Is FARS2 p.Pro47fs (c.139_161del) pathogenic?

FARS2 p.Pro47fs (c.139161del) is classified Likely pathogenic in FARS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-07-28). Associated with FARS2-related disorder.

What condition is associated with FARS2 p.Pro47fs (c.139_161del)?

FARS2 p.Pro47fs (c.139_161del) is associated with FARS2-related disorder (ClinVar).

FARS2 p.Pro47fs

c.139_161del · VCV4973563

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

FARS2-related disorder

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 2 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.049	GERP -2.5

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

Variant & gene context

Gene: FARS2
Protein: p.Pro47fs
Coding: c.139_161del
MANE Select: NM_006567
Type: Deletion
Location: chr6:5368706 (GRCh38)
Gene constraint: LOEUF 1.015 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.17 · 9 PDB

Full FARS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

FARS2-related disorder

Similar variants

FARS2 p.Pro47Ser Uncertain significance ★★ ⚠ same residue
FARS2 p.Pro47= Likely benign ★ same residue
FARS2 p.Arg307Ter Pathogenic/Likely pathogenic ★★ same condition
FARS2 p.Thr156Met Pathogenic/Likely pathogenic ★★ ⚠ same condition
FARS2 p.Tyr144Cys Pathogenic ★★ same condition
FARS2 p.Ala170Val Uncertain significance ★ ⚠ same condition
FARS2 p.Asp265fs Pathogenic/Likely pathogenic ★★ same type
FARS2 p.Leu316fs Pathogenic/Likely 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/fars2-p-pro47fs (accessed [today's date]).

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