Is MT-ND5 m.12400A>G pathogenic?

MT-ND5 m.12400A>G is classified Benign in MT-ND5 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-17). GnomAD v4.1's mitochondrial callset is not in our release; Associated with Leigh syndrome.

What condition is associated with MT-ND5 m.12400A>G?

MT-ND5 m.12400A>G is associated with Leigh syndrome (ClinVar).

How is Leigh syndrome inherited?

Typically Mitochondrial (maternal) (Orphanet). A genetic counselor can assess individual risk for a family.

MT-ND5 m.12400A>G

Q: How common is MT-ND5 m.12400A>G in the general population?

MT-ND5 m.12400A>G is gnomAD v4.1's mitochondrial callset is not in our release (gnomAD).

rs201405598 · VCV693433

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

gnomAD v4.1's mitochondrial callset is not in our release

Conditions

Leigh syndrome

Computational evidence

Protein change
AlphaMissense does not cover mitochondrial-encoded proteins.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Non-coding constraint	—	not assessed · autosomes only, so chrMT has no window · absence ≠ unconstrained

Population frequency

gnomAD v4.1 · exomes + genomes

GnomAD v4.1's mitochondrial callset is not in our release. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MT-ND5
Mitochondrial: m.12400A>G
dbSNP: rs201405598
Type: single nucleotide variant
Location: chrMT:12400 (GRCh38)
Structure: AlphaFold pLDDT 92.67 · 7 PDB

Full MT-ND5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Leigh syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Leigh syndrome (Orphanet):

Inheritance: Mitochondrial (maternal)
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

MT-ND5 m.13513G>A Pathogenic ★★★ same condition
MT-ND5 m.13514A>G Likely pathogenic ★★★ same condition
MT-ND5 p.Phe124Leu Likely pathogenic ★★★ same condition
MT-ND6 m.14459G>A Pathogenic ★★★ same condition
MT-ND5 m.12544A>G Uncertain significance ★★★ same condition
MT-ND5 m.13063G>A Uncertain significance ★★★ same condition
MT-ND5 m.12811T>C Benign ★★★ same condition
MT-ND5 m.13528A>G Likely benign ★★★ 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/mt-nd5-m-12400a-g (accessed [today's date]).

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