Is AGAP2 p.Ala11Val (c.32C>T) pathogenic?

AGAP2 p.Ala11Val (c.32C>T) is classified Likely benign in AGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-05). Rare (popmax 0.58%, sas); Associated with AGAP2-related disorder.

What condition is associated with AGAP2 p.Ala11Val (c.32C>T)?

AGAP2 p.Ala11Val (c.32C>T) is associated with AGAP2-related disorder (ClinVar).

How common is AGAP2 p.Ala11Val (c.32C>T) in the general population?

AGAP2 p.Ala11Val (c.32C>T) is rare (popmax 0.58%, sas) (gnomAD).

AGAP2 p.Ala11Val

c.32C>T · rs201928942 · VCV3052503

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.58%, sas)

Conditions

AGAP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.102	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Overall
CADD	20.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.58% South Asian · 528/91,078 alleles

Filtering AF 0.539% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.523%

Overall 0.0605% 977/1,614,088 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.58%	172
Middle Eastern	0.0495%	2,021
European (non-Finnish)	0.0362%	2,763
Remaining individualsnot grpmax-eligible	0.0192%	5,209
African / African-American	0.00533%	18,755
Admixed American	0.00333%	30,011
East Asian	0.00223%	44,872

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.Ala11Val
Coding: c.32C>T
MANE Select: NM_001122772 · reported on NM_014770
dbSNP: rs201928942
Type: single nucleotide variant
Location: chr12:57742040 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 60.04 · 3 PDB
Residue 11: the 'interaction with epb41l1' region

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

Disease context

AGAP2-related disorder

Similar variants

AGAP2 p.Arg11Pro Uncertain significance ★ same residue
AGAP2 p.Gly462Arg Uncertain significance ★ same condition
AGAP2 p.Val881Ala Uncertain significance ★ same condition
AGAP2 p.Arg984Leu Uncertain significance same condition
AGAP2 p.Gln598= Likely benign same condition
AGAP2 p.Glu438Gln Benign same condition
AGAP2 p.Gly507Ser Likely benign same condition
AGAP2 p.His1096= Likely 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-ala11val (accessed [today's date]).

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