Is AP2A2 p.Gly679Ser (c.2035G>A) pathogenic?

AP2A2 p.Gly679Ser (c.2035G>A) is classified Uncertain significance in AP2A2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-08-26). AlphaMissense: likely benign (0.068); Ultra-rare (popmax 0.0846%, afr).

How common is AP2A2 p.Gly679Ser (c.2035G>A) in the general population?

AP2A2 p.Gly679Ser (c.2035G>A) is ultra-rare (popmax 0.0846%, afr) (gnomAD).

What do computational predictors say about AP2A2 p.Gly679Ser (c.2035G>A)?

AlphaMissense predicts likely benign (score 0.068) — an in-silico prediction, not a clinical call.

AP2A2 p.Gly679Ser

c.2035G>A · rs570397060 · VCV2459287

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.068 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0846%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.068	likely benign
REVEL	0.02	moderately benign-leaning
SaProt	LLR -5.87	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 1.1	GERP -2.6, phastCons 0.45
Regional constraint	o/e 1.16	unconstrained · MANE · 6,363 bp · p 0.14 · regional, not allelic
Overall
CADD	7.848	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 0.0846% African / African-American · 62/73,310 alleles

Filtering AF 0.0677% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0616%

Overall 0.00526% 81/1,540,892 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0846%	1,182
Remaining individualsnot grpmax-eligible	0.0133%	7,507
Admixed American	0.00779%	12,837
South Asian	0.00119%	84,160
European (non-Finnish)	0.000523%	191,352

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: AP2A2
Protein: p.Gly679Ser
Coding: c.2035G>A
MANE Select: NM_012305
dbSNP: rs570397060
Type: single nucleotide variant
Location: chr11:1000510 (GRCh38)
Gene constraint: LOEUF 0.437 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.30
Residue 679: the 'disordered' region

Full AP2A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AP2A2 p.Ala136Ser Uncertain significance ★ ⚠ same type
AP2A2 p.Ala136Thr Uncertain significance ★ ⚠ same type
AP2A2 p.Ala168Thr Uncertain significance ★ ⚠ same type
AP2A2 p.Ala274Pro Uncertain significance ★ ⚠ same type
AP2A2 p.Ala304Val Uncertain significance ★ ⚠ same type
AP2A2 p.Ala375Thr Uncertain significance ★ ⚠ same type
AP2A2 p.Ala3Val Uncertain significance ★ ⚠ same type
AP2A2 p.Ala435Val 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/ap2a2-p-gly679ser (accessed [today's date]).

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