Is AGAP2 p.Pro129= (c.387C>T) pathogenic?

AGAP2 p.Pro129= (c.387C>T) is classified Likely benign in AGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-20). Rare (popmax 0.206%, eas); Associated with AGAP2-related disorder.

What condition is associated with AGAP2 p.Pro129= (c.387C>T)?

AGAP2 p.Pro129= (c.387C>T) is associated with AGAP2-related disorder (ClinVar).

How common is AGAP2 p.Pro129= (c.387C>T) in the general population?

AGAP2 p.Pro129= (c.387C>T) is rare (popmax 0.206%, eas) (gnomAD).

AGAP2 p.Pro129=

c.387C>T · rs932350430 · VCV3058368

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.206%, eas)

Conditions

AGAP2-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 -4	GERP -2.4
Overall
CADD	5.527	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.206% East Asian · 77/37,356 alleles

Filtering AF 0.169% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.155%

Overall 0.00538% 78/1,451,066 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.206%	485
Remaining individualsnot grpmax-eligible	0.00179%	55,864

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.Pro129=
Coding: c.387C>T
MANE Select: NM_001122772
dbSNP: rs932350430
Type: single nucleotide variant
Location: chr12:57737860 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 60.04 · 3 PDB
Residue 129: 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.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-pro129 (accessed [today's date]).

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