Is AGO2 p.Ser798Pro (c.2392T>C) pathogenic?

AGO2 p.Ser798Pro (c.2392T>C) is classified Uncertain significance in AGO2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-19). AlphaMissense: likely pathogenic (0.9985); Absent from gnomAD v4.1; Associated with AGO2-related disorder.

What condition is associated with AGO2 p.Ser798Pro (c.2392T>C)?

AGO2 p.Ser798Pro (c.2392T>C) is associated with AGO2-related disorder (ClinVar).

How common is AGO2 p.Ser798Pro (c.2392T>C) in the general population?

AGO2 p.Ser798Pro (c.2392T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AGO2 p.Ser798Pro (c.2392T>C)?

AlphaMissense predicts likely pathogenic (score 0.9985) — an in-silico prediction, not a clinical call.

AGO2 p.Ser798Pro

c.2392T>C · rs2540672241 · VCV2633636

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9985 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

AGO2-related disorder

Computational evidence

Protein change
AlphaMissense	0.9985	likely pathogenic · top 8% in AGO2
REVEL	0.664	pathogenic-leaning
SaProt	LLR -13.75	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 0.78, phastCons 1
Regional constraint	o/e 0.42	unconstrained · MANE · 25 kb · p 1.2e-55 · regional, not allelic
Overall
CADD	28.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: AGO2
Protein: p.Ser798Pro
Coding: c.2392T>C
MANE Select: NM_012154
dbSNP: rs2540672241
Type: single nucleotide variant
Location: chr8:140532495 (GRCh38)
Gene constraint: LOEUF 0.102 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 92.82 · 71 PDB
Residue 798: the 'interaction with guide rna' region; the piwi domain

Full AGO2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

AGO2-related disorder

Similar variants

AGO2 p.Thr738Ser Uncertain significance ★★ ⚠ same condition
AGO2 p.Met364Ile Likely pathogenic ★ ⚠ same condition
AGO2 p.Thr734Arg Likely pathogenic ★ same condition
AGO2 c.1404-5T>G Uncertain significance ★ same condition
AGO2 p.Lys241Arg Uncertain significance ★ ⚠ same condition
AGO2 p.Val450Met Uncertain significance ⚠ same condition
AGO2 c.337-3C>A Likely benign same condition
AGO2 p.Arg714Trp Pathogenic/Likely pathogenic ★★ 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/ago2-p-ser798pro (accessed [today's date]).

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