Is APOBEC3D p.Arg156Cys (c.466C>T) pathogenic?

APOBEC3D p.Arg156Cys (c.466C>T) is classified Uncertain significance in APOBEC3D (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-20). AlphaMissense: likely benign (0.1672); Ultra-rare (popmax 0.0183%, amr).

How common is APOBEC3D p.Arg156Cys (c.466C>T) in the general population?

APOBEC3D p.Arg156Cys (c.466C>T) is ultra-rare (popmax 0.0183%, amr) (gnomAD).

What do computational predictors say about APOBEC3D p.Arg156Cys (c.466C>T)?

AlphaMissense predicts likely benign (score 0.1672) — an in-silico prediction, not a clinical call.

APOBEC3D p.Arg156Cys

c.466C>T · rs530222573 · VCV2354357

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1672 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0183%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1672	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -8.58	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 -15	GERP -3.3
Regional constraint	o/e 1.00	unconstrained · MANE · 11 kb · p 0.98 · regional, not allelic
Overall
CADD	14.57	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 0.0183% Admixed American · 11/60,012 alleles

Filtering AF 0.0102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00785%

Overall 0.00118% 19/1,614,040 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0183%	5,456
Remaining individualsnot grpmax-eligible	0.0032%	31,252
African / African-American	0.00133%	75,006
European (non-Finnish)	0.000424%	235,997

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: APOBEC3D
Protein: p.Arg156Cys
Coding: c.466C>T
MANE Select: NM_152426
dbSNP: rs530222573
Type: single nucleotide variant
Location: chr22:39025325 (GRCh38)
Gene constraint: LOEUF 1.029 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.72

Full APOBEC3D gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

APOBEC3D p.Ala121Ser Uncertain significance ★ ⚠ same type
APOBEC3D p.Ala133Thr Uncertain significance ★ ⚠ same type
APOBEC3D p.Ala191Thr Uncertain significance ★ ⚠ same type
APOBEC3D p.Ala263Val Uncertain significance ★ ⚠ same type
APOBEC3D p.Ala305Val Uncertain significance ★ ⚠ same type
APOBEC3D p.Ala79Pro Uncertain significance ★ ⚠ same type
APOBEC3D p.Arg11Gln Uncertain significance ★ ⚠ same type
APOBEC3D p.Arg134Cys 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/apobec3d-p-arg156cys (accessed [today's date]).

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