Case1: Female, Anglo-Celtic, Birth onset

CasePresentingHPOs: HP:0001511, HP:0008872, HP:0025404, HP:0000737, HP:0010845, HP:0001263, HP:0001290, HP:0002059, HP:0012448, HP:0002079, HP:0002474, HP:0002421 (Intrauterine growth retardation, Feeding difficulties in infancy, Abnormal visual fixation, Irritability, EEG with genaralized slow activity, Developmental delay, Hypotonia, Cerebral atrophy, Delayed myelination, Thinning of the corpus callosum, Communication delay, Poor head control)

HPOsFreeText: Birth weight was 2160 g, Inability to follow with eyes at four months, EEG showed poorly modulated background, MRI showed markedly increased signals in the brain stem, upper pons, basal ganglia and thalami, Inability to sit unsupported

CaseNotHPOs: HP:0001250, HP:0001946 (Seizures, Ketosis)

NotHPOsFreeText: N/A

CaseAddInfo: Parents were not consanguineous, parental testing confirms in trans

CasePreviousTesting: Routine metabolic investigations at 4 months (plasma and CSF amino acids, urine amino and organic acids, transferrin isoforms, very long chain fatty acids) were uninformative, Increased excretion of SCPC, Increased levels of urine metabolites derived from methacrylate such as S-(2-carboxypropyl)cysteine (18,27 μmol/mmol of creatinine; reference <5.3), N-acetyl-S-(2-carboxypropyl)cysteine (30,42 μmol/mmol of creatinine; reference <4.2), S-(2-carboxypropyl)cysteine carnitine ester (5.8,5.3 μmol/mmol of creatinine; reference <1.0), and S-(2-carboxypropyl)cysteamine (13,16 μmol/mmol of creatinine; reference <10), Increased erythro-2,3-dihydroxy-2-methylbutyrate compared to controls, The coding region of the E1α gene was sequenced and was found normal

CaseGenotypingMethod: The HIBCH gene was sequenced after the metabolite testing. Other details were not described.

Variant1: NM_014362.4(HIBCH):c.1033G>A (p.Gly345Ser)

ClinVar: 208532 https://www.ncbi.nlm.nih.gov/clinvar/variation/208532/

gnomAD: European (Non-Finnish) 8.805e-6, Overall 3.982e-6 https://gnomad.broadinstitute.org/variant/2-191073618-C-T

Variant2: NM_014362.4(HIBCH):c.129dup (p.Gly44Argfs*20)

ClinVar: 208531 https://www.ncbi.nlm.nih.gov/clinvar/variation/208531/

gnomAD: South Asian 9.834e-5, Overall 1.597e-5 https://gnomad.broadinstitute.org/variant/2-191161628-C-CT

CaseIV-2: Female, 4 months onset, Lebanese

CasePresentingHPOs: HP:0002463, HP:0002376, HP:0001332, HP:0002510, HP:0002522, HP:0000648, HP:0011471, HP:0011968, HP:0001508, HP:0002453, HP:0007374, HP:0002518, HP:0007042, HP:0011931, HP:0012751, HP:0200147, HP:0000252, HP:0001141, HP:0000486, HP:0002300, HP:0002421, HP:0002540, HP:0008936, HP:0002509, HP:0040288, HP:0002650, HP:0002828, HP:0002827, HP:0010465, (Language impairment, Developmental regression, Dystonia, Spastic quadriplegia, Areflexia of lower limbs, Optic atrophy, Gastrostomy tube feeding in infancy, Poor feeding, Failure to thrive, Abnormality of the globus pallidus, Atrophy/Degeneration involving the caudate nucleus, Abnormality of the periventricular white matter, Focal white matter lesion, Abnormality of the cerebellar peduncle, Abnormal basal ganglia MRI signal intensity, Neuronal loss in basal ganglia, Microcephaly, Severe visual impairment, Strabismus, Mutism, Poor head control, Inability to walk, Truncal hypotonia, Limb hypertonia, Nasogastric tube feeding, Scoliosis, Multiple joint contractures, Hip dislocation, Precocious puberty in females,

HPOsFreeText: Normal early developmental milestones, Not able to bear weight, Unable to fix or follow, Intermittent roving eye movement,

CaseNotHPOs: HP:0000240, HP:0001999, HP:0025336, (Abnormality of head circumference, Dysmorphic facies, Delayed ability to sit,

NotHPOsFreeText:

CaseAddInfo: Parents are consanguinous (first cousins),

CasePreviousTesting: Elevated hydroxy-C4-carnitine at 0.88 μM for patient 1 (control < 0.3 μM).

CaseGenotypingMethod: Whole exome sequencing was performed on the proband's sibling, with all SNVs and variants detected called, investigated, and filtered for pathogenicity. Mitochondrial DNA mutation tests were negative, as well as a southern blot for deletions in the muscle. Sanger sequencing of SURF1, SCO1, SCO2, COX10, NDUFV1, NDUFS7, and PANK2 revealed no pathogenic mutation. The WES identified a homozygous variant in HIBCH that was orthogonally validated. PCR-based Sanger sequencing was performed on the proband and the parents to confirm the presence of the mutations and recessive inheritance.

Variant: NM_014362.3:c.196C>T (p.Arg66Trp)

ClinVar: 190268 https://www.ncbi.nlm.nih.gov/clinvar/variation/190268/

gnomAD: Latino 2.892e-5, Overall 1.193e-5 https://gnomad.broadinstitute.org/variant/2-191161562-G-A

Case1: Male, 3 months diagnosis/death, Egypt, African

CasePresentingHPOs: HP:0001999, HP:0011968, HP:0001531, HP:0001270, HP:0001252, HP:0003468, HP:0001636, HP:0001274 (Dysmorphic facial features, Poor feeding, Failure to thrive in infancy, Motor delay, Muscle hypotonia, Abnormal vertebrae, Tetraology of Fallot, Agenesis of corpus callosum)

HPOsFreeText: Agenesis of the cingulate gyrus

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: Parents are consanguinous, Proband is homozygous for this mutation, Died a few days after hospital admission in infancy

CasePreviousTesting: Increased levels of S-2-carboxypropyl-cysteamine and S-2-carboxypropyl-cysteine, Fibroblast and liver homogenates of patient 1 showed normal hydratase activities towards methacrylyl-CoA (as well as crotonyl-CoA and tiglyl-CoA),

CasePMIDs: 7122152

CaseGenotypingMethod: After confirming low HICBH activity in fibroblasts of the patients, the gene was analyzed at the genomic level and the mRNA level in both patients using sequence analysis.

Variant: NM_014362.3:c.220-9T>G

ClinVar: 1144 https://www.ncbi.nlm.nih.gov/clinvar/variation/1144/

gnomAD: Not in gnomAD

Case2: Male, Caucasian, 9 months onset

CasePresentingHPOs: HP:0011968, HP:0001270, HP:0001251, HP:0002376, HP:0002121, HP:0000737, HP:0002317, HP:0002599, HP:0002078, HP:0012389, HP:0001310, HP:0001337, HP:0001254, HP:0001942, HP:0002329, HP:0001308, HP:0002599, HP:0001332, HP:0002181, HP:0002134 (Poor feeding, Delayed motor milestones, Ataxia, Developmental regression, Absence seizures, Irritability, Unsteady gait, Head titubation, Truncal ataxia, Appendicular hypotonia, Dysmetria, Tremor, Lethargy, Metabolic acidosis, Drowsiness, Tongue fasciculation, Head titubation, Dystonia, Cerebral edema, Abnormality of the basal ganglia)

HPOsFreeText: Head bobbing at 4 months, Rolled over at 5 mo but lost the ability at 10 mo, Reaching out and grasping objects at 4 mo but lost the ability at 13 mo, Eye rolling episodes at 9 months, Lost ability to finger feed at 10 months, Inability to sit unsupported, At 14 months blood pH was 7.29 with a base deficit of 15.8 mmol/L, Sluggish papillary responses, Pooling of secretions in the mouth, No improvement on treatment with thiamine or a combination of vitamin C, vitamin E, and ubiquinone, Signal abnormalities in the globus pallidus and the midbrain

CaseNotHPOs: HP:0000639, HP:0002151, HP:0001987, HP:0003116, HP:0012443 (Nystagmus, Increased serum lactate, Hyperammonemia, Abnormal echocardiogram, Abnormality of brain morphology)

NotHPOsFreeText: N/A

CaseAddInfo: Parents were nonconsanguinous, Proband is compound heterozygous for these mutations with parental testing

CasePreviousTesting: Pyruvate dehydrogenase and pyruvate carboxylase in cultured human skin fibroblasts, Activities of respiratory chain complexes in a muscle biopsy, Marked reduction of complex I (patient 0.089, controls 0.104–0.268) and a borderline reduction of complex IV (patient 0.013, controls 0.014–0.034), Organic acid analysis during ketotic episodes showed excessive excretion of 3-hydroxybutyrate and acetoacetate and moderate excretion of lactate, 2-hydroxyisovalerate, 2-oxoisocaproate, dicarboxylic acids (C6, C8, C10), and methylmalonate, with normal levels of methylcitrate as opposed to normal levels when well, Urine amino acid analysis, Elevated levels of hydroxy-C4-carnitine (patient 0.45-1.73 μM, controls <0.4 μM) even when not ketotic

CaseGenotypingMethod: After confirming low HICBH activity in fibroblasts of the patients, the gene was analyzed at the genomic level and the mRNA level in both patients using sequence analysis.

Variant1: NM_014362.4:c.365A>G (p.Tyr122Cys)

ClinVar: 1145 https://www.ncbi.nlm.nih.gov/clinvar/variation/1145/

gnomAD: Latino 4.338e-4, Overall 6.373e-5 https://gnomad.broadinstitute.org/variant/2-191155151-T-C

Variant2: NM_014362.3:c.79-3C>G

ClinVar: 1146 https://www.ncbi.nlm.nih.gov/clinvar/variation/1146/

gnomAD: Not in gnomAD

Case1: Male, 15 months onset, Iran

CasePresentingHPOs: HP:0006579, HP:0001324, HP:0001336, HP:0000639, HP:0002134, HP:0002282, HP:0002453, HP:0002540, HP:0002463, HP:0006801, HP:0001252, HP:0011443, HP:0001251, HP:0001310, HP:0000565, HP:0001510 (Neonatal jaundice, Muscle weakness, Myoclonus, Nystagmus, Abnormality of the basal ganglia, Heterotopia, Abnormality of the globus pallidus, Inability to walk, Language impairment, Hyperactive deep tendon reflexes, Muscular hypotonia, Abnormality of coordination, Ataxia, Dysmetria, Esotropia, Growth delay)

HPOsFreeText:

CaseNotHPOs: HP:0012443, HP:0012447 (Abnormality of brain morphology, Abnormal myelination)

NotHPOsFreeText:

CaseAddInfo: No parental consanguinity,

CasePreviousTesting: Plasma amino acids and plasma acylcarnitine profile were normal. The organic acid in the urine showed an elevated 3‐hydroxyisovaleric acid (110 mmol/mol creatinine, normal <44 mmol/mol creatinine). Serum biotinidase activity was normal. Blood lactate and ammonia were normal in repeated measurements.

CaseGenotypingMethod: Patient had the IVD exons and exon-intron boundaries analyzed using PCR/Sanger sequencing to follow up on suspected IVA, with no variants found. Whole Exome Sequencing was performed to determine the correct genetic cause of the disorder by evaluating all known exons and their flanking regions. This found two heterozygous missense mutations in HIBCH consistent with the diagnosis. Trio PCR/Sanger sequencing confirmed parental heterozygosity and the variants in the patient.

Variant1: NM_014362.3:c.641C>T (p.Thr214Ile)

CAID: CA349890265 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_014362.3%3Ac.641C%3ET

gnomAD: Not in gnomAD

Variant2: NM_014362.3:c.913A>G (p.Thr305Ala)

CAID: CA62635843 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_014362.3%3Ac.913A%3EG

gnomAD: European (Non-Finnish) 1.767e-5, Overall 7.978e-6 https://gnomad.broadinstitute.org/variant/2-191077780-T-C

CaseII-2: Female, Japanese, 4 years death

CasePresentingHPOs: HP:0001290, HP:0001263, HP:0002453, HP:0004372, HP:0001942, HP:0045011, HP:0002339, HP:0002138, HP:0002795, HP:0007695, HP:0008000, HP:0001635, HP:0001942 (Generalized hypotonia, Developmental delay, Abnormality of the globus pallidus, Lowered consciousness, Metabolic acidosis, Decreased urine bicarbonate concentration, Abnormality of the caudate nucleus, Subarachnoid hemorrhage, Abnormal respiration, Abnormal pupillary light reflex, Decreased corneal reflex, Heart failure, Metabolic acidosis)

HPOsFreeText: Her birth weight was 2714 g, She measured 44 cm (− 2.6 SD) in length, Had an occipitofrontal circumference of 32.5 cm (− 0.5 SD), Could hold her head up at 5 months and roll over at 10 months, Febrile illness at 15 months, Required ventilator support, Absence of brain activity, Auditory brainstem response audiometry showed no response

CaseNotHPOs: HP:0009782, HP:0001250, HP:0001332 (Aplasia/Hypoplasia of the biceps, Seizures, Dystonia)

NotHPOsFreeText:

CaseAddInfo: Parents are nonconsanguineous, Older sister of patient II-2 who is also homozygous for the mutation and has the disorder, Parents are confirmed heterozygous for the mutation

CasePreviousTesting: Lactate and pyruvate levels in arterial blood (16.5 mg/dL and 1.48 mg/dL, respectively; normal range: 5–20 mg/dL and 0.3–0.9 mg/dL, respectively) and cerebrospinal liquor (13.5 mg/dL and 1.12 mg/dL, respectively; normal range: 9.1–18.8 mg/dL and 0.26–1.32 mg/dL, respectively) were almost normal, Arterial blood ketone bodies, pH, pCO2, and base excess were (8700 μmol/L; normal range: < 130 μmol/L), 7.051, 6.7 mm Hg, and − 26.9 mEq/L, respectively, CSF lactate at 1.5 (< 2.0 mmol/L reference)

CaseGenotypingMethod: Whole exome analysis was performed on the parents and the proband. Afterwards, genomic DNA was extracted from peripheral blood leukocytes and targeted sequences were amplified and sequenced. All SNVs and Indels were evaluated and filtered to confirm the mutations. Afterwards, after identifying the exon 4 mutation, a DNA segment was amplified via PCR and sequenced to confirm these findings.

Variant: NM_014362.3:c.287C>A (p.Ala96Asp)

CAID: CA349896230 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_014362.3%3Ac.287C%3EA

gnomAD: Not in gnomAD

Case1: Male, 3 months onset, Pakistan,

CasePresentingHPOs: HP:0002376, HP:0008947, HP:0001336, HP:0002197, HP:0002490, HP:0012240, HP:0002572, HP:0000737, HP:0002360, HP:0002453, HP:0002352, HP:0002283, HP:0001332, HP:0002871, HP:0000648, HP:0000365, HP:0000252 (Developmental regression, Infantile hypotonia, Myoclonic jerks, Generalized seizures, Increased CSF lactate, Increased muscle lipid droplets, Episodic vomiting, Irritability, Sleep disturbance, Abnormality of the globus pallidus, Leukoencephalopathy, Global brain atrophy, Dystonia, Central apnea, Optic atrophy, Hearing loss, Microcephaly)

HPOsFreeText: Born at term weighing 3.2 kg, Loss of smile

CaseNotHPOs: HP:0002151, HP:0003200, HP:0003688, HP:0010663, HP:0006846 (Increased serum lactate, Ragged-red fibres, Cytochrome C oxidase-negative muscle fibers, Abnormality of thalamus morphology, Acute encephalopathy)

NotHPOsFreeText: N/A

CaseAddInfo: Parents were distantly related, Died at 3 years, Has a younger brother with the same variant, Has a family history of neurological/neuromuscular disorders, Variant was confirmed by parental testing

CasePreviousTesting: At 8 months Nissen fundoplication was performed because of persistent vomiting, Mildly elevated CSF lactate at 2.2 mmol/l (reference range <2 mmol/l) at 8 months, with a normal venous blood lactate of 1.7 mmol/l (reference range < 1.8 mmol/l), Complex I at 0.068 (Reference; 0.104-0.268 ratio to citrate synthase activity), Complexes II + III at 0.010 (0.040-0.204 ratio to citrate synthase activity), Complex IV (COX) at 0.010 (0.014-0.034 ratio to citrate synthase activity)

CaseGenotypingMethod: Genomic DNA was extracted from skin fibroblasts. Exons and flanking intronic sequences of HIBCH was sequenced after PCR amplification. Sequence data was compared to the reference sequence and filtered for variants.

Variant: NM_014362.3:c.950G>A (p.Gly317Glu)

ClinVar: 187864 https://www.ncbi.nlm.nih.gov/clinvar/variation/187864/

gnomAD: Not in gnomAD

Case1: Male, 3 months onset, China, Asian

CasePresentingHPOs: HP:0011968, HP:0001290, HP:0001263, HP:0001508, HP:0000023, HP:0002793, HP:0004691, HP:0001999, HP:0000369, HP:0000218, HP:0000954, HP:0006802, HP:0100952, HP:0002079, HP:0002151, HP:0012736, HP:0002421 (Poor feeding, Generalized hypotonia, Psychomotor delay, Poor weight gain, Inguinal hernia, Abnormal pattern of respiration, 2-3 toe syndactyly, Dysmorphic facies, Low-set ears, High-arched palate, Transverse palmar crease, Abnormality of the anterior horn cells, Enlarged lateral sulcus, Thinning of the corpus callosum, Increased serum lactate, Profound global developmental delay, Poor head control)

HPOsFreeText: 3 kg birth weight, Breath-holding spells, The parameters at 5 months were as follows: weight, 4 kg (<0.4th percentile); length, 58 cm (<0.4th percentile), head circumference, 36.5 cm (<0.4th percentile), Enlarged anterior portion of bilateral ventricles and thinning surrounding whiter, Abnormal infant EEG

CaseNotHPOs: HP:0001946, HP:0003542, HP:0000364, HP:0003457 (Ketosis, Increased serum pyruvate, Hearing abnormality, EMG abnormality)

NotHPOsFreeText: N/A

CaseAddInfo: Parents are non-consanguineous, parental heterozygosity is confirmed, Both variants are predicted to destroy normal splicing sites and cause a null protein with Variant 1 skipping exon 4 and Variant 2 skipping exon 12

CasePreviousTesting: Mild elevation of hydroxyl-C4-carnitine (0.79; reference: 0.03–0.70), Normal venous blood lactate at 3 months (1.1 mmol/L; reference 0.44–1.78 mmol/L) and elevated at 5 months (3.2 mmol/L; reference: 1.42–1.90 mmol/L), Ketone and pyruvate levels at 5 months were normal, Karyotype analysis was performed to confirm normality. Low-coverage massively parallel CNV sequencing was used to confirm any copy number variation, which showed normal results.

CaseGenotypingMethod: Genomic DNA was extracted from lymphocytes and whole exome sequencing was performed. The identified variants were filtered for pathogenicity and confirmed via Sanger sequencing. cDNA sequence analysis was also performed to determine the effect of these variants on the protein.

Variant1: NM_014362.3:c.304+3A>G (p.=)

CAID: CA913203579 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203579

gnomAD: Not in gnomAD

Variant2: NM_014362.3:c.1010_1011+3delTGGTA

CAID: CA2027408 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_014362.3%3Ac.1010_1011%2B3delTGGTA

gnomAD: Not in gnomAD