Is AGAP2 p.Gln598= (c.1794G>A) pathogenic?

AGAP2 p.Gln598= (c.1794G>A) is classified Likely benign in AGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-07-12). Very rare (popmax 0.00402%, afr); Associated with AGAP2-related disorder.

What condition is associated with AGAP2 p.Gln598= (c.1794G>A)?

AGAP2 p.Gln598= (c.1794G>A) is associated with AGAP2-related disorder (ClinVar).

How common is AGAP2 p.Gln598= (c.1794G>A) in the general population?

AGAP2 p.Gln598= (c.1794G>A) is very rare (popmax 0.00402%, afr) (gnomAD).

AGAP2 p.Gln598=

c.1794G>A · rs551915207 · VCV3049551

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00402%, afr)

Conditions

AGAP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.136	moderately benign-leaning
Splicing
SpliceAI	Δ0.20	donor gain · deltas
Constraint at this position
Conservation	phyloP 6	GERP 1.6, phastCons 1
Overall
CADD	22.0	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00402% African / African-American · 3/74,670 alleles

Filtering AF 0.00123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00105%

Overall 0.00157% 25/1,594,762 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00402%	24,890
European (non-Finnish)	0.00188%	53,167

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: AGAP2
Protein: p.Gln598=
Coding: c.1794G>A
MANE Select: NM_001122772
dbSNP: rs551915207
Type: single nucleotide variant
Location: chr12:57732403 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 60.04 · 3 PDB
Residue 598: the 'disordered' region

Full AGAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

AGAP2-related disorder

Similar variants

AGAP2 p.Gly462Arg Uncertain significance ★ same condition
AGAP2 p.Val881Ala Uncertain significance ★ same condition
AGAP2 p.Arg984Leu Uncertain significance same condition
AGAP2 p.Ala11Val Likely benign same condition
AGAP2 p.Glu438Gln Benign same condition
AGAP2 p.Gly507Ser Likely benign same condition
AGAP2 p.His1096= Likely benign same condition
AGAP2 p.Leu582= 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/agap2-p-gln598 (accessed [today's date]).

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