Is DARS2 p.Lys196Arg (c.587A>G) pathogenic?

DARS2 p.Lys196Arg (c.587A>G) is classified Benign in DARS2 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-25). AlphaMissense: likely benign (0.0764); Common (popmax 8.8%, afr) — too common for a highly-penetrant pathogenic allele; Associated with leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome.

What do computational predictors say about DARS2 p.Lys196Arg (c.587A>G)?

AlphaMissense predicts likely benign (score 0.0764) — an in-silico prediction, not a clinical call.

DARS2 p.Lys196Arg

Q: What condition is associated with DARS2 p.Lys196Arg (c.587A>G)?

DARS2 p.Lys196Arg (c.587A>G) is associated with leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome (ClinVar).

Q: How common is DARS2 p.Lys196Arg (c.587A>G) in the general population?

DARS2 p.Lys196Arg (c.587A>G) is common (popmax 8.8%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

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.587A>G · rs35515638 · VCV21547

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.0764 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 8.8%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

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

Computational evidence

Protein change
AlphaMissense	0.0764	likely benign
REVEL	0.224	benign-leaning
SaProt	LLR -6.57	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 2.3	GERP -1.8, phastCons 0.88
Regional constraint	o/e 0.87	unconstrained · MANE · 32 kb · p 0.00036 · regional, not allelic
Overall
CADD	15.62	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 8.8% African / African-American · 6,599/75,022 alleles

Filtering AF 8.62% ClinGen BA1/BS1 input FAF95, joint · FAF99 8.55%

Overall 0.454% 7,335/1,614,146 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	8.8%	11
Remaining individualsnot grpmax-eligible	0.534%	187
Admixed American	0.421%	237
Middle Eastern	0.248%	404
South Asian	0.0132%	7,590
European (non-Finnish)	0.0103%	9,672

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.Lys196Arg
Coding: c.587A>G
MANE Select: NM_018122
dbSNP: rs35515638
Type: single nucleotide variant
Location: chr1:173833470 (GRCh38)
Gene constraint: LOEUF 0.923 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.91 · 1 PDB
Residue 196: a UniProt-annotated variant site (in)

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 c.228-15C>A Pathogenic/Likely pathogenic ★★ same condition
DARS2 c.228-16C>A Pathogenic/Likely pathogenic ★★ same condition
DARS2 c.397-2A>G Pathogenic/Likely pathogenic ★★ same condition
DARS2 c.492+2T>C Pathogenic ★★ same condition
DARS2 c.493-1G>C Likely pathogenic ★★ same condition
DARS2 p.Ala262Val Likely pathogenic ★★ ⚠ same condition
DARS2 p.Arg179His Pathogenic/Likely pathogenic ★★ same condition
DARS2 p.Arg188Ter 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/dars2-p-lys196arg (accessed [today's date]).

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