Is CD79A p.Arg124Cys (c.370C>T) pathogenic?

CD79A p.Arg124Cys (c.370C>T) is classified Uncertain significance in CD79A (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-07). AlphaMissense: likely pathogenic (0.6787); Ultra-rare (popmax 0.0292%, nfe); Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Arg124Cys (c.370C>T)?

CD79A p.Arg124Cys (c.370C>T) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Arg124Cys (c.370C>T) in the general population?

CD79A p.Arg124Cys (c.370C>T) is ultra-rare (popmax 0.0292%, nfe) (gnomAD).

What do computational predictors say about CD79A p.Arg124Cys (c.370C>T)?

AlphaMissense predicts likely pathogenic (score 0.6787) — an in-silico prediction, not a clinical call.

CD79A p.Arg124Cys

c.370C>T · rs144006380 · VCV450253

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.6787 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0292%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.6787	likely pathogenic
REVEL	0.535	indeterminate
SaProt	LLR -7.68	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 1.8, phastCons 0.99
Regional constraint	o/e 0.79	unconstrained · MANE · 3,672 bp · p 0.00029 · regional, not allelic
Overall
CADD	28.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0292% European (non-Finnish) · 344/1,179,888 alleles

Filtering AF 0.0265% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0256%

Overall 0.0235% 379/1,612,408 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0292%	3,430
Remaining individualsnot grpmax-eligible	0.0256%	3,904
South Asian	0.011%	9,107
Finnishnot grpmax-eligible	0.0064%	15,628
African / African-American	0.004%	25,011
East Asian	0.00223%	44,876
Admixed American	0.00167%	60,000

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.Arg124Cys
Coding: c.370C>T
MANE Select: NM_001783
dbSNP: rs144006380
Type: single nucleotide variant
Location: chr19:41879280 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 124: 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.Arg124His Uncertain significance ★★ ⚠ same residue
CD79A p.Arg124= Likely benign ★★ same residue
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
CD79A p.Gly179Arg Uncertain significance ★★ ⚠ same condition
CD79A p.Ile151Thr 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-arg124cys (accessed [today's date]).

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