Is CD79B p.Ala188Pro (c.562G>C) pathogenic?

CD79B p.Ala188Pro (c.562G>C) is classified Uncertain significance in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-02). AlphaMissense: likely benign (0.1022); Very rare (popmax 0.0022%, sas); Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Ala188Pro (c.562G>C)?

CD79B p.Ala188Pro (c.562G>C) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Ala188Pro (c.562G>C) in the general population?

CD79B p.Ala188Pro (c.562G>C) is very rare (popmax 0.0022%, sas) (gnomAD).

What do computational predictors say about CD79B p.Ala188Pro (c.562G>C)?

AlphaMissense predicts likely benign (score 0.1022) — an in-silico prediction, not a clinical call.

CD79B p.Ala188Pro

c.562G>C · VCV3722090

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1022 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0022%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

agammaglobulinemia 6, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.1022	likely benign
REVEL	0.134	moderately benign-leaning
SaProt	LLR -6.07	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 -0.49	GERP -3.2
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	10.04	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

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0022% South Asian · 2/91,086 alleles

Filtering AF 0.000365% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000136%

Overall 0.000205% 3/1,461,632 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0022%	45,543
Admixed American	0.00167%	60,014

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: CD79B
Protein: p.Ala188Pro
Coding: c.562G>C
MANE Select: NM_000626
Type: single nucleotide variant
Location: chr17:63929463 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 188: the itam domain

Full CD79B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

agammaglobulinemia 6, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD79B p.Ala188Gly Uncertain significance ★ same residue
CD79B p.Ala5Val Uncertain significance ★★ ⚠ same condition
CD79B p.Arg36Trp Uncertain significance ★★ ⚠ same condition
CD79B p.Gly216Arg Uncertain significance ★★ ⚠ same condition
CD79B p.Leu91Pro Uncertain significance ★★ ⚠ same condition
CD79B p.Met96Val Uncertain significance ★★ ⚠ same condition
CD79B p.Thr212Met Uncertain significance ★★ ⚠ same condition
CD79B p.Val175Met 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/cd79b-p-ala188pro (accessed [today's date]).

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