Is AGAP1 p.Ala797= (c.2391C>T) pathogenic?

AGAP1 p.Ala797= (c.2391C>T) is classified Likely benign in AGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-12). Ultra-rare (popmax 0.0721%, afr).

How common is AGAP1 p.Ala797= (c.2391C>T) in the general population?

AGAP1 p.Ala797= (c.2391C>T) is ultra-rare (popmax 0.0721%, afr) (gnomAD).

AGAP1 p.Ala797=

c.2391C>T · rs149073997 · VCV2150710

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0721%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.055	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.068	GERP 0.67, phastCons 0.91
Overall
CADD	9.039	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0721% African / African-American · 54/74,886 alleles

Filtering AF 0.0567% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0512%

Overall 0.00347% 56/1,613,252 alleles · ultra-rare exomes 27/1,461,076 · genomes 29/152,176 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0721%	1,387
Remaining individualsnot grpmax-eligible	0.0032%	31,214

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: AGAP1
Protein: p.Ala797=
Coding: c.2391C>T
MANE Select: NM_001037131
dbSNP: rs149073997
Type: single nucleotide variant
Location: chr2:236123939 (GRCh38)
Gene constraint: LOEUF 0.366 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 72.01 · 2 PDB

Full AGAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AGAP1 p.Ala418Ser Uncertain significance ★★ ⚠ same type
AGAP1 p.Ala52Ser Uncertain significance ★★ ⚠ same type
AGAP1 p.Ala570Gly Uncertain significance ★★ same type
AGAP1 p.Ala809Ser Uncertain significance ★★ ⚠ same type
AGAP1 p.Arg14Trp Uncertain significance ★★ ⚠ same type
AGAP1 p.Arg313His Uncertain significance ★★ ⚠ same type
AGAP1 p.Arg696Trp Uncertain significance ★★ ⚠ same type
AGAP1 p.Arg770Cys 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/agap1-p-ala797 (accessed [today's date]).

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