Is CD79B p.Phe121Cys (c.362T>G) pathogenic?

CD79B p.Phe121Cys (c.362T>G) is classified Uncertain significance in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-27). AlphaMissense: likely pathogenic (0.722); Absent from gnomAD v4.1; Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Phe121Cys (c.362T>G)?

CD79B p.Phe121Cys (c.362T>G) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Phe121Cys (c.362T>G) in the general population?

CD79B p.Phe121Cys (c.362T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD79B p.Phe121Cys (c.362T>G)?

AlphaMissense predicts likely pathogenic (score 0.722) — an in-silico prediction, not a clinical call.

CD79B p.Phe121Cys

c.362T>G · rs2509268615 · VCV2139982

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.722 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

agammaglobulinemia 6, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.722	likely pathogenic
REVEL	0.602	indeterminate
SaProt	LLR -11.04	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP -0.071, phastCons 0.2
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD79B
Protein: p.Phe121Cys
Coding: c.362T>G
MANE Select: NM_000626
dbSNP: rs2509268615
Type: single nucleotide variant
Location: chr17:63930142 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 121: a β-strand; the ig-like v-type 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.Phe121= Likely benign ★ 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-phe121cys (accessed [today's date]).

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