Is AARS2 p.Gln798fs (c.2393del) pathogenic?

AARS2 p.Gln798fs (c.2393del) is classified Pathogenic in AARS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-16). Absent from gnomAD.

How common is AARS2 p.Gln798fs (c.2393del) in the general population?

AARS2 p.Gln798fs (c.2393del) is absent from gnomAD (gnomAD).

AARS2 p.Gln798fs

c.2393del · rs2534652321 · VCV2980940

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 18 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.36	GERP 0.85, phastCons 0.99

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AARS2
Protein: p.Gln798fs
Coding: c.2393del
MANE Select: NM_020745
dbSNP: rs2534652321
Type: Deletion
Location: chr6:44302485 (GRCh38)
Gene constraint: LOEUF 0.752 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.05 · 3 PDB

Full AARS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AARS2 p.Gln798Ter Likely pathogenic ★★ same residue
AARS2 p.Gln261fs Pathogenic/Likely pathogenic ★★ same type
AARS2 p.Gly647fs Pathogenic/Likely pathogenic ★★ same type
AARS2 p.Glu314del Uncertain significance ★★ same type
AARS2 c.(759+1_760-1 Likely pathogenic ★ same type
AARS2 p.Gln568fs Pathogenic ★ same type
AARS2 p.Glu314fs Pathogenic ★ same type
AARS2 p.Glu686fs 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/aars2-p-gln798fs (accessed [today's date]).

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