Is APBA2 p.Arg52Gln (c.155G>A) pathogenic?

APBA2 p.Arg52Gln (c.155G>A) is classified Benign in APBA2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-26). AlphaMissense: likely benign (0.0686); Low-frequency (popmax 1.97%, nfe); Associated with APBA2-related disorder.

What condition is associated with APBA2 p.Arg52Gln (c.155G>A)?

APBA2 p.Arg52Gln (c.155G>A) is associated with APBA2-related disorder (ClinVar).

How common is APBA2 p.Arg52Gln (c.155G>A) in the general population?

APBA2 p.Arg52Gln (c.155G>A) is low-frequency (popmax 1.97%, nfe) (gnomAD).

What do computational predictors say about APBA2 p.Arg52Gln (c.155G>A)?

AlphaMissense predicts likely benign (score 0.0686) — an in-silico prediction, not a clinical call.

APBA2 p.Arg52Gln

c.155G>A · rs117098828 · VCV3037758

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0686 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.97%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

APBA2-related disorder

Computational evidence

Protein change
AlphaMissense	0.0686	likely benign
REVEL	0.073	moderately benign-leaning
SaProt	LLR -5.73	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 4.9	GERP -2.1, phastCons 1
Overall
CADD	19.28	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.97% European (non-Finnish) · 23,202/1,180,028 alleles

Filtering AF 1.95% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.94%

Overall 1.68% 27,163/1,613,814 alleles · low-frequency

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	1.97%	51
Finnishnot grpmax-eligible	1.72%	58
Remaining individualsnot grpmax-eligible	1.58%	63
Middle Eastern	1.26%	79
Ashkenazi Jewishnot grpmax-eligible	0.969%	103
South Asian	0.836%	120
Admixed American	0.811%	123
African / African-American	0.354%	282
East Asian	0.00223%	44,852

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: APBA2
Protein: p.Arg52Gln
Coding: c.155G>A
MANE Select: NM_001353788
dbSNP: rs117098828
Type: single nucleotide variant
Location: chr15:29054039 (GRCh38)
Gene constraint: LOEUF 0.524 · pLI 0.78 (gnomAD)
Structure: AlphaFold pLDDT 59.74
Residue 52: the 'disordered' region

Full APBA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

APBA2-related disorder

Similar variants

APBA2 c.1070-9C>T Likely benign same condition
APBA2 c.952-3825C>T Likely benign same condition
APBA2 c.*7C>T Likely benign same condition
APBA2 p.Asn704= Likely benign same condition
APBA2 p.Asn722Ser Likely benign same condition
APBA2 p.Asp162= Likely benign same condition
APBA2 p.Gln408= Likely benign same condition
APBA2 p.Gly603= Benign same condition

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/apba2-p-arg52gln (accessed [today's date]).

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