Is CD79B p.Phe121= (c.363C>T) pathogenic?

CD79B p.Phe121= (c.363C>T) is classified Likely benign in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-11). Very rare (popmax 0.00322%, nfe); Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Phe121= (c.363C>T)?

CD79B p.Phe121= (c.363C>T) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Phe121= (c.363C>T) in the general population?

CD79B p.Phe121= (c.363C>T) is very rare (popmax 0.00322%, nfe) (gnomAD).

CD79B p.Phe121=

c.363C>T · rs1221118585 · VCV2166286

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00322%, nfe)

Conditions

agammaglobulinemia 6, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 1.1, phastCons 1
Overall
CADD	12.21	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00322% European (non-Finnish) · 38/1,180,020 alleles

Filtering AF 0.00239% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0021%

Overall 0.00248% 40/1,614,078 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00322%	31,053
Remaining individualsnot grpmax-eligible	0.0016%	62,486
South Asian	0.0011%	91,090

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.Phe121=
Coding: c.363C>T
MANE Select: NM_000626
dbSNP: rs1221118585
Type: single nucleotide variant
Location: chr17:63930141 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 121: a disulfide bond; 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.Phe121Cys 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-phe121 (accessed [today's date]).

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