Is APBA2 p.Ala57Val (c.170C>T) pathogenic?

APBA2 p.Ala57Val (c.170C>T) is classified Likely benign in APBA2 (ClinVar, Single submitter, 2 submitters). AlphaMissense: likely benign (0.0609); Rare (popmax 0.175%, amr).

How common is APBA2 p.Ala57Val (c.170C>T) in the general population?

APBA2 p.Ala57Val (c.170C>T) is rare (popmax 0.175%, amr) (gnomAD).

What do computational predictors say about APBA2 p.Ala57Val (c.170C>T)?

AlphaMissense predicts likely benign (score 0.0609) — an in-silico prediction, not a clinical call.

APBA2 p.Ala57Val

c.170C>T · rs141358568 · VCV3036076

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0609 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.175%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0609	likely benign
REVEL	0.047	moderately benign-leaning
SaProt	LLR -6.24	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	GERP -2.1
Overall
CADD	7.281	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 0.175% Admixed American · 105/60,028 alleles

Filtering AF 0.148% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.138%

Overall 0.0693% 1,118/1,613,878 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.175%	572
European (non-Finnish)	0.0794%	1,259
Remaining individualsnot grpmax-eligible	0.0624%	1,602
African / African-American	0.0386%	2,588
Middle Eastern	0.0171%	5,836
Finnishnot grpmax-eligible	0.00937%	10,670
South Asian	0.0011%	91,068

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.Ala57Val
Coding: c.170C>T
MANE Select: NM_001353788
dbSNP: rs141358568
Type: single nucleotide variant
Location: chr15:29054054 (GRCh38)
Gene constraint: LOEUF 0.524 · pLI 0.78 (gnomAD)
Structure: AlphaFold pLDDT 59.74
Residue 57: the 'disordered' region

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

Similar variants

APBA2 p.Ala57Thr Likely benign ★ same residue
APBA2 p.Val77Met Uncertain significance ★★ ⚠ same type
APBA2 c.1216-9T>C Benign ★★ same type
APBA2 c.1525-8C>G Likely benign ★★ same type
APBA2 c.1705-9C>T Benign ★★ same type
APBA2 p.Asp87= Benign ★★ same type
APBA2 p.Gly206= Benign ★★ same type
APBA2 p.His127= Benign ★★ 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/apba2-p-ala57val (accessed [today's date]).

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