Is MDH2 p.Lys74= (c.222A>G) pathogenic?

MDH2 p.Lys74= (c.222A>G) is classified Likely benign in MDH2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-27). Rare (popmax 0.43%, mid); Associated with Inborn genetic diseases.

What condition is associated with MDH2 p.Lys74= (c.222A>G)?

MDH2 p.Lys74= (c.222A>G) is associated with Inborn genetic diseases (ClinVar).

How common is MDH2 p.Lys74= (c.222A>G) in the general population?

MDH2 p.Lys74= (c.222A>G) is rare (popmax 0.43%, mid) (gnomAD).

MDH2 p.Lys74=

c.222A>G · rs769743658 · VCV1662161

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.43%, mid)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	phastCons 1
Overall
CADD	6.367	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.43% Middle Eastern · 26/6,044 alleles

Filtering AF 0.301% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.258%

Overall 0.0193% 312/1,613,468 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.43%	232
Admixed American	0.0568%	1,762
Ashkenazi Jewishnot grpmax-eligible	0.0507%	1,973
European (non-Finnish)	0.0189%	5,290
Remaining individualsnot grpmax-eligible	0.008%	12,499
South Asian	0.0066%	15,162
African / African-American	0.004%	24,999

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: MDH2
Protein: p.Lys74=
Coding: c.222A>G
MANE Select: NM_005918
dbSNP: rs769743658
Type: single nucleotide variant
Location: chr7:76054985 (GRCh38)
Gene constraint: LOEUF 0.984 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.49 · 7 PDB
Residue 74: a β-strand

Full MDH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MDH2 p.Lys74Asn Uncertain significance ★ ⚠ same residue
MDH2 p.Lys74Thr Uncertain significance ★ ⚠ same residue
MDH2 p.Ala135Gly Uncertain significance ★★ ⚠ same condition
MDH2 p.Ala141Thr Uncertain significance ★★ same condition
MDH2 p.Ala177Thr Uncertain significance ★★ ⚠ same condition
MDH2 p.Ala21Val Uncertain significance ★★ ⚠ same condition
MDH2 p.Ala242Val Uncertain significance ★★ ⚠ same condition
MDH2 p.Ala256Thr 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/mdh2-p-lys74 (accessed [today's date]).

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