Is AARS2 p.Val586Met (c.1756G>A) pathogenic?

AARS2 p.Val586Met (c.1756G>A) is classified Uncertain significance in AARS2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-08-24). AlphaMissense: likely benign (0.1012); Ultra-rare (popmax 0.0546%, afr); Associated with Inborn genetic diseases.

What condition is associated with AARS2 p.Val586Met (c.1756G>A)?

AARS2 p.Val586Met (c.1756G>A) is associated with Inborn genetic diseases (ClinVar).

How common is AARS2 p.Val586Met (c.1756G>A) in the general population?

AARS2 p.Val586Met (c.1756G>A) is ultra-rare (popmax 0.0546%, afr) (gnomAD).

What do computational predictors say about AARS2 p.Val586Met (c.1756G>A)?

AlphaMissense predicts likely benign (score 0.1012) — an in-silico prediction, not a clinical call.

AARS2 p.Val586Met

c.1756G>A · rs201873561 · VCV379680

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1012 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0546%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1012	likely benign
REVEL	0.085	moderately benign-leaning
SaProt	LLR -7.35	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 2.2	GERP 2.2, phastCons 0.98
Regional constraint	o/e 0.90	unconstrained · MANE · 13 kb · p 0.00019 · regional, not allelic
Overall
CADD	18.46	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 0.0546% African / African-American · 41/75,042 alleles

Filtering AF 0.0413% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0367%

Overall 0.00874% 141/1,614,142 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0546%	1,830
Admixed American	0.0117%	8,575
Remaining individualsnot grpmax-eligible	0.0112%	8,930
European (non-Finnish)	0.0072%	13,882
South Asian	0.0011%	91,078

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.Val586Met
Coding: c.1756G>A
MANE Select: NM_020745
dbSNP: rs201873561
Type: single nucleotide variant
Location: chr6:44304530 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AARS2 p.Arg958Ter Pathogenic/Likely pathogenic ★★ same condition
AARS2 p.Met1Thr Likely pathogenic ★★ same condition
AARS2 p.Ala275Val Uncertain significance ★★ ⚠ same condition
AARS2 p.Ala37Thr Uncertain significance ★★ ⚠ same condition
AARS2 p.Ala566Thr Uncertain significance ★★ ⚠ same condition
AARS2 p.Ala737Gly Uncertain significance ★★ ⚠ same condition
AARS2 p.Ala741Thr Uncertain significance ★★ ⚠ same condition
AARS2 p.Ala9Ser 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-val586met (accessed [today's date]).

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