Is APOBEC3B p.Gln167Pro (c.500A>C) pathogenic?

APOBEC3B p.Gln167Pro (c.500A>C) is classified Uncertain significance in APOBEC3B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-15). AlphaMissense: likely benign (0.0376); Rare (popmax 0.936%, afr); Associated with APOBEC3B-related condition.

What condition is associated with APOBEC3B p.Gln167Pro (c.500A>C)?

APOBEC3B p.Gln167Pro (c.500A>C) is associated with APOBEC3B-related condition (ClinVar).

How common is APOBEC3B p.Gln167Pro (c.500A>C) in the general population?

APOBEC3B p.Gln167Pro (c.500A>C) is rare (popmax 0.936%, afr) (gnomAD).

What do computational predictors say about APOBEC3B p.Gln167Pro (c.500A>C)?

AlphaMissense predicts likely benign (score 0.0376) — an in-silico prediction, not a clinical call.

APOBEC3B p.Gln167Pro

c.500A>C · VCV3779920

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0376 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.936%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

APOBEC3B-related condition

Computational evidence

Protein change
AlphaMissense	0.0376	likely benign
REVEL	0.076	moderately benign-leaning
SaProt	LLR -2.74	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 -7.6	GERP -2.9
Regional constraint	o/e 0.94	unconstrained · MANE · 3,632 bp · p 0.41 · regional, not allelic
Overall
CADD	0.003	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

Grpmax group 0.936% African / African-American · 696/74,386 alleles

Filtering AF 0.878% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.855%

Overall 0.0534% 851/1,593,914 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.936%	107
Admixed American	0.062%	1,614
Remaining individualsnot grpmax-eligible	0.0537%	1,862
Middle Eastern	0.05%	2,001
South Asian	0.00788%	12,685
East Asian	0.00744%	13,443
European (non-Finnish)	0.00631%	15,847

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: APOBEC3B
Protein: p.Gln167Pro
Coding: c.500A>C
MANE Select: NM_004900
Type: single nucleotide variant
Location: chr22:38986343 (GRCh38)
Gene constraint: LOEUF 0.854 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.94 · 13 PDB
Residue 167: an α-helix

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

Disease context

APOBEC3B-related condition

Similar variants

APOBEC3B p.Arg351Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
APOBEC3B p.Phe296Ser Uncertain significance ★ ⚠ same condition
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

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-gln167pro (accessed [today's date]).

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