Is CD79A p.Val125= (c.375G>A) pathogenic?

CD79A p.Val125= (c.375G>A) is classified Likely benign in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-23). Very rare (popmax 0.000254%, nfe); Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Val125= (c.375G>A)?

CD79A p.Val125= (c.375G>A) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Val125= (c.375G>A) in the general population?

CD79A p.Val125= (c.375G>A) is very rare (popmax 0.000254%, nfe) (gnomAD).

CD79A p.Val125=

c.375G>A · rs1600631350 · VCV732168

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.42	donor gain · deltas
Constraint at this position
Conservation	phyloP 0.74	GERP -2.1, phastCons 1
Overall
CADD	14.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,179,890 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000186% 3/1,612,038 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.Val125=
Coding: c.375G>A
MANE Select: NM_001783
dbSNP: rs1600631350
Type: single nucleotide variant
Location: chr19:41879285 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 125: 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.Val125Met Uncertain significance ★★ ⚠ same residue
CD79A p.Val125Gly Uncertain significance ★ ⚠ 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-val125 (accessed [today's date]).

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