Is CD79B p.Pro38Ser (c.112C>T) pathogenic?

CD79B p.Pro38Ser (c.112C>T) is classified Uncertain significance in CD79B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-18). AlphaMissense: likely benign (0.1012); Absent from gnomAD v4.1.

How common is CD79B p.Pro38Ser (c.112C>T) in the general population?

CD79B p.Pro38Ser (c.112C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD79B p.Pro38Ser (c.112C>T)?

AlphaMissense predicts likely benign (score 0.1012) — an in-silico prediction, not a clinical call.

CD79B p.Pro38Ser

c.112C>T · VCV3264877

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1012 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1012	likely benign
REVEL	0.092	moderately benign-leaning
SaProt	LLR -5.86	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 -0.64	GERP -3.6
Regional constraint	o/e 0.73	unconstrained · MANE · 3,032 bp · p 2.7e-06 · regional, not allelic
Overall
CADD	0.08	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD79B
Protein: p.Pro38Ser
Coding: c.112C>T
MANE Select: NM_000626
Type: single nucleotide variant
Location: chr17:63931341 (GRCh38)
Gene constraint: LOEUF 0.421 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.02 · 6 PDB
Residue 38: the ig-like v-type domain

Full CD79B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD79B p.Ala5Val Uncertain significance ★★ ⚠ same type
CD79B p.Arg36Trp Uncertain significance ★★ ⚠ same type
CD79B p.Gly216Arg Uncertain significance ★★ ⚠ same type
CD79B p.Leu91Pro Uncertain significance ★★ ⚠ same type
CD79B p.Met96Val Uncertain significance ★★ ⚠ same type
CD79B p.Thr212Met Uncertain significance ★★ ⚠ same type
CD79B p.Val175Met Uncertain significance ★★ same type
CD79B c.118+12C>T Benign/Likely benign ★★ same type

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/cd79b-p-pro38ser (accessed [today's date]).

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