Is CD79A p.Ala23fs (c.67_73del) pathogenic?

CD79A p.Ala23fs (c.6773del) is classified Pathogenic in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-03). Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Ala23fs (c.67_73del)?

CD79A p.Ala23fs (c.67_73del) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

CD79A p.Ala23fs

c.67_73del · VCV4781785

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP -0.41, phastCons 0.86

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: CD79A
Protein: p.Ala23fs
Coding: c.67_73del
MANE Select: NM_001783
Type: Microsatellite
Location: chr19:41877362 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB

Full CD79A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

agammaglobulinemia 3, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD79A p.Arg124Cys Uncertain significance ★★ ⚠ same condition
CD79A p.Arg124His Uncertain significance ★★ ⚠ same condition
CD79A p.Arg168Gln Uncertain significance ★★ ⚠ same condition
CD79A p.Arg204Gln Uncertain significance ★★ ⚠ same condition
CD79A p.Asn60Ser Uncertain significance ★★ ⚠ same condition
CD79A p.Asn63Ser Uncertain significance ★★ ⚠ same condition
CD79A p.Gly179Arg Uncertain significance ★★ ⚠ same condition
CD79A p.Ile151Thr 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/cd79a-p-ala23fs (accessed [today's date]).

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