Is DARS2 p.Ala392fs (c.1173_1179del) pathogenic?

DARS2 p.Ala392fs (c.11731179del) is classified Pathogenic/Likely pathogenic in DARS2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-01-22). Very rare (popmax 0.005%, amr); Associated with leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome.

How common is DARS2 p.Ala392fs (c.1173_1179del) in the general population?

DARS2 p.Ala392fs (c.1173_1179del) is very rare (popmax 0.005%, amr) (gnomAD).

DARS2 p.Ala392fs

Q: What condition is associated with DARS2 p.Ala392fs (c.1173_1179del)?

DARS2 p.Ala392fs (c.1173_1179del) is associated with leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome (ClinVar).

Q: How is Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1173_1179del · rs770447116 · VCV1324208

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Conditions

leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome

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 12 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.9	GERP -0.64, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.005% Admixed American · 3/60,002 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.000206% 3/1,459,176 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: DARS2
Protein: p.Ala392fs
Coding: c.1173_1179del
MANE Select: NM_018122
dbSNP: rs770447116
Type: Deletion
Location: chr1:173845272 (GRCh38)
Gene constraint: LOEUF 0.923 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.91 · 1 PDB

Full DARS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal

Similar variants

DARS2 p.Gly365fs Likely pathogenic ★★ same condition
DARS2 p.Gly467fs Pathogenic ★★ same condition
DARS2 p.Leu187fs Pathogenic/Likely pathogenic ★★ same condition
DARS2 p.Lys362fs Pathogenic/Likely pathogenic ★★ same condition
DARS2 p.Pro317fs Pathogenic/Likely pathogenic ★★ same condition
DARS2 c.228-10del Benign ★★ same condition
DARS2 c.664-17_664-14del Likely benign ★★ same condition
DARS2 c.294+2_294+7del 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/dars2-p-ala392fs (accessed [today's date]).

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