Is CD79A p.Arg68His (c.203G>A) pathogenic?

CD79A p.Arg68His (c.203G>A) is classified Conflicting classifications of pathogenicity in CD79A (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-03-01). AlphaMissense: likely benign (0.1159); Ultra-rare (popmax 0.0133%, afr); Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Arg68His (c.203G>A)?

CD79A p.Arg68His (c.203G>A) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Arg68His (c.203G>A) in the general population?

CD79A p.Arg68His (c.203G>A) is ultra-rare (popmax 0.0133%, afr) (gnomAD).

What do computational predictors say about CD79A p.Arg68His (c.203G>A)?

AlphaMissense predicts likely benign (score 0.1159) — an in-silico prediction, not a clinical call.

CD79A p.Arg68His

c.203G>A · rs782507150 · VCV834558

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1159 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

agammaglobulinemia 3, autosomal recessive

Computational evidence

Protein change
AlphaMissense	0.1159	likely benign
REVEL	0.103	moderately benign-leaning
SaProt	LLR -6.36	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -3.7
Regional constraint	o/e 0.79	unconstrained · MANE · 3,672 bp · p 0.00029 · regional, not allelic
Overall
CADD	2.778	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 0.0133% African / African-American · 10/74,912 alleles

Filtering AF 0.00723% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0055%

Overall 0.00149% 24/1,613,976 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0133%	7,491
South Asian	0.0022%	45,546
Remaining individualsnot grpmax-eligible	0.0016%	62,484
Finnishnot grpmax-eligible	0.00156%	63,948
European (non-Finnish)	0.000847%	118,003

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.Arg68His
Coding: c.203G>A
MANE Select: NM_001783
dbSNP: rs782507150
Type: single nucleotide variant
Location: chr19:41879113 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 68: 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.Arg68Cys Uncertain significance ★ ⚠ same residue
CD79A p.Arg68= Likely benign ★ 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-arg68his (accessed [today's date]).

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