Is MT-TC m.5800A>G pathogenic?

MT-TC m.5800A>G is classified Likely benign in MT-TC (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-12). GnomAD v4.1's mitochondrial callset is not in our release; Associated with MELAS syndrome.

What condition is associated with MT-TC m.5800A>G?

MT-TC m.5800A>G is associated with MELAS syndrome (ClinVar).

How is MELAS inherited?

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

MT-TC m.5800A>G

Q: How common is MT-TC m.5800A>G in the general population?

MT-TC m.5800A>G is gnomAD v4.1's mitochondrial callset is not in our release (gnomAD).

rs1603220125 · VCV689995

Likely benign Single submitter

Classification

Likely 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

MELAS 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-TC
Mitochondrial: m.5800A>G
dbSNP: rs1603220125
Type: single nucleotide variant
Location: chrMT:5800 (GRCh38)

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

Disease context

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

For MELAS (Orphanet):

Inheritance: Mitochondrial (maternal)
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 1 000 000 (Japan)

Similar variants

MT-TC m.5816A>G Uncertain significance ★★★ same condition
MT-TC m.5814T>C Likely benign ★★★ same condition
MT-TC m.5791G>A Uncertain significance ★ same condition
MT-TC m.5793A>G Uncertain significance ★ same condition
MT-TC m.5802T>C Uncertain significance ★ same condition
MT-TC m.5804A>G Uncertain significance ★ same condition
MT-TC m.5809G>A Uncertain significance ★ same condition
MT-TC m.5819T>C Uncertain significance ★ 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-tc-m-5800a-g (accessed [today's date]).

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