Is CD79A p.Leu81Ser (c.242T>C) pathogenic?

CD79A p.Leu81Ser (c.242T>C) is classified Uncertain significance in CD79A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-04). AlphaMissense: likely benign (0.3176); Very rare (popmax 0.000169%, nfe); Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Leu81Ser (c.242T>C)?

CD79A p.Leu81Ser (c.242T>C) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Leu81Ser (c.242T>C) in the general population?

CD79A p.Leu81Ser (c.242T>C) is very rare (popmax 0.000169%, nfe) (gnomAD).

What do computational predictors say about CD79A p.Leu81Ser (c.242T>C)?

AlphaMissense predicts likely benign (score 0.3176) — an in-silico prediction, not a clinical call.

CD79A p.Leu81Ser

c.242T>C · rs2074205887 · VCV2106718

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3176 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.3176	likely benign
REVEL	0.062	moderately benign-leaning
SaProt	LLR -12.42	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.6	GERP -0.28, phastCons 0.001
Regional constraint	o/e 0.79	unconstrained · MANE · 3,672 bp · p 0.00029 · regional, not allelic
Overall
CADD	4.81	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 0.000169% European (non-Finnish) · 2/1,180,014 alleles

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

Overall 0.000137% 2/1,461,794 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.Leu81Ser
Coding: c.242T>C
MANE Select: NM_001783
dbSNP: rs2074205887
Type: single nucleotide variant
Location: chr19:41879152 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 81: a disulfide bond; a β-strand; the ig-like c2-type domain

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.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
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-leu81ser (accessed [today's date]).

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