Case10: Patient LeM (found in the GT database) gender and age are not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000979, HP:0000967 (Purpura/petechiae)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: <5% of normal expression

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

Variant: NM_000419.3:c.1366_1371del

LegacyVariant: N/A

ClinVar: 2898

CAiD: CA8603160

gnomAD: MAF in the European (non-Finnish) population is 0.000008791 https://gnomad.broadinstitute.org/variant/17-42458268-TGTCTAC-T

PreviouslyPublished: Reference number 21 in this article

Case#: 19 years (report), male, Italian

CasePresentingHPOs: HP:0002240, HP:0002329, HP:0002919, HP:0003738, HP:0001324, HP:0006852, HP:0001069, HP:0000980, HP:0003648, HP:0001513, HP:0002910, HP:0003124, HP:0002155, HP:0002151, HP:0008344

HPOFreeText: Infancy: hepatomegaly, episodes of drowsiness, ketonuria. 3 years: muscle pain, weakness, perioral cyanosis during physical activity. 4.5 years: episode of lethargy, hypotonia, sweating, pallor after fasting. Cytolysis, mild acidosis, ketonuria. Urinary lactic aciduria and mildly elevated alpha-keto acids. Enlarged and hyperechogenic liver with swollen hypatocytes with centrally placed nuclei, vacuolated cytoplasm, PAS-positive cytoplasmic glycogen deposits. 15 years: myalgia, exertional fatigue, numbness/weakness of lower limbs. 17 years: obesity, hepatomegaly, muscle weakness, worsening exertional fatigue. Intermittent hyperckemia, increase of LDH, elevated transaminases and gamma-GT, mild hypercholesterolemia, hypertrigylceridemia. Elevated blood lactate, plasma BCAAs, increased secretion of lactate, pyruvate, alpha-ketoglutarate, and branched chain alpha-hydroxy and alpha keto-acids. Responsive to riboflavin supplementation.

NotHPOs: Normal blood ammonia and creatine kinase. Brain CT scan and MRI normal.

CasePreviousTesting: 4.5 years: cytolysis (ASAT 199/ALAT 209 UI/L; nv < 40), mild acidosis (base excess -7.6). 17 years: hyperckemia (20x), LDL (10x), ASAT 60/ALAT137, gamma-GT (70-80 UI/L; nv < 40), blood lactate (1.5-6.0 mmol/L; nv < 1.2), valine (479 mmol/L, nv 150-320), isoleucine (146 mmol/L, nv 30-100), leucine (307 mmol/L, nv 50-190), alloisoleucine (2-13 mmol/L, nv 0).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Coding exons and exon-intron boundaries of nuclear-encoded DLD were PCR amplified followed by bidirectional sequencing. Mutations confirmed in family members.

Variant: 1. NM_000108.4(DLD):c.118+1G>T 2. NM_000108.4(DLD):c.1382G>A (p.Gly461Glu)

ClinVar: 1. 557660 2. 203685

**gnomAD: **

VariantEvidence: For the splice site mutation, RNA was extracted from fibroblasts and RT-PCR was performed. Variant causes skipping of exon 2 and predicts a frameshift resulting in truncated protein.For the missense variant, molecular modeling predicts an inability of E3 to homodimerize.

CaseAddInfo: Variants confirmed in trans. Western blot in muscle biopsy shows ~97% reduction. Muscle biopsy also showed mitochondrial proliferation with increased SDH and COX staining with absence of COX negative fibers. Enzymatic activities of PDHc, KGDHc, and BCKDHc in isolated fibroblast mitochondria were reduced (experimental evidence).

Case#: Male, 3 days (onset)

CasePresentingHPOs: HP:0001250, HP:0002791, HP:0002240, HP:0001943, HP:0001942, HP:0002151, HP:0011968, HP:0003128, HP:0000648

HPOFreeText: 3 days: seizures, hypoventilation, circulatory failure, hepatomegaly, hypoglycemia, metabolic acidosis, elevated lactate. 2 months: poor feeding, somnolence, liver was normal. Developed lactic acidosis in hospital. Increased alanine, alpha-aminobutyrate, leucine, isoleucine, valine, glycine, threonine, methionine, mildy increased phenylalanine, cystathionine, cysteine, histidine. Urine analysis: increased lactic, pyruvic, and alpha-keto- and/or alpha-hydroxy-isovaleric, isocaproic, butyric, and glutaric acids. 15 months: head small (7th percentile), delayed development, progressive optic atrophy. Died at 5.5 years following acute illness.

CaseNotHPOs:

CasePreviousTesting: 3 days: metabolic acidosis (pH 7.05), and elevated lactate (12.8 mM, normal: 0.6–2.5). 2 months: lactic acidosis (10-16 mM). Increased alanine (1348 μM; normal: 132–455), α-aminobutyrate (106 μM; normal: 4–24), leucine (300 μM; normal: 61–183), isoleucine (120 μM; normal: 27–80), valine (345 μM; normal: 78–142), glycine (553 μM; normal 106–254), threonine (236 μM; normal: 65–147), methionine (151 μM; normal: 6–36).

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod: E3 cDNA prepared by RT-PCR from fibroblasts of proband and parents. For proband's E3 cDNA anlaysis, 1.5kb fragment was isolated from agarose gel and transformed into E. coli, followed by sequencing of the entire E3 cDNA. Direct sequencing was performed with genomic DNA to confirm variants in proband and parents.

Variant: 1. NM_000108.4(DLD):c.1123G>A (p.Glu375Lys); 2. NM_000108.4:c.405_407del (p.Gly136del)

ClinVar: 1. 11971

CAID: 2. CA891842420

gnomAD: 1. MAF (Ashkenazi Jewish): 0.002219 (23/10366); 2. Not in gnomAD

VariantEvidence: In vitro and in vivo functional studies for the missense variant show reduced enzyme activity compared to wild type (Ambrus et al., 2011; Vaubel et al., 2011).

CaseAddInfo: E3 activity in blood lymphocytes and fibroblasts were 9% ad 3% respectively; PDC activity was 13% of controls; KGDC activity was 6% of controls. Protein levels were not changed.

Case#: Male, 3 days (onset)

CasePresentingHPOs: HP:0001250, HP:0002791, HP:0002240, HP:0001943, HP:0001942, HP:0002151, HP:0011968, HP:0003128, HP:0000648

HPOFreeText: 3 days: seizures, hypoventilation, circulatory failure, hepatomegaly, hypoglycemia, metabolic acidosis, elevated lactate. 2 months: poor feeding, somnolence, liver was normal. Developed lactic acidosis in hospital. Increased alanine, alpha-aminobutyrate, leucine, isoleucine, valine, glycine, threonine, methionine, mildy increased phenylalanine, cystathionine, cysteine, histidine. Urine analysis: increased lactic, pyruvic, and alpha-keto- and/or alpha-hydroxy-isovaleric, isocaproic, butyric, and glutaric acids. 15 months: head small (7th percentile), delayed development, progressive optic atrophy. Died at 5.5 years following acute illness.

CaseNotHPOs:

CasePreviousTesting: 3 days: metabolic acidosis (pH 7.05), and elevated lactate (12.8 mM, normal: 0.6–2.5). 2 months: lactic acidosis (10-16 mM). Increased alanine (1348 μM; normal: 132–455), α-aminobutyrate (106 μM; normal: 4–24), leucine (300 μM; normal: 61–183), isoleucine (120 μM; normal: 27–80), valine (345 μM; normal: 78–142), glycine (553 μM; normal 106–254), threonine (236 μM; normal: 65–147), methionine (151 μM; normal: 6–36).

CaseMethod1:

CaseMethod2:

CaseGenotypingMethod: E3 cDNA prepared by RT-PCR from fibroblasts of proband and parents. For proband's E3 cDNA anlaysis, 1.5kb fragment was isolated from agarose gel and transformed into E. coli, followed by sequencing of the entire E3 cDNA. Direct sequencing was performed with genomic DNA to confirm variants in proband and parents.

Variant: 1. NM_000108.4(DLD):c.1123G>A (p.Glu375Lys); 2. NM_000108.4:c.405_407del (p.Gly136del)

ClinVar: 1. 11971

CAID: 2. CA891842420

gnomAD: 1. MAF (Ashkenazi Jewish): 0.002219 (23/10366); 2. Not in gnomAD

VariantEvidence: In vitro and in vivo functional studies for the missense variant show reduced enzyme activity compared to wild type (Ambrus et al., 2011; Vaubel et al., 2011).

CaseAddInfo: E3 activity in blood lymphocytes and fibroblasts were 9% ad 3% respectively; PDC activity was 13% of controls; KGDC activity was 6% of controls. Protein levels were not changed.