single calibrated threshold — expert panels disagree |
ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0214% | 4,669 |
| European (non-Finnish) | 0.00565% | 17,689 |
| Remaining individualsnot grpmax-eligible | 0.00331% | 30,176 |
| East Asian | 0.00242% | 41,362 |
| South Asian | 0.00236% | 42,434 |
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.Asp538Asn
- Coding
- c.1612G>A
- MANE Select
- NM_001770
- dbSNP
- rs542387169
- Type
- single nucleotide variant
- Location
- chr16:28938904 (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 538
- the 'disordered' region
Similar variants
- CD19 p.Arg234Cys Uncertain significance ★★ ⚠ same condition
- CD19 p.Arg321Lys Uncertain significance ★★ ⚠ same condition
- CD19 p.Arg549Cys Uncertain significance ★★ ⚠ same condition
- CD19 p.Arg549Leu Uncertain significance ★★ ⚠ same condition
- CD19 p.Arg54Trp Uncertain significance ★★ ⚠ same condition
- CD19 p.Arg5His Uncertain significance ★★ ⚠ same condition
- CD19 p.Gly438Ser Uncertain significance ★★ ⚠ same condition
- CD19 p.His282Gln Uncertain significance ★★ ⚠ same condition
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-asp538asn (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown