Is CD79A p.Thr140= (c.420C>T) pathogenic?

CD79A p.Thr140= (c.420C>T) is classified Likely benign in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-03). Very rare (popmax 0.00017%, nfe); Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Thr140= (c.420C>T)?

CD79A p.Thr140= (c.420C>T) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Thr140= (c.420C>T) in the general population?

CD79A p.Thr140= (c.420C>T) is very rare (popmax 0.00017%, nfe) (gnomAD).

CD79A p.Thr140=

c.420C>T · VCV4753386

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Conditions

agammaglobulinemia 3, 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 -0.061	GERP 0.24, phastCons 0.68
Overall
CADD	12.37	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00017% European (non-Finnish) · 2/1,179,196 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000137% 2/1,459,536 alleles · very rare

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: CD79A
Protein: p.Thr140=
Coding: c.420C>T
MANE Select: NM_001783
Type: single nucleotide variant
Location: chr19:41879575 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 140: a β-strand

Full CD79A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

agammaglobulinemia 3, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD79A p.Thr140Ile Uncertain significance ★★ ⚠ same residue
CD79A p.Thr140Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
CD79A p.Arg124Cys Uncertain significance ★★ ⚠ same condition
CD79A p.Arg124His Uncertain significance ★★ ⚠ same condition
CD79A p.Arg168Gln Uncertain significance ★★ ⚠ same condition
CD79A p.Arg204Gln Uncertain significance ★★ ⚠ same condition
CD79A p.Asn60Ser Uncertain significance ★★ ⚠ same condition
CD79A p.Asn63Ser 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/cd79a-p-thr140 (accessed [today's date]).

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