Is AARS2 p.Ala740Pro (c.2218G>C) pathogenic?

AARS2 p.Ala740Pro (c.2218G>C) is classified Uncertain significance in AARS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-09). AlphaMissense: likely benign (0.1835); Very rare (popmax 0.000169%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with AARS2 p.Ala740Pro (c.2218G>C)?

AARS2 p.Ala740Pro (c.2218G>C) is associated with Cardiovascular phenotype (ClinVar).

How common is AARS2 p.Ala740Pro (c.2218G>C) in the general population?

AARS2 p.Ala740Pro (c.2218G>C) is very rare (popmax 0.000169%, nfe) (gnomAD).

What do computational predictors say about AARS2 p.Ala740Pro (c.2218G>C)?

AlphaMissense predicts likely benign (score 0.1835) — an in-silico prediction, not a clinical call.

AARS2 p.Ala740Pro

c.2218G>C · rs755023355 · VCV3895181

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1835 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000169%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.1835	likely benign
REVEL	0.179	moderately benign-leaning
SaProt	LLR -9.92	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 2.1, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 13 kb · p 0.00019 · regional, not allelic
Overall
CADD	20.6	PHRED · no single calibrated threshold — expert panels disagree

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

Grpmax group 0.000169% European (non-Finnish) · 2/1,180,050 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000124% 2/1,613,996 alleles · very rare

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: AARS2
Protein: p.Ala740Pro
Coding: c.2218G>C
MANE Select: NM_020745
dbSNP: rs755023355
Type: single nucleotide variant
Location: chr6:44303103 (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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AARS2 p.Ala740Thr Uncertain significance ★★ ⚠ same residue
AARS2 p.Ala740Val Uncertain significance ★★ ⚠ same residue
AARS2 p.Ala740= Likely benign ★ same residue
AARS2 p.Arg769Cys Uncertain significance ★★ ⚠ same condition
AARS2 p.His225Tyr Uncertain significance ★★ ⚠ same condition
AARS2 p.Ile224Leu Uncertain significance ★★ ⚠ same condition
AARS2 p.Ile766Ser Uncertain significance ★★ ⚠ same condition
AARS2 p.Leu118Val Uncertain significance ★★ ⚠ 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/aars2-p-ala740pro (accessed [today's date]).

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