Is CD79B p.Thr60= (c.180G>A) pathogenic?

CD79B p.Thr60= (c.180G>A) is classified Likely benign in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-26). Ultra-rare (popmax 0.0164%, mid); Associated with agammaglobulinemia 6, autosomal recessive.

What condition is associated with CD79B p.Thr60= (c.180G>A)?

CD79B p.Thr60= (c.180G>A) is associated with agammaglobulinemia 6, autosomal recessive (ClinVar).

How common is CD79B p.Thr60= (c.180G>A) in the general population?

CD79B p.Thr60= (c.180G>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

CD79B p.Thr60=

c.180G>A · VCV4755136

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Conditions

agammaglobulinemia 6, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.6	GERP -4.3
Overall
CADD	7.846	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0164% Middle Eastern · 1/6,084 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00309%

Overall 0.000991% 16/1,614,048 alleles · ultra-rare exomes 9/1,461,810 · genomes 7/152,238 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,084
African / African-American	0.00934%	10,705
European (non-Finnish)	0.000678%	147,506

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.Thr60=
Coding: c.180G>A
MANE Select: NM_000626
Type: single nucleotide variant
Location: chr17:63930324 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 60: 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.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-thr60 (accessed [today's date]).

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