Is CD79A p.Cys155Leu (c.463_464delinsCT) pathogenic?

CD79A p.Cys155Leu (c.463464delinsCT) is classified Uncertain significance in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-12). Absent from gnomAD; Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Cys155Leu (c.463_464delinsCT)?

CD79A p.Cys155Leu (c.463_464delinsCT) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Cys155Leu (c.463_464delinsCT) in the general population?

CD79A p.Cys155Leu (c.463_464delinsCT) is absent from gnomAD (gnomAD).

CD79A p.Cys155Leu

c.463_464delinsCT · rs2513700375 · VCV1938028

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP 1.5, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 3,672 bp · p 0.00029 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CD79A
Protein: p.Cys155Leu
Coding: c.463_464delinsCT
MANE Select: NM_001783
dbSNP: rs2513700375
Type: Indel
Location: chr19:41879618 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 155: an α-helix

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.Cys155Ter Pathogenic ★ same residue
CD79A p.Cys155= Likely benign ★ same residue
CD79A p.Ala156Leu Uncertain significance ★ same condition
CD79A c.567+20_567+21delinsAT Likely benign ★ same condition
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

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-cys155leu (accessed [today's date]).

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