Is CD79B p.Phe114Cys (c.341T>G) pathogenic?

CD79B p.Phe114Cys (c.341T>G) is classified Uncertain significance in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-12). AlphaMissense: likely pathogenic (0.6862); Absent from gnomAD v4.1; Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Phe114Cys (c.341T>G)?

CD79B p.Phe114Cys (c.341T>G) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Phe114Cys (c.341T>G) in the general population?

CD79B p.Phe114Cys (c.341T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD79B p.Phe114Cys (c.341T>G)?

AlphaMissense predicts likely pathogenic (score 0.6862) — an in-silico prediction, not a clinical call.

CD79B p.Phe114Cys

c.341T>G · rs1908032776 · VCV1005019

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6862 · 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	0.6862	likely pathogenic
REVEL	0.328	indeterminate
SaProt	LLR -12.74	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.32 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.35	GERP -4.3
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	16.12	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.Phe114Cys
Coding: c.341T>G
MANE Select: NM_000626
dbSNP: rs1908032776
Type: single nucleotide variant
Location: chr17:63930163 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 114: a disulfide bond; an α-helix; 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.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-phe114cys (accessed [today's date]).

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