Is CD79B p.Arg214Gln (c.641G>A) pathogenic?

CD79B p.Arg214Gln (c.641G>A) is classified Uncertain significance in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-03). AlphaMissense: ambiguous (0.5419); Very rare (popmax 0.00525%, nfe); Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Arg214Gln (c.641G>A)?

CD79B p.Arg214Gln (c.641G>A) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Arg214Gln (c.641G>A) in the general population?

CD79B p.Arg214Gln (c.641G>A) is very rare (popmax 0.00525%, nfe) (gnomAD).

What do computational predictors say about CD79B p.Arg214Gln (c.641G>A)?

AlphaMissense predicts ambiguous (score 0.5419) — an in-silico prediction, not a clinical call.

CD79B p.Arg214Gln

c.641G>A · rs1169314441 · VCV1986905

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5419 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00525%, nfe)

Conditions

agammaglobulinemia 6, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.5419	ambiguous
REVEL	0.56	indeterminate
SaProt	LLR -7.05	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	31.0	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

Grpmax group 0.00525% European (non-Finnish) · 62/1,179,960 alleles

Filtering AF 0.00418% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0038%

Overall 0.00403% 65/1,613,930 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00525%	19,032
Remaining individualsnot grpmax-eligible	0.0048%	20,829

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.Arg214Gln
Coding: c.641G>A
MANE Select: NM_000626
dbSNP: rs1169314441
Type: single nucleotide variant
Location: chr17:63929275 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB

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.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
CD79B c.118+12C>T Benign/Likely benign ★★ 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-arg214gln (accessed [today's date]).

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