Is APBA2 p.Asp162= (c.486C>T) pathogenic?

APBA2 p.Asp162= (c.486C>T) is classified Likely benign in APBA2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-29). Ultra-rare (popmax 0.0491%, eas); Associated with APBA2-related disorder.

What condition is associated with APBA2 p.Asp162= (c.486C>T)?

APBA2 p.Asp162= (c.486C>T) is associated with APBA2-related disorder (ClinVar).

How common is APBA2 p.Asp162= (c.486C>T) in the general population?

APBA2 p.Asp162= (c.486C>T) is ultra-rare (popmax 0.0491%, eas) (gnomAD).

APBA2 p.Asp162=

c.486C>T · rs372649988 · VCV3040331

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0491%, eas)

Conditions

APBA2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -13	GERP -2.5
Overall
CADD	0.819	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0491% East Asian · 22/44,850 alleles

Filtering AF 0.0332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.028%

Overall 0.00471% 76/1,614,114 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0491%	2,039
African / African-American	0.0426%	2,345
Middle Eastern	0.033%	3,031
Remaining individualsnot grpmax-eligible	0.0064%	15,628
Finnishnot grpmax-eligible	0.00469%	21,324
South Asian	0.00439%	22,772
European (non-Finnish)	0.000763%	131,114

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.Asp162=
Coding: c.486C>T
MANE Select: NM_001353788
dbSNP: rs372649988
Type: single nucleotide variant
Location: chr15:29054370 (GRCh38)
Gene constraint: LOEUF 0.524 · pLI 0.78 (gnomAD)
Structure: AlphaFold pLDDT 59.74
Residue 162: 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.Arg52Gln Benign same condition
APBA2 p.Asn704= Likely benign same condition
APBA2 p.Asn722Ser 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-asp162 (accessed [today's date]).

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