Is GARS1 p.Ala58Pro (c.172G>C) pathogenic?

GARS1 p.Ala58Pro (c.172G>C) is classified Uncertain significance in GARS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-06). AlphaMissense: likely benign (0.0826); Very rare (popmax 0.00236%, sas); Associated with Charcot-Marie-Tooth disease type 2.

What condition is associated with GARS1 p.Ala58Pro (c.172G>C)?

GARS1 p.Ala58Pro (c.172G>C) is associated with Charcot-Marie-Tooth disease type 2 (ClinVar).

How common is GARS1 p.Ala58Pro (c.172G>C) in the general population?

GARS1 p.Ala58Pro (c.172G>C) is very rare (popmax 0.00236%, sas) (gnomAD).

What do computational predictors say about GARS1 p.Ala58Pro (c.172G>C)?

AlphaMissense predicts likely benign (score 0.0826) — an in-silico prediction, not a clinical call.

GARS1 p.Ala58Pro

c.172G>C · VCV3707584

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0826 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00236%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Charcot-Marie-Tooth disease type 2

Computational evidence

Protein change
AlphaMissense	0.0826	likely benign
REVEL	0.226	benign-leaning
SaProt	LLR -8.21	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 0.74	GERP -0.65, phastCons 0.92
Regional constraint	o/e 1.12	unconstrained · MANE · 5,108 bp · p 0.097 · regional, not allelic
Overall
CADD	14.39	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 0.00236% South Asian · 2/84,802 alleles

Filtering AF 0.000392% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000147%

Overall 0.000144% 2/1,391,560 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: GARS1
Protein: p.Ala58Pro
Coding: c.172G>C
MANE Select: NM_002047
Type: single nucleotide variant
Location: chr7:30595093 (GRCh38)
Gene constraint: LOEUF 0.648 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.61 · 14 PDB

Full GARS1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Charcot-Marie-Tooth disease type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GARS1 p.Ala58= Likely benign ★★ same residue
GARS1 p.Asp200Asn Pathogenic/Likely pathogenic ★★ same condition
GARS1 p.Gly294Arg Pathogenic/Likely pathogenic ★★ same condition
GARS1 p.Gly339Arg Pathogenic/Likely pathogenic ★★ same condition
GARS1 p.His472Arg Pathogenic ★★ same condition
GARS1 p.Ile334Asn Pathogenic/Likely pathogenic ★★ same condition
GARS1 p.Ile334Phe Pathogenic ★★ same condition
GARS1 p.Ile334Thr Pathogenic/Likely pathogenic ★★ 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/gars1-p-ala58pro (accessed [today's date]).

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