Case1: Male, 5 years onset, African

CasePresentingHPOs: HP:0410020, HP:0003750, HP:0030234 (Fish odor, Muscle fatigue, Highly elevated creatine phosphokinase)

HPOsFreeText: Increased fish odor under stress or effort, Elevated plasma creatine kinase (1066 U/L; reference 30–270), Riboflavin (10 mg/day) had no effect, High N,N-dimethylglycine in urine (449 mmol DMG/mol; over 20x normal)

CaseNotHPOs: HP:0001249, HP:0040126, HP:0003138, HP:0040087, HP:0010919, HP:0010901, HP:0003614, HP:0001871, HP:0001410 (Intellectual disability, Abnormal serum cobalamin level, Increased blood urea nitrogen, Abnormal serum folate, Abnormality of homocysteine metabolism, Abnormality of methionine metabolism, Trimethylaminuria, Hematological abnormality, Liver dysfunction)

NotHPOsFreeText: Normal serum cobalamin (222 pmol/L; reference 150–400) and urea (5 mmol/L; reference 2.5–7.5), Normal plasma folate (9.7 nmol/L; reference 4–15) and homocysteine (12 μmol/L; reference 8–18)

CasePMIDs: 10767172, 10102904

CaseAddInfo: Consanguinity of the parents is unknown, Brothers, sisters, and the two sons of the patient were without signs or symptoms, Patient is homozygous for this mutation

CasePreviousTesting: Nuclear magnetic resonance (NMR) spectroscopy, Conventional metabolic screening techniques, Gas chromatography (GC) analysis, Analysis of the very-long-chain fatty acids and a carnitine ester profile in serum, Amino acid and organic acid analyses of blood and urine

CaseGenotypingMethod: cDNA was prepared from the patient and control fibroblast cultures. PCR amplification was performed and the DMGDH gene was sequenced. After the mutation was confirmed, the area around it was again amplified and sequenced.

Variant: NM_013391.3:c.326A>G (p.His109Arg)

ClinVar: 4742 https://www.ncbi.nlm.nih.gov/clinvar/variation/4742/

gnomAD: African 4.737e-3, Overall 5.205e-4 https://gnomad.broadinstitute.org/variant/5-78351682-T-C

Variant: NM_013391.3:c.326A>G (p.His109Arg)

VariantEvidence: The above variant was expressed in E coli through an expression vector and DMGDH activity was measured and purified for both the mutant and the wild-type. The flavination in the mutant protein showed a 2-fold decrease compared to the wild-type and the under-flavinated mutant revealed a 27-fold decrease in enzyme activity compared to the flavinated wild-type. Experiments with trypsin digestion also confirmed that the under-flavinated variants may be less stable than the wild-type enzyme.