Is CD19 p.Trp52Cys (c.156G>C) pathogenic?

CD19 p.Trp52Cys (c.156G>C) is classified Pathogenic in CD19 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2016-09-13). AlphaMissense: likely pathogenic (0.9778); Absent from gnomAD v4.1; Associated with immunodeficiency, common variable, 3.

What condition is associated with CD19 p.Trp52Cys (c.156G>C)?

CD19 p.Trp52Cys (c.156G>C) is associated with immunodeficiency, common variable, 3 (ClinVar).

How common is CD19 p.Trp52Cys (c.156G>C) in the general population?

CD19 p.Trp52Cys (c.156G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD19 p.Trp52Cys (c.156G>C)?

AlphaMissense predicts likely pathogenic (score 0.9778) — an in-silico prediction, not a clinical call.

CD19 p.Trp52Cys

c.156G>C · rs886037920 · VCV254195

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9778 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

immunodeficiency, common variable, 3

Computational evidence

Protein change
AlphaMissense	0.9778	likely pathogenic ✓ concordant with ClinVar · top 1% in CD19
REVEL	0.534	indeterminate
SaProt	LLR -14.15	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 6,959 bp · p 0.00041 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD19
Protein: p.Trp52Cys
Coding: c.156G>C
MANE Select: NM_001770
dbSNP: rs886037920
Type: single nucleotide variant
Location: chr16:28932413 (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 52: a disulfide bond; a β-strand; the ig-like c2-type 1 domain

Full CD19 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency, common variable, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD19 c.835+3A>G Uncertain significance ★★ same condition
CD19 p.Arg163His Uncertain significance ★★ ⚠ same condition
CD19 p.Arg263His Uncertain significance ★★ ⚠ same condition
CD19 p.Arg490Gln Uncertain significance ★★ ⚠ same condition
CD19 p.Arg76Ser Uncertain significance ★★ ⚠ same condition
CD19 p.Gln345His Uncertain significance ★★ ⚠ same condition
CD19 p.Glu21Gln Uncertain significance ★★ ⚠ same condition
CD19 p.Glu29Gln 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-trp52cys (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown