Is CD79A p.Thr90= (c.270G>A) pathogenic?

CD79A p.Thr90= (c.270G>A) is classified Conflicting classifications of pathogenicity in CD79A (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-11-08). Ultra-rare (popmax 0.022%, sas); Associated with agammaglobulinemia 3, autosomal recessive.

What condition is associated with CD79A p.Thr90= (c.270G>A)?

CD79A p.Thr90= (c.270G>A) is associated with agammaglobulinemia 3, autosomal recessive (ClinVar).

How common is CD79A p.Thr90= (c.270G>A) in the general population?

CD79A p.Thr90= (c.270G>A) is ultra-rare (popmax 0.022%, sas) (gnomAD).

CD79A p.Thr90=

c.270G>A · rs781875393 · VCV1082880

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.022%, sas)

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	Δ0.46	donor loss · deltas
Constraint at this position
Conservation	phyloP 0.13	GERP -3.6, phastCons 0.006
Overall
CADD	8.433	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.022% South Asian · 20/91,088 alleles

Filtering AF 0.0145% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0121%

Overall 0.0039% 63/1,613,890 alleles · ultra-rare exomes 61/1,461,750 · genomes 2/152,140 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.022%	4,554
Middle Eastern	0.0164%	6,084
Admixed American	0.00667%	15,001
Remaining individualsnot grpmax-eligible	0.0048%	20,829
European (non-Finnish)	0.00297%	33,715

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.Thr90=
Coding: c.270G>A
MANE Select: NM_001783
dbSNP: rs781875393
Type: single nucleotide variant
Location: chr19:41879180 (GRCh38)
Gene constraint: LOEUF 0.991 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.56 · 6 PDB
Residue 90: 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.Thr90Met 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
CD79A p.Gly179Arg 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-thr90 (accessed [today's date]).

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