Is APOBEC3B p.Pro96Arg (c.287C>G) pathogenic?

APOBEC3B p.Pro96Arg (c.287C>G) is classified Uncertain significance in APOBEC3B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-04). AlphaMissense: likely pathogenic (0.7782); Absent from gnomAD v4.1.

How common is APOBEC3B p.Pro96Arg (c.287C>G) in the general population?

APOBEC3B p.Pro96Arg (c.287C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APOBEC3B p.Pro96Arg (c.287C>G)?

AlphaMissense predicts likely pathogenic (score 0.7782) — an in-silico prediction, not a clinical call.

APOBEC3B p.Pro96Arg

c.287C>G · VCV3417222

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7782 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.7782	likely pathogenic · top 10% in APOBEC3B
REVEL	0.587	indeterminate
SaProt	LLR -13.06	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.7, phastCons 1
Regional constraint	o/e 0.39	unconstrained · MANE · 127 bp · p 1.5e-05 · regional, not allelic
Overall
CADD	18.96	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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: APOBEC3B
Protein: p.Pro96Arg
Coding: c.287C>G
MANE Select: NM_004900
Type: single nucleotide variant
Location: chr22:38985924 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.94 · 13 PDB
Residue 96: the cmp/dcmp-type deaminase 1 domain; an α-helix

Full APOBEC3B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

APOBEC3B p.Asn23= Benign ★★ same type
APOBEC3B p.Pro206= Benign ★★ same type
APOBEC3B c.174+1G>T Uncertain significance ★ same type
APOBEC3B p.Ala242Ser Uncertain significance ★ ⚠ same type
APOBEC3B p.Ala331Ser Uncertain significance ★ ⚠ same type
APOBEC3B p.Ala375Val Uncertain significance ★ ⚠ same type
APOBEC3B p.Arg183Cys Uncertain significance ★ ⚠ same type
APOBEC3B p.Arg212Leu Uncertain significance ★ ⚠ 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/apobec3b-p-pro96arg (accessed [today's date]).

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