Is GARS1 p.Ser232Phe (c.695C>T) pathogenic?

GARS1 p.Ser232Phe (c.695C>T) is classified Uncertain significance in GARS1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-20). AlphaMissense: likely benign (0.2993); Very rare (popmax 0.00133%, afr); Associated with Charcot-Marie-Tooth disease type 2.

What condition is associated with GARS1 p.Ser232Phe (c.695C>T)?

GARS1 p.Ser232Phe (c.695C>T) is associated with Charcot-Marie-Tooth disease type 2 (ClinVar).

How common is GARS1 p.Ser232Phe (c.695C>T) in the general population?

GARS1 p.Ser232Phe (c.695C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about GARS1 p.Ser232Phe (c.695C>T)?

AlphaMissense predicts likely benign (score 0.2993) — an in-silico prediction, not a clinical call.

GARS1 p.Ser232Phe

c.695C>T · rs1791422922 · VCV1957973

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2993 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Charcot-Marie-Tooth disease type 2

Computational evidence

Protein change
AlphaMissense	0.2993	likely benign
REVEL	0.432	indeterminate
SaProt	LLR -14.38	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 34 kb · p 2.2e-07 · regional, not allelic
Overall
CADD	28.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,046 alleles

Overall 6.2e-05% 1/1,613,888 alleles · very rare exomes 1/1,461,588 · genomes 0/152,300 · joint denominator

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.Ser232Phe
Coding: c.695C>T
MANE Select: NM_002047
dbSNP: rs1791422922
Type: single nucleotide variant
Location: chr7:30603532 (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.Ser232fs Uncertain significance ★ 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-ser232phe (accessed [today's date]).

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