Is APOBEC3D p.Arg30Gln (c.89G>A) pathogenic?

APOBEC3D p.Arg30Gln (c.89G>A) is classified Uncertain significance in APOBEC3D (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). AlphaMissense: likely benign (0.1419); Ultra-rare (popmax 0.0978%, sas).

How common is APOBEC3D p.Arg30Gln (c.89G>A) in the general population?

APOBEC3D p.Arg30Gln (c.89G>A) is ultra-rare (popmax 0.0978%, sas) (gnomAD).

What do computational predictors say about APOBEC3D p.Arg30Gln (c.89G>A)?

AlphaMissense predicts likely benign (score 0.1419) — an in-silico prediction, not a clinical call.

APOBEC3D p.Arg30Gln

c.89G>A · rs770105306 · VCV2471683

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1419 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0978%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1419	likely benign
REVEL	0.359	indeterminate
SaProt	LLR -6.94	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.59	GERP -1.8
Regional constraint	o/e 1.00	unconstrained · MANE · 11 kb · p 0.98 · regional, not allelic
Overall
CADD	15.49	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 0.0978% South Asian · 89/91,028 alleles

Filtering AF 0.0813% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0752%

Overall 0.00638% 103/1,613,320 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0978%	1,023
Remaining individualsnot grpmax-eligible	0.00481%	20,811
East Asian	0.00446%	22,436
African / African-American	0.00134%	74,856
European (non-Finnish)	0.000678%	147,499

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.Arg30Gln
Coding: c.89G>A
MANE Select: NM_152426
dbSNP: rs770105306
Type: single nucleotide variant
Location: chr22:39022893 (GRCh38)
Gene constraint: LOEUF 1.029 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.72
Residue 30: the cmp/dcmp-type deaminase 1 domain

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-arg30gln (accessed [today's date]).

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