Is CD79B p.Leu104= (c.312C>T) pathogenic?

CD79B p.Leu104= (c.312C>T) is classified Benign in CD79B (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-26). Low-frequency (popmax 2.75%, afr); Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Leu104= (c.312C>T)?

CD79B p.Leu104= (c.312C>T) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Leu104= (c.312C>T) in the general population?

CD79B p.Leu104= (c.312C>T) is low-frequency (popmax 2.75%, afr) (gnomAD).

CD79B p.Leu104=

c.312C>T · rs116625909 · VCV471350

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.75%, afr)

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 -0.88	GERP -4
Overall
CADD	3.552	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.75% African / African-American · 2,062/75,060 alleles

Filtering AF 2.65% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.61%

Overall 0.145% 2,341/1,614,228 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.75%	36
Remaining individualsnot grpmax-eligible	0.197%	508
Admixed American	0.17%	589
Middle Eastern	0.148%	674
South Asian	0.00988%	10,121
European (non-Finnish)	0.00305%	32,779

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.Leu104=
Coding: c.312C>T
MANE Select: NM_000626
dbSNP: rs116625909
Type: single nucleotide variant
Location: chr17:63930192 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 104: a disulfide bond; 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-leu104 (accessed [today's date]).

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