Is CD79A p.Pro226Gln (c.677C>A) pathogenic?

CD79A p.Pro226Gln (c.677C>A) is classified Uncertain significance in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2020-07-20). AlphaMissense: likely pathogenic (0.9848); Absent from gnomAD v4.1; Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Pro226Gln (c.677C>A)?

CD79A p.Pro226Gln (c.677C>A) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Pro226Gln (c.677C>A) in the general population?

CD79A p.Pro226Gln (c.677C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD79A p.Pro226Gln (c.677C>A)?

AlphaMissense predicts likely pathogenic (score 0.9848) — an in-silico prediction, not a clinical call.

CD79A p.Pro226Gln

c.677C>A · rs1555844167 · VCV860381

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9848 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,556,504)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.9848	likely pathogenic · top 6% in CD79A
REVEL	0.607	indeterminate
SaProt	LLR -6.77	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 1, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 3,672 bp · p 0.00029 · regional, not allelic
Overall
CADD	25.1	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

No allele count reported in gnomAD v4.1 (AN 1,556,504). 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.Pro226Gln
Coding: c.677C>A
MANE Select: NM_001783
dbSNP: rs1555844167
Type: single nucleotide variant
Location: chr19:41880976 (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.Pro226Leu Uncertain significance ★ ⚠ same residue
CD79A p.Pro226= Likely benign ★ same residue
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

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-pro226gln (accessed [today's date]).

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