P5
Case5: Female, Chinese, 1.6 y (onset)
HPOsFreeText: 1.6 y onset
NotHPOsFreeText: Not responsive to vitamin B12
Case5 (Level 2):
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.1106G>A (p.Arg369His)
ClinVar: 203846
CAID: CA312764
gnomAD: 0.0001504 (East Asian)
CaseAddInfo: homozygous mutations, lost to follow up
P3
Case3: Female, Chinese, 4 mo (end of study)
HPOsFreeText: Responsive to vitamin B12
Case3 (Level 2):
CasePreviousTesting: NBS
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.599T>C (p.Ille200Thr)
ClinVar: n/a
CAID: CA364404381
gnomAD: n/a
CaseAddInfo: homozygous mutations, asymptomatic
P2
Case2: Male, Chinese, 3 mo (age at death)
HPOsFreeText: Neonatal onset
NotHPOsFreeText: Not responsive to vitamin B12
Case2 (Level 2):
CasePreviousTesting: NBS (newborn screening)
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.482G>T (p.Gly161Val)
ClinVar: n/a
CAID: CA364404636
gnomAD: n/a
CaseAddInfo: homozygous mutations, novel mutation
43 patients
GroupPresentingHPOs: HP:0001987, HP:0001942, HP:0003128, HP:0002912 (hyperammonemia, metabolic acidosis, lactic acidosis, methylmalonic acidemia)
HPOsFreeText: elevated blood levels of propionylcarnitine (C3) (median 13.56 umol/L), and elevated C3 to acetylcarnitine (C2) ratio (median 0.85). elevated urine methylmalonate levels (median 598.96 mmol/mol creatinine). 28/73.7% displayed recurrent vomiting (HP:0002572). 28/73.7% displayed disturbances of consciousness (HP:0004372). 23/60.5% displayed feeding difficulties in infancy (HP:0008872), 20/52.6% displayed respiratory distress (HP:0002098), 20/52.6% displayed failure to thrive (HP:0001508), 20/52.6% displayed dystonia (HP:0001332), 14/36.8% displayed mental retardation, 12/31.6% displayed convulsions.
GroupNotHPOs: normal plasma total homocysteine
NotHPOsFreeText:
NumberMales: 27
NumberFemales: 16
CountryOrigin: China
Ethnicity: Chinese
AgeRange: 33d- 10.3 y at last follow up
TotalNumber 43
FamilyInfo: 43
NoFamily: 0
GroupAddInfo: 9 identified by NBS, 34 recruited after being suspected of inherited metabolism disorders. 42 families from 14 provinces of the Mainland of China. 8 died during acute metabolic crisis, 7 lost to follow up, 28 alive at end of study.
Group (Level 2)
VariantCount: 43 (35 had two mutant alleles)
NonVariant: 0
OtherVariant: 0
GroupPreviousTesting: tandem mass spectrometry for blood levels, gas chromatography-mass spectrometry for urine,
GroupMethod1: PCR
GroupGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes from patients and their parents. Exonic and flanking intronic regions of the MUT gene were amplified through PCR. PCR products were sequenced directly using forward and reverse primers on ABI 3700 sequencer. Mutation analysis using MUT reference NM_000255.3. Nucleotide numbering reflects cDNA numbering (initiation codon= codon1). All detected mutations were confirmed in the patients' parents. Novel variants were screened in 100 alleles from 50 control children. Novel variants were considered pathogenic when predicted to be deleterious by two algorithms.
P1
Case1: Male, Chinese, 11 mo (at end of study)
Case1HPOs: HP:0012736 (profound psychomotor retardation)
HPOsFreeText: 10 mo at onset, poor neurological outcome
NotHPOsFreeText: not responsive to vitamin B12
Case1 (Level 2)
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3(MMUT):c.323G>A (p.Arg108His)
ClinVar: 100707
CAID: CA235522
gnomAD: 0.00006152 (African)
CaseAddInfo: homozygous mutations
P4
Case4: Male, Chinese, 2.8 y (end of study)
HPOsFreeText: poor neurologic outcome, neonatal onset
NotHPOsFreeText: not responsive to vitamin B12
Case4 (Level 2):
CasePreviousTesting: NBS
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.729_730insTT (p.Asp244LeufsTer?)
ClinVar: 552079
CAID: CA3847064
gnomAD: 0.0002008 (East Asian)
CaseAddInfo: homozygous mutations
P5
Case5: Female, Chinese, 1.6 y (onset)
HPOsFreeText: 1.6 y onset
NotHPOsFreeText: Not responsive to vitamin B12
Case5 (Level 2):
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.1106G>A (p.Arg369His)
ClinVar: 203846
CAID: CA312764
gnomAD: 0.0001504 (East Asian)
CaseAddInfo: homozygous mutations, lost to follow up
P3
Case3: Female, Chinese, 4 mo (end of study)
HPOsFreeText: Responsive to vitamin B12
Case3 (Level 2):
CasePreviousTesting: NBS
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.599T>C (p.Ille200Thr)
ClinVar: n/a
CAID: CA364404381
gnomAD: n/a
CaseAddInfo: homozygous mutations, asymptomatic
P2
Case2: Male, Chinese, 3 mo (age at death)
HPOsFreeText: Neonatal onset
NotHPOsFreeText: Not responsive to vitamin B12
Case2 (Level 2):
CasePreviousTesting: NBS (newborn screening)
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000255.3:c.482G>T (p.Gly161Val)
ClinVar: n/a
CAID: CA364404636
gnomAD: n/a
CaseAddInfo: homozygous mutations, novel mutation
Patient 1
CaseSA1: Male, Serbia
CasePresentingHPOs: HP:0025190, HP:0001987, HP:0000825, HP:0001988, HP:0001252, HP:0025502, HP:0001263 (Generalized tonic-clonic seizure, Hyperammonemia, Hyperinsulinemic hypoglycemia, Recurrent hypoglycemia, Muscular hypotonia, Overweight, Global developmental delay)
HPOsFreeText: Born at term with a birth weight of 3850 g, birth length of 51 cm, and an Apgar score of 10
CaseNotHPOs: HP:0002353 (EEG abnormality)
NotHPOsFreeText: N/A
CaseAddInfo: Parents are healthy and non-consanguineous with no family history,
CasePreviousTesting: At 9 weeks blood glucose at 2.0 mmol/L, serum insulin level of 32.4 mIU/L, plasma ammonia level was of 277 μmol/L; No abnormalities in plasma amino acid levels nor in urinary organic acid concentrations
CaseGenotypingMethod: Genetic analysis was perfomed on the GLUD1 gene.
Variant: NM_005271.5(GLUD1):c.1493C>T (p.Ser498Leu)
ClinVar: 16122, https://www.ncbi.nlm.nih.gov/clinvar/variation/16122/
gnomAD: Not in gnomAD
Patient 1
CaseSA1: Male, Serbia
CasePresentingHPOs: HP:0025190, HP:0001987, HP:0000825, HP:0001988, HP:0001252, HP:0025502, HP:0001263 (Generalized tonic-clonic seizure, Hyperammonemia, Hyperinsulinemic hypoglycemia, Recurrent hypoglycemia, Muscular hypotonia, Overweight, Global developmental delay)
HPOsFreeText: Born at term with a birth weight of 3850 g, birth length of 51 cm, and an Apgar score of 10
CaseNotHPOs: HP:0002353 (EEG abnormality)
NotHPOsFreeText: N/A
CaseAddInfo: Parents are healthy and non-consanguineous with no family history,
CasePreviousTesting: At 9 weeks blood glucose at 2.0 mmol/L, serum insulin level of 32.4 mIU/L, plasma ammonia level was of 277 μmol/L; No abnormalities in plasma amino acid levels nor in urinary organic acid concentrations
CaseGenotypingMethod: Genetic analysis was perfomed on the GLUD1 gene.
Variant: NM_005271.5(GLUD1):c.1493C>T (p.Ser498Leu)
ClinVar: 16122, https://www.ncbi.nlm.nih.gov/clinvar/variation/16122/
gnomAD: Not in gnomAD
Patient 2
Case2: Female, Austria, 18 yrs report
CasePresentingHPOs: HP:0010628, HP:0002643, HP:0002015, HP:0040288, HP:0001260, HP:0003690, HP:0003798, HP:0001511, HP:0001561, HP:0005216, HP:0002540, HP:0002650 (Facial weakness, Neonatal respiratory distress, Swallowing difficulties, Nasogastric tube feeding, Dysarthric speech, Limb weakness, Nemaline bodies, Intrauterine growth restriction, Polyhydramnios, Chewing difficulties, Non-ambulatory, Scoliosis)
HPOsFreeText: 3/3/5 Apgar score
CaseNotHPOs: HP:0002015 (Swallowing difficulties)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: Whole exome sequencing of the proband revealed these homozygous LMOD3 mutations.
Variant1: NM_198271.4:c.1648C>T (p.Leu550Phe)
ClinVar: 374498 https://www.ncbi.nlm.nih.gov/clinvar/variation/374498/
gnomAD: Not in gnomAD
Variant2: NM_198271.4:c.1004A>G (p.Gln335Arg)
ClinVar: 374499 https://www.ncbi.nlm.nih.gov/clinvar/variation/374499/
gnomAD: Not in gnomAD
Patients 3
Case3: Male, Germany, 20 yrs report
CasePresentingHPOs: HP:0010628, HP:0002015, HP:0040288, HP:0001260, HP:0003690, HP:0003798, HP:0002650 (Facial weakness, Swallowing difficulties, Nasogastric tube feeding, Dysarthric speech, Limb weakness, Nemaline bodies, Scoliosis)
HPOsFreeText: 7/8/9 Apgar score
CaseNotHPOs: HP:0002015, HP:0002540, , HP:0002098 (Swallowing difficulties, Non-ambulatory, Respiratory distress)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: Next generation sequnecing-based panel analysis detected the below variants in LMOD3.
Variant1: NM_198271.4:c.1648C>T (p.Leu550Phe)
ClinVar: 374498 https://www.ncbi.nlm.nih.gov/clinvar/variation/374498/
gnomAD: Not in gnomAD
Variant2: NM_198271.4:c.1004A>G (p.Gln335Arg)
ClinVar: 374499 https://www.ncbi.nlm.nih.gov/clinvar/variation/374499/
gnomAD: Not in gnomAD
Patient 2
Case2: Female, Austria, 18 yrs report
CasePresentingHPOs: HP:0010628, HP:0002643, HP:0002015, HP:0040288, HP:0001260, HP:0003690, HP:0003798, HP:0001511, HP:0001561, HP:0005216, HP:0002540, HP:0002650 (Facial weakness, Neonatal respiratory distress, Swallowing difficulties, Nasogastric tube feeding, Dysarthric speech, Limb weakness, Nemaline bodies, Intrauterine growth restriction, Polyhydramnios, Chewing difficulties, Non-ambulatory, Scoliosis)
HPOsFreeText: 3/3/5 Apgar score
CaseNotHPOs: HP:0002015 (Swallowing difficulties)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: Whole exome sequencing of the proband revealed these homozygous LMOD3 mutations.
Variant1: NM_198271.4:c.1648C>T (p.Leu550Phe)
ClinVar: 374498 https://www.ncbi.nlm.nih.gov/clinvar/variation/374498/
gnomAD: Not in gnomAD
Variant2: NM_198271.4:c.1004A>G (p.Gln335Arg)
ClinVar: 374499 https://www.ncbi.nlm.nih.gov/clinvar/variation/374499/
gnomAD: Not in gnomAD
Patients 3
Case3: Male, Germany, 20 yrs report
CasePresentingHPOs: HP:0010628, HP:0002015, HP:0040288, HP:0001260, HP:0003690, HP:0003798, HP:0002650 (Facial weakness, Swallowing difficulties, Nasogastric tube feeding, Dysarthric speech, Limb weakness, Nemaline bodies, Scoliosis)
HPOsFreeText: 7/8/9 Apgar score
CaseNotHPOs: HP:0002015, HP:0002540, , HP:0002098 (Swallowing difficulties, Non-ambulatory, Respiratory distress)
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: Next generation sequnecing-based panel analysis detected the below variants in LMOD3.
Variant1: NM_198271.4:c.1648C>T (p.Leu550Phe)
ClinVar: 374498 https://www.ncbi.nlm.nih.gov/clinvar/variation/374498/
gnomAD: Not in gnomAD
Variant2: NM_198271.4:c.1004A>G (p.Gln335Arg)
ClinVar: 374499 https://www.ncbi.nlm.nih.gov/clinvar/variation/374499/
gnomAD: Not in gnomAD
All nine affected individuals presented with various skeletal dysplasias. In four families (A and C–E), X-rays revealed severe platyspondyly leading to disproportionate stature (Figure 1). Lumbar gibbus and kyphoscoliosis were observed in families C and D, respectively. Three individuals (from families D and E) had cervical malformations and a hypoplastic odontoid peg with cervical instability. Short stature was also present in families A and B but appeared to be the result of limb shortening. Metaphyseal abnormalities of the long bones were found in families A and E, whereas families B–D showed epiphyseal abnormalities (Figure 1). Brachydactyly was observed in affected individuals from families A, B, and D. In addition to showing skeletal abnormalities, all affected individuals in families B and C had intellectual disability (ID). This could not be assessed for individuals A:II-1, E:II-1, and E:II-2 because of their early death at 7 weeks, 6 months, and 10 months of age, respectively. Both siblings of family B were severely disabled and unable to speak and are currently wheelchair bound. Dysmorphic facial features were non-discriminatingly mild but included coarse facial features, a prominent nose, and full cheeks in almost all affected individuals (Figure S1). A single palmar crease was also observed in six of nine affected individuals. A striking phenotype present in three of the five families was T-cell-negative SCID. Affected individuals from families A and B showed a lack of T cells, whereas B cell numbers were normal (Figure 4). Family E showed idiopathic CD4+ lymphopenia and an absolute lack of naive T cells (both CD4+CD45RA+ and CD8+CD45RA+ T cells were missing). In families B and E, a typical skin rash prompted further evaluation of the blood cells. Maternal T cells were excluded, and the oligoclonal T cell reaction found in the presence of eosinophilia was compatible with an Omenn-like presentation of SCID.1,2 Worth mentioning are also the liver cysts seen in affected individuals from families A and E. Although the phenotypes were widely variable and partly contrasting (e.g., severe versus no ID, severe versus mild platyspondyly, and epiphyseal versus metaphyseal changes), all major malformations and features occurred in three organ systems only: the immune system, the skeleton, and the neurological system. All together, we classify these five families as having phenotypic variability of an EXTL3-related neuro-immuno-skeletal dysplasia phenotype. The affected individuals from families A and E died in early infancy, whereas the others are currently between 2 and 38 years of age. Individual III-1 from family D died at 30 years of age from a unknown cause. Table 1 gives an overview of the most affected organ systems in all affected individuals. Detailed case reports and clinical data for each affected individual can be found in the Supplemental Note.
Case 1: Family A: AII-1, female
Born at 37 weeks, consanguineous family, APGAR = 9, tachypnea developed shortly after birth. At 20 weeks, skeletal abnormalities and kidney and liver cysts were detected. Died at 7 weeks from renal insufficiency.
HPO Terms: HP:0002652, HP:0001999, HP:0002789, HP:0005562, HP:0001407, HP:0009826, HP:0000926, HP:0001156, HP:0000085, HP:0000083, HP:0002079, HP:0002119, HP:0030747, HP:0011839
Previous Testing: Found autosomal recessive variant in CHST9 (MIM: 610191; c.1133A>G [p.Asn378Ser] [GenBank: NM_031422])
Genotyping Method: WES, CNV performed on WES data, EXTL3 fibroblast localization tested and compared to non-affected controls using immunocytochemistry
Variant: p.Arg513Cys, g.28575113, c.1537C>T
ClinVar ID: n/a
gnomAD: http://gnomad.broadinstitute.org/variant/8-28575113-C-T
Inheritance: autosomal recessive
Variant Evidence:
All nine affected individuals presented with various skeletal dysplasias. In four families (A and C–E), X-rays revealed severe platyspondyly leading to disproportionate stature (Figure 1). Lumbar gibbus and kyphoscoliosis were observed in families C and D, respectively. Three individuals (from families D and E) had cervical malformations and a hypoplastic odontoid peg with cervical instability. Short stature was also present in families A and B but appeared to be the result of limb shortening. Metaphyseal abnormalities of the long bones were found in families A and E, whereas families B–D showed epiphyseal abnormalities (Figure 1). Brachydactyly was observed in affected individuals from families A, B, and D. In addition to showing skeletal abnormalities, all affected individuals in families B and C had intellectual disability (ID). This could not be assessed for individuals A:II-1, E:II-1, and E:II-2 because of their early death at 7 weeks, 6 months, and 10 months of age, respectively. Both siblings of family B were severely disabled and unable to speak and are currently wheelchair bound. Dysmorphic facial features were non-discriminatingly mild but included coarse facial features, a prominent nose, and full cheeks in almost all affected individuals (Figure S1). A single palmar crease was also observed in six of nine affected individuals. A striking phenotype present in three of the five families was T-cell-negative SCID. Affected individuals from families A and B showed a lack of T cells, whereas B cell numbers were normal (Figure 4). Family E showed idiopathic CD4+ lymphopenia and an absolute lack of naive T cells (both CD4+CD45RA+ and CD8+CD45RA+ T cells were missing). In families B and E, a typical skin rash prompted further evaluation of the blood cells. Maternal T cells were excluded, and the oligoclonal T cell reaction found in the presence of eosinophilia was compatible with an Omenn-like presentation of SCID.1,2 Worth mentioning are also the liver cysts seen in affected individuals from families A and E. Although the phenotypes were widely variable and partly contrasting (e.g., severe versus no ID, severe versus mild platyspondyly, and epiphyseal versus metaphyseal changes), all major malformations and features occurred in three organ systems only: the immune system, the skeleton, and the neurological system. All together, we classify these five families as having phenotypic variability of an EXTL3-related neuro-immuno-skeletal dysplasia phenotype. The affected individuals from families A and E died in early infancy, whereas the others are currently between 2 and 38 years of age. Individual III-1 from family D died at 30 years of age from a unknown cause. Table 1 gives an overview of the most affected organ systems in all affected individuals. Detailed case reports and clinical data for each affected individual can be found in the Supplemental Note.
Case 1: Family A: AII-1, female
Born at 37 weeks, consanguineous family, APGAR = 9, tachypnea developed shortly after birth. At 20 weeks, skeletal abnormalities and kidney and liver cysts were detected. Died at 7 weeks from renal insufficiency.
HPO Terms: HP:0002652, HP:0001999, HP:0002789, HP:0005562, HP:0001407, HP:0009826, HP:0000926, HP:0001156, HP:0000085, HP:0000083, HP:0002079, HP:0002119, HP:0030747, HP:0011839
Previous Testing: Found autosomal recessive variant in CHST9 (MIM: 610191; c.1133A>G [p.Asn378Ser] [GenBank: NM_031422])
Genotyping Method: WES, CNV performed on WES data, EXTL3 fibroblast localization tested and compared to non-affected controls using immunocytochemistry
Variant: p.Arg513Cys, g.28575113, c.1537C>T
ClinVar ID: n/a
gnomAD: http://gnomad.broadinstitute.org/variant/8-28575113-C-T
Inheritance: autosomal recessive
Variant Evidence:
Case 3
Case#: 3, female, 12 days (onset), 4 y (current- this differs than what is in table 1), Chinese
CasePresentingHPOs: HP: 0008344, HP: 0012088, HP:0011968, HP: 0002013, HP:0011344, HP: 0002543, HP: 0012751 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, vomiting, severe global developmental delay, abnormal globus pallidus, abnormal basal ganglia)
HPOsFreeText: Bilateral damage to capsula interna and externa, Blood ammonia: 205 uM, Hemoglobin: 118 g/L, Leucin: 891.90 uM, Valine: 502.50 uM, Isoleucine: 165.99 uM, Alloisoleucine: 90.12 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 2 different variants, unsure of cis or trans
CasePreviousTesting: n/a
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000709.3(BCKDHA):c.178G>T (p.Glu60Ter), NM_000709.3(BCKDHA):c.1214_1219dupCCAACC (p.Asn406Leu407insProGln)
ClinVar: n/a
CAID: CA406004676 , CA658820662
gnomAD: neither in gnomAD
8 patients
GroupPresentingHPOs: HP:0008344 (elevated A keto acids in urine)
HPOsFreeText:
GroupNotHPOs:
NotHPOsFreeText:
NumberMales: 4
NumberFemales: 4
CountryOrigin: mainland China
Ethnicity:
Race: Chinese
AgeRange: 2 y 3 mo- 4 y 3 mo (present age)
TotalNumber: 8
VariantCount: 8 (subunits of BKDC: either BCKDHA, BCKDHB, or DBT)
NonVariant: 0
OtherVariant: 0
GroupPreviousTesting: n/a
GroupMethod1: PCR
GroupMethod2: Multiple sequence alignments
GroupGenotypingMethod: genomic DNA extracted from peripheral blood lymphocytes of patients and parents using TIANamp Blood DNA Kit. Exons and flanking intronic regions of BCKDHA, BCKDHB, and DBT were amplified with PCR and sequenced. Results compared with reference sequences in UCSC genome (BCKDHA (NM_000709), BCKDHB (NM_183050), DLD (NM_000108), DBT (NM_001918)), and compared with integrated set of variants from 1000 Genome Project to identify mutations. PolyPhen-2 and Mutationtaster program predicted the impact of missense alterations on protein function. Multiple sequence alignments obtained using BLAST.
Case 6
Case#: 6, male, 18 m (onset), 2 y 6 m (current), Chinese
CasePresentingHPOs: HP: 0008344, HP; 0012088, HP: 0011342, HP: 0001332, HP:0002543, HP: 0012751, HP:0012747 (elevated A keto acids in urine, abnormal urinary odor, mild global developmental delay, dystonia, abnormal globus pallidus, abnormal basal ganglia, abnormal brainstem MRI signal intensity)
HPOsFreeText: damage to cerebellar dentate nucleus, damage to corpora quadrigemina, damage to frontal lobe, damage to insular cortex, Isoleucine: 167.13 uM, Alloisoleucine: 44.88 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: unsure cis or trans
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_183050.3:c.767A>G (p.Tyr256Cys), NM_183050.3:c.768C>G (p.Tyr256Ter)
ClinVar: neither found
CAID: CA364659935, CA142287564
gnomAD: 0.000008820 (European, non-Finnish), not found
Case 8
Case#: 8, male, 13 days (onset), 1 y 6 m (current), Chinese
CasePresentingHPOs: HP: 0008344, HP:0012088, HP:0011968, HP:0001254, HP:0002415, HP: 0006989 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, lethargy, leukodystrophy, dysplastic corpus callosum)
FreeTextHPOs: blood ammonia: 96 uM, hemoglobin: 98 g/L, leucin: 1047.24 uM, isoleucine: 261.09 uM, alloisoleucine: 127.05 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: homozygous mutation
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_001918.3:c.1A>G (p.Met1Val)
ClinVar: not found
CAID: CA969877
gnomAD: not found
Case 1
Case#: 1, male, 3 days (onset), 2 y 8 mo (current), Chinese
CasePresentingHPOs: HP:0008344 HP: 0012088, HP: 0001250, HP: 0011968, HP: 0001941, HP: 0001943, HP: 0001987, HP: 0001903, HP:0012751, HP:0002543, HP: 0001276, HP:0011343 (elevated A keto acids in urine, abnormal urinary odor, seizures, feeding difficulties, acidosis, hypoglycemia, hyperammonemia, anemia, abnormal basal ganglia MRI signal intensity, abnormal globus pallidus signals, hypertonia, moderate global developmental delay)
HPOsFreeText: Blood ammonia: 75 uM, Valine: 532.83 uM, Isoleucine: 384.90 uM, Alloisoleucine: 213.09 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: variants also found in parents
Case (Level 2)
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000709.3(BCKDHA): IVS6+1delG (can't search this format of an intronic mutations, how do I change it?)
ClinVar: not sure how to search for BCKDHA IVS6 + 1delG
CAID:
gnomAD:
Variant2: NM_000709.3(BCKDHA):c.740A>G (p.His247Arg)
ClinVar: not found
CAID: CA406012849
gnomAD: not in gnomAD
There are two variants listed for every patient except, one. The text said that all the mutations found were also found in the parents so does that mean they would be in trans?
(didn't see this template at first, so still need to apply it to the other entries)
Case 3
Case#: 3, female, 12 days (onset), 4 y (current- this differs than what is in table 1), Chinese
CasePresentingHPOs: HP: 0008344, HP: 0012088, HP:0011968, HP: 0002013, HP:0011344, HP: 0002543, HP: 0012751 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, vomiting, severe global developmental delay, abnormal globus pallidus, abnormal basal ganglia)
HPOsFreeText: Bilateral damage to capsula interna and externa, Blood ammonia: 205 uM, Hemoglobin: 118 g/L, Leucin: 891.90 uM, Valine: 502.50 uM, Isoleucine: 165.99 uM, Alloisoleucine: 90.12 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: 2 different variants, unsure of cis or trans
CasePreviousTesting: n/a
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_000709.3(BCKDHA):c.178G>T (p.Glu60Ter), NM_000709.3(BCKDHA):c.1214_1219dupCCAACC (p.Asn406Leu407insProGln)
ClinVar: n/a
CAID: CA406004676 , CA658820662
gnomAD: neither in gnomAD
8 patients
GroupPresentingHPOs: HP:0008344 (elevated A keto acids in urine)
HPOsFreeText:
GroupNotHPOs:
NotHPOsFreeText:
NumberMales: 4
NumberFemales: 4
CountryOrigin: mainland China
Ethnicity:
Race: Chinese
AgeRange: 2 y 3 mo- 4 y 3 mo (present age)
TotalNumber: 8
VariantCount: 8 (subunits of BKDC: either BCKDHA, BCKDHB, or DBT)
NonVariant: 0
OtherVariant: 0
GroupPreviousTesting: n/a
GroupMethod1: PCR
GroupMethod2: Multiple sequence alignments
GroupGenotypingMethod: genomic DNA extracted from peripheral blood lymphocytes of patients and parents using TIANamp Blood DNA Kit. Exons and flanking intronic regions of BCKDHA, BCKDHB, and DBT were amplified with PCR and sequenced. Results compared with reference sequences in UCSC genome (BCKDHA (NM_000709), BCKDHB (NM_183050), DLD (NM_000108), DBT (NM_001918)), and compared with integrated set of variants from 1000 Genome Project to identify mutations. PolyPhen-2 and Mutationtaster program predicted the impact of missense alterations on protein function. Multiple sequence alignments obtained using BLAST.
Case 6
Case#: 6, male, 18 m (onset), 2 y 6 m (current), Chinese
CasePresentingHPOs: HP: 0008344, HP; 0012088, HP: 0011342, HP: 0001332, HP:0002543, HP: 0012751, HP:0012747 (elevated A keto acids in urine, abnormal urinary odor, mild global developmental delay, dystonia, abnormal globus pallidus, abnormal basal ganglia, abnormal brainstem MRI signal intensity)
HPOsFreeText: damage to cerebellar dentate nucleus, damage to corpora quadrigemina, damage to frontal lobe, damage to insular cortex, Isoleucine: 167.13 uM, Alloisoleucine: 44.88 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: unsure cis or trans
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_183050.3:c.767A>G (p.Tyr256Cys), NM_183050.3:c.768C>G (p.Tyr256Ter)
ClinVar: neither found
CAID: CA364659935, CA142287564
gnomAD: 0.000008820 (European, non-Finnish), not found
Case 8
Case#: 8, male, 13 days (onset), 1 y 6 m (current), Chinese
CasePresentingHPOs: HP: 0008344, HP:0012088, HP:0011968, HP:0001254, HP:0002415, HP: 0006989 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, lethargy, leukodystrophy, dysplastic corpus callosum)
FreeTextHPOs: blood ammonia: 96 uM, hemoglobin: 98 g/L, leucin: 1047.24 uM, isoleucine: 261.09 uM, alloisoleucine: 127.05 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: homozygous mutation
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant: NM_001918.3:c.1A>G (p.Met1Val)
ClinVar: not found
CAID: CA969877
gnomAD: not found
Case 1
Case#: 1, male, 3 days (onset), 2 y 8 mo (current), Chinese
CasePresentingHPOs: HP:0008344 HP: 0012088, HP: 0001250, HP: 0011968, HP: 0001941, HP: 0001943, HP: 0001987, HP: 0001903, HP:0012751, HP:0002543, HP: 0001276, HP:0011343 (elevated A keto acids in urine, abnormal urinary odor, seizures, feeding difficulties, acidosis, hypoglycemia, hyperammonemia, anemia, abnormal basal ganglia MRI signal intensity, abnormal globus pallidus signals, hypertonia, moderate global developmental delay)
HPOsFreeText: Blood ammonia: 75 uM, Valine: 532.83 uM, Isoleucine: 384.90 uM, Alloisoleucine: 213.09 uM
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: variants also found in parents
Case (Level 2)
CasePreviousTesting: same as group
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000709.3(BCKDHA): IVS6+1delG (can't search this format of an intronic mutations, how do I change it?)
ClinVar: not sure how to search for BCKDHA IVS6 + 1delG
CAID:
gnomAD:
Variant2: NM_000709.3(BCKDHA):c.740A>G (p.His247Arg)
ClinVar: not found
CAID: CA406012849
gnomAD: not in gnomAD
There are two variants listed for every patient except, one. The text said that all the mutations found were also found in the parents so does that mean they would be in trans?
(didn't see this template at first, so still need to apply it to the other entries)
VI-4 Son
CaseVI-4: Male, 3.5 years, Turkey
CasePresentingHPOs: HP:0004912, HP:0002540, HP:0002970 (Hypophosphatemic rickets, Inability to walk, Genu varum)
HPOsFreeText: -3.76 standard deviation score
CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)
NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2
CaseAddInfo: Variant is asserted de novo and confirmed by parental testing, Proband is hemizygous for this mutation
CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.8 mg/dL; reference 3.8-6.5), Elevated serum ALP (925 IU/L; reference 90-325), 25OHD3 levels (35 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (62.2 ng/L), TPR levels (69.7), Decreased TmP/GFR levels (1.95; reference 2.9-6.1)
CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.
Variant: NM_000444.5:c.1217G>T (p.Cys406Phe)
CAID: CA412573391 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.1217G%3ET
gnomAD: Not in gnomAD
VI-4 Son
CaseVI-4: Male, 3.5 years, Turkey
CasePresentingHPOs: HP:0004912, HP:0002540, HP:0002970 (Hypophosphatemic rickets, Inability to walk, Genu varum)
HPOsFreeText: -3.76 standard deviation score
CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)
NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2
CaseAddInfo: Variant is asserted de novo and confirmed by parental testing, Proband is hemizygous for this mutation
CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.8 mg/dL; reference 3.8-6.5), Elevated serum ALP (925 IU/L; reference 90-325), 25OHD3 levels (35 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (62.2 ng/L), TPR levels (69.7), Decreased TmP/GFR levels (1.95; reference 2.9-6.1)
CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.
Variant: NM_000444.5:c.1217G>T (p.Cys406Phe)
CAID: CA412573391 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.1217G%3ET
gnomAD: Not in gnomAD
Patient 1
Case1: Male, 3 months onset, Australia
CasePresentingHPOs: HP:0002878, HP:0002460, HP:0001270, HP:0003701, HP:0000467, HP:0001488, HP:0002938, HP:0003691, HP:0003391, HP:0003803, HP:0003755 (Respiratory failure, Distal muscle weakness, Motor delay, Proximal muscle weakness, Neck muscle weakness, Bilateral ptosis, Lumbar hyperlordosis, Scapular winging, Gowers sign, Type 1 muscle fiber predominance, Type 1 fibers relatively smaller than type 2 fibers)
HPOsFreeText: BiPAP from 3.5 yrs, Type 2B fibers absent
CaseNotHPOs: HP:0003798, HP:0030177, HP:0031237 (Nemaline bodies, Abnormal nerve conduction study, Internally nucleated skeletal muscle fibers)
NotHPOsFreeText: N/A
CaseAddInfo: Variant is de novo with parental testing confirmed
CasePreviousTesting: Patients were diagnosed with CFTD via clinical notes and muscle biopsies at pathology centers throughout Australia and several international centers.
CaseGenotypingMethod: Two methods were used for genotyping. In 16 patients, the 10 exons spliced onto the muscle-specific isoform of TPM3 were bidirectionally sequenced from genomic DNA. For the other 7 patients, complementary DNA was generated from patient muscle and isoform-specific primers were used to sequence the transcript. Paternity was confirmed in isolated patients using microsatellite markers.
Variant: NM_152263.4(TPM3):c.733A>G (p.Arg245Gly)
ClinVar: 42117 https://www.ncbi.nlm.nih.gov/clinvar/variation/42117/
gnomAD: Not in gnomAD
Patient 2
Case2: Male, Birth onset, Australia
CasePresentingHPOs: HP:0008947, HP:0002460, HP:0001270, HP:0003701, HP:0000467, HP:0001488, HP:0002938, HP:0010628, HP:0003391, HP:0002942, HP:0003803, HP:0003755 (Infantile muscular hypotonia, Distal muscle weakness, Motor delay, Proximal muscle weakness, Neck muscle weakness, Bilateral ptosis, Lumbar hyperlordosis, Facial palsy, Gowers sign, Thoracic kyphosis, Type 1 muscle fiber predominance, Type 1 fibers relatively smaller than type 2 fibers)
HPOsFreeText: Type 2B fibers absent
CaseNotHPOs: HP:0003798, HP:0030177, HP:0030877, HP:0031237 (Nemaline bodies, Abnormal nerve conduction study, Obstructive deficit on pulmonary function testing, Internally nucleated skeletal muscle fibers)
NotHPOsFreeText: N/A
CaseAddInfo: Variant is de novo with parental testing confirmation
CasePreviousTesting: Patients were diagnosed with CFTD via clinical notes and muscle biopsies at pathology centers throughout Australia and several international centers.
CaseGenotypingMethod: Two methods were used for genotyping. In 16 patients, the 10 exons spliced onto the muscle-specific isoform of TPM3 were bidirectionally sequenced from genomic DNA. For the other 7 patients, complementary DNA was generated from patient muscle and isoform-specific primers were used to sequence the transcript. Paternity was confirmed in isolated patients using microsatellite markers.
Variant: NM_152263.4(TPM3):c.505A>G (p.Lys169Glu)
ClinVar: 42115 https://www.ncbi.nlm.nih.gov/clinvar/variation/42115/
gnomAD: Not in gnomAD
Patient 1
Case1: Male, 3 months onset, Australia
CasePresentingHPOs: HP:0002878, HP:0002460, HP:0001270, HP:0003701, HP:0000467, HP:0001488, HP:0002938, HP:0003691, HP:0003391, HP:0003803, HP:0003755 (Respiratory failure, Distal muscle weakness, Motor delay, Proximal muscle weakness, Neck muscle weakness, Bilateral ptosis, Lumbar hyperlordosis, Scapular winging, Gowers sign, Type 1 muscle fiber predominance, Type 1 fibers relatively smaller than type 2 fibers)
HPOsFreeText: BiPAP from 3.5 yrs, Type 2B fibers absent
CaseNotHPOs: HP:0003798, HP:0030177, HP:0031237 (Nemaline bodies, Abnormal nerve conduction study, Internally nucleated skeletal muscle fibers)
NotHPOsFreeText: N/A
CaseAddInfo: Variant is de novo with parental testing confirmed
CasePreviousTesting: Patients were diagnosed with CFTD via clinical notes and muscle biopsies at pathology centers throughout Australia and several international centers.
CaseGenotypingMethod: Two methods were used for genotyping. In 16 patients, the 10 exons spliced onto the muscle-specific isoform of TPM3 were bidirectionally sequenced from genomic DNA. For the other 7 patients, complementary DNA was generated from patient muscle and isoform-specific primers were used to sequence the transcript. Paternity was confirmed in isolated patients using microsatellite markers.
Variant: NM_152263.4(TPM3):c.733A>G (p.Arg245Gly)
ClinVar: 42117 https://www.ncbi.nlm.nih.gov/clinvar/variation/42117/
gnomAD: Not in gnomAD
Patient 2
Case2: Male, Birth onset, Australia
CasePresentingHPOs: HP:0008947, HP:0002460, HP:0001270, HP:0003701, HP:0000467, HP:0001488, HP:0002938, HP:0010628, HP:0003391, HP:0002942, HP:0003803, HP:0003755 (Infantile muscular hypotonia, Distal muscle weakness, Motor delay, Proximal muscle weakness, Neck muscle weakness, Bilateral ptosis, Lumbar hyperlordosis, Facial palsy, Gowers sign, Thoracic kyphosis, Type 1 muscle fiber predominance, Type 1 fibers relatively smaller than type 2 fibers)
HPOsFreeText: Type 2B fibers absent
CaseNotHPOs: HP:0003798, HP:0030177, HP:0030877, HP:0031237 (Nemaline bodies, Abnormal nerve conduction study, Obstructive deficit on pulmonary function testing, Internally nucleated skeletal muscle fibers)
NotHPOsFreeText: N/A
CaseAddInfo: Variant is de novo with parental testing confirmation
CasePreviousTesting: Patients were diagnosed with CFTD via clinical notes and muscle biopsies at pathology centers throughout Australia and several international centers.
CaseGenotypingMethod: Two methods were used for genotyping. In 16 patients, the 10 exons spliced onto the muscle-specific isoform of TPM3 were bidirectionally sequenced from genomic DNA. For the other 7 patients, complementary DNA was generated from patient muscle and isoform-specific primers were used to sequence the transcript. Paternity was confirmed in isolated patients using microsatellite markers.
Variant: NM_152263.4(TPM3):c.505A>G (p.Lys169Glu)
ClinVar: 42115 https://www.ncbi.nlm.nih.gov/clinvar/variation/42115/
gnomAD: Not in gnomAD
The index patient (V-1)
CaseV-1: Male, 27 yrs onset, China, Asian
CasePresentingHPOs: HP:0002875, HP:0001639, HP:0002027, HP:0001712, HP:0001671, HP:0032092, HP:0001645 (Exertional dyspnea, Hypertrophic cardiomyopathy, Abdominal pain, Left ventricular hypertrophy, Abnormal cardiac septum morphology, Left ventricular outflow tract obstruction, Sudden cardiac death)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Family is consanguineous, The MYPBC3 variant was the only one to segregate with the disease, with the CACNB2 variant also being present in individuals with "severe" forms of the disease. CACNB2+ MYH7- individuals showed no symptoms of cardiomyopathy, supporting a modifying effect leading to the clinical heterogeneity of this family, MYBPC3 variant leads to a premature termination and a loss of 49 amino acids which is predicted to undergo NMD but is also associated with incomplete penetrance
CasePreviousTesting: Marked hypertrophic septum (27 mm) and a left-ventricular outflow obstruction (LVOTO) of 32 mmHg, Clinical features in Table 1, No members showed Brugada syndrome phenotypes, Proband also has polymorphisms in TGFB1 and AKAP9 but no other affected family member contains them suggesting a benign pathogenicity
CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood. PCR amplification was performed and sanger sequencing was performed for MYH7 and MYPBC3 mutations. After positive confirmation of the MYBPC3 mutation, RAAS genes were genotyped for a possible modifying effect. Negative findings led to a targeted NGS for the index patient using all known 104 causing/closely related genes of cardiomyopathy and chanelopathy. These variants were then filtered and analyzed for pathogenicity and confirmed in family members via Sanger sequencing.
Variant: NM_201597.3:c.1598C>T (p.Ser533Leu)
ClinVar: 190730 https://www.ncbi.nlm.nih.gov/clinvar/variation/190730/
gnomAD: 0.01004, https://gnomad.broadinstitute.org/variant/10-18828340-C-T
MultipleGeneVariants
MYBPC3 Variant
Variant: NM_000256.3(MYBPC3):c.3624del (p.Lys1209fs)
ClinVar: 42727 https://www.ncbi.nlm.nih.gov/clinvar/variation/42727/
gnomAD: 0.00005140, https://gnomad.broadinstitute.org/variant/11-47354119-TG-T
DSP Variant
Variant: NM_004415.4(DSP):c.3923G>A (p.Arg1308Gln)
ClinVar: 178028 https://www.ncbi.nlm.nih.gov/clinvar/variation/178028/
gnomAD: 0.01680, https://gnomad.broadinstitute.org/variant/6-7580346-G-A
The index patient (V-1)
CaseV-1: Male, 27 yrs onset, China, Asian
CasePresentingHPOs: HP:0002875, HP:0001639, HP:0002027, HP:0001712, HP:0001671, HP:0032092, HP:0001645 (Exertional dyspnea, Hypertrophic cardiomyopathy, Abdominal pain, Left ventricular hypertrophy, Abnormal cardiac septum morphology, Left ventricular outflow tract obstruction, Sudden cardiac death)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Family is consanguineous, The MYPBC3 variant was the only one to segregate with the disease, with the CACNB2 variant also being present in individuals with "severe" forms of the disease. CACNB2+ MYH7- individuals showed no symptoms of cardiomyopathy, supporting a modifying effect leading to the clinical heterogeneity of this family, MYBPC3 variant leads to a premature termination and a loss of 49 amino acids which is predicted to undergo NMD but is also associated with incomplete penetrance
CasePreviousTesting: Marked hypertrophic septum (27 mm) and a left-ventricular outflow obstruction (LVOTO) of 32 mmHg, Clinical features in Table 1, No members showed Brugada syndrome phenotypes, Proband also has polymorphisms in TGFB1 and AKAP9 but no other affected family member contains them suggesting a benign pathogenicity
CaseGenotypingMethod: Genomic DNA was extracted from peripheral blood. PCR amplification was performed and sanger sequencing was performed for MYH7 and MYPBC3 mutations. After positive confirmation of the MYBPC3 mutation, RAAS genes were genotyped for a possible modifying effect. Negative findings led to a targeted NGS for the index patient using all known 104 causing/closely related genes of cardiomyopathy and chanelopathy. These variants were then filtered and analyzed for pathogenicity and confirmed in family members via Sanger sequencing.
Variant: NM_201597.3:c.1598C>T (p.Ser533Leu)
ClinVar: 190730 https://www.ncbi.nlm.nih.gov/clinvar/variation/190730/
gnomAD: 0.01004, https://gnomad.broadinstitute.org/variant/10-18828340-C-T
MultipleGeneVariants
MYBPC3 Variant
Variant: NM_000256.3(MYBPC3):c.3624del (p.Lys1209fs)
ClinVar: 42727 https://www.ncbi.nlm.nih.gov/clinvar/variation/42727/
gnomAD: 0.00005140, https://gnomad.broadinstitute.org/variant/11-47354119-TG-T
DSP Variant
Variant: NM_004415.4(DSP):c.3923G>A (p.Arg1308Gln)
ClinVar: 178028 https://www.ncbi.nlm.nih.gov/clinvar/variation/178028/
gnomAD: 0.01680, https://gnomad.broadinstitute.org/variant/6-7580346-G-A
o determine the frequency of MYOZ2 mutation in HCM, we screened all exons and exon–intron boundaries of MYOZ2 in 516 probands by direct sequencing. We detected another heterozygous missense A→G mutation at nucleotide 50 278 in a white proband who had 2 deceased siblings with HCM. The mutation changed amino acid isoleucine 246, a conserved amino acid, to methionine
Case 2: male, Dx = n/a, variant identified via direct sequencing
HP:0001712 (left ventricular hypertrophy)
Variant: NM_016599.4(MYOZ2):c.738A>G (p.Ile246Met)
non-LOF
ClinVar ID: 30509, conflicting interpretations of pathogenicity,<br /> https://www.ncbi.nlm.nih.gov/clinvar/variation/30509/
ExAC Score: 0.001897, http://gnomad.broadinstitute.org/variant/4-120107298-A-G
o determine the frequency of MYOZ2 mutation in HCM, we screened all exons and exon–intron boundaries of MYOZ2 in 516 probands by direct sequencing. We detected another heterozygous missense A→G mutation at nucleotide 50 278 in a white proband who had 2 deceased siblings with HCM. The mutation changed amino acid isoleucine 246, a conserved amino acid, to methionine
Case 2: male, Dx = n/a, variant identified via direct sequencing
HP:0001712 (left ventricular hypertrophy)
Variant: NM_016599.4(MYOZ2):c.738A>G (p.Ile246Met)
non-LOF
ClinVar ID: 30509, conflicting interpretations of pathogenicity,<br /> https://www.ncbi.nlm.nih.gov/clinvar/variation/30509/
ExAC Score: 0.001897, http://gnomad.broadinstitute.org/variant/4-120107298-A-G
Dutch patient
Case1: Female, 12 yrs onset, Dutch
CasePresentingHPOs: HP:0002093, HP:0001288, HP:0003690, HP:0010628, HP:0003722, HP:0003202, HP:0003798 (Respiratory insufficiency, Gait difficulties, Limb muscle weakness, Facial muscle weakness, Neck flexor weakness, Muscle hypotrophy, Nemaline rods)
HPOsFreeText: Mild form of nemaline myopathy, Wheelchair from the age of 48, Selective hypotrophy of Type 1 muscle fibres
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: No family history of neuromuscular disorders, Variant was not detected in healthy mother or 7 unaffected siblings, Father was deceased so no sample was available
CasePreviousTesting: N/A
CaseGenotypingMethod: Genomic DNA and RNA was extracted from blood or lymphoblastoid cell lines. SSCP was used to analyze all 10 exons of TPM2. After locating the mutations, RT-PCR was used to confirm the mutated allele expression and haplotype analysis was performed on the probands and their family.
Variant: NM_003289.3:c.440A>C (p.Gln147Pro)
ClinVar: 12461 https://www.ncbi.nlm.nih.gov/clinvar/variation/12461/
gnomAD: Not in gnomAD
Dutch patient
Case1: Female, 12 yrs onset, Dutch
CasePresentingHPOs: HP:0002093, HP:0001288, HP:0003690, HP:0010628, HP:0003722, HP:0003202, HP:0003798 (Respiratory insufficiency, Gait difficulties, Limb muscle weakness, Facial muscle weakness, Neck flexor weakness, Muscle hypotrophy, Nemaline rods)
HPOsFreeText: Mild form of nemaline myopathy, Wheelchair from the age of 48, Selective hypotrophy of Type 1 muscle fibres
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: No family history of neuromuscular disorders, Variant was not detected in healthy mother or 7 unaffected siblings, Father was deceased so no sample was available
CasePreviousTesting: N/A
CaseGenotypingMethod: Genomic DNA and RNA was extracted from blood or lymphoblastoid cell lines. SSCP was used to analyze all 10 exons of TPM2. After locating the mutations, RT-PCR was used to confirm the mutated allele expression and haplotype analysis was performed on the probands and their family.
Variant: NM_003289.3:c.440A>C (p.Gln147Pro)
ClinVar: 12461 https://www.ncbi.nlm.nih.gov/clinvar/variation/12461/
gnomAD: Not in gnomAD
two unrelated patients
CaseRoma: France
CasePresentingHPOs: HP:0006785, HP:0003236, (Limb-girdle muscular dystrophy, Elevated serum creatine kinase)
HPOsFreeText: Wheelchair bound before 14 yrs
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Probands are from consanguineous gypsy families supporting a founder event, This mutation segregated with the disease in 18 patients and all asymptomatic parents were heterozygous, 15 siblings were heterozygous and asymptomatic except for a moderate increase in Serum CK in some
CasePreviousTesting: Duchenne-like clinical presentation, Males and females equally affected, Normal dystrophin and decreased level of α- and γ-SG in muscle specimens
CaseGenotypingMethod: DNA was isolated from peripheral blood leukocytes and subject to PCR amplification for linkage analysis. Total RNA was extracted from muscle biopsies and cDNA synthesis was performed and amplified. This was sequenced and analyzed for mutations.
Variant: NM_000231.2(SGCG):c.848G>A (p.Cys283Tyr)
ClinVar: 2006 https://www.ncbi.nlm.nih.gov/clinvar/variation/2006/
gnomAD: 0.000008796, https://gnomad.broadinstitute.org/variant/13-23898652-G-A
Affected: 18
Unaffected: At least 29
Segregations: N/A
SegregationAddInfo: Candidate Gene Sequencing
two unrelated patients
CaseRoma: France
CasePresentingHPOs: HP:0006785, HP:0003236, (Limb-girdle muscular dystrophy, Elevated serum creatine kinase)
HPOsFreeText: Wheelchair bound before 14 yrs
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Probands are from consanguineous gypsy families supporting a founder event, This mutation segregated with the disease in 18 patients and all asymptomatic parents were heterozygous, 15 siblings were heterozygous and asymptomatic except for a moderate increase in Serum CK in some
CasePreviousTesting: Duchenne-like clinical presentation, Males and females equally affected, Normal dystrophin and decreased level of α- and γ-SG in muscle specimens
CaseGenotypingMethod: DNA was isolated from peripheral blood leukocytes and subject to PCR amplification for linkage analysis. Total RNA was extracted from muscle biopsies and cDNA synthesis was performed and amplified. This was sequenced and analyzed for mutations.
Variant: NM_000231.2(SGCG):c.848G>A (p.Cys283Tyr)
ClinVar: 2006 https://www.ncbi.nlm.nih.gov/clinvar/variation/2006/
gnomAD: 0.000008796, https://gnomad.broadinstitute.org/variant/13-23898652-G-A
Affected: 18
Unaffected: At least 29
Segregations: N/A
SegregationAddInfo: Candidate Gene Sequencing
Patient 2
Case2: Female, Birth onset, Germany
CasePresentingHPOs: HP:0003552, HP:0001558, HP:0002375, HP:0002747, HP:0004887, HP:0001385, HP:0001537, HP:0000023, HP:0012418, HP:0000278, HP:0000347, HP:0000470, HP:0001276, HP:0002808, HP:0001376, HP:0002063, HP:0011968, HP:0000975, HP:0003236, HP:0000938, HP:0009803, HP:0030084, HP:0001561, HP:0002828, HP:0005949, HP:0001284, HP:0003198, HP:0003557, HP:0003687, HP:0010602 (Muscle stiffness, Decreased fetal movement, Hypokinesia, Respiratory insufficiency due to muscle weakness, Respiratory failure requiring assisted ventilation, Hip dysplasia, Umbilical hernia, Inguinal hernia, Hypoxemia, Retrognathia, Micrognathia, Short neck, Hypertonia, Kyphosis, Limited joint motion, Rigidity, Feeding difficulties, Profuse sweating, Elevated serum creatine phosphokinase, Osteopenia, Shortened phalanges, Clinodactyly, Polyhydramnios, Multiple joint contractures, Apneic episodes in infancy, Areflexia, Myopathic changes, Increased variability in muscle fiber diameter, Centrally nucleated skeletal muscle fibers, Type 2 muscle fiber predominance)
HPOsFreeText: Tracheostomy performed, Bladder catheter required, Inability to sit or roll, Increased echogenicity on muscle ultrasound, Treatment with carbamazepine, benzodiazepines, and baclofen reportedly provided no substantial benefit, Difficulty sitting due to hyperactivity of hip extensors, Mini rods and z-band broadening were seen in atrophic fibers
CaseNotHPOs: HP:0100543, HP:0003730, HP:0002486, HP:0002353, HP:0002363, HP:0000496, HP:0003202, HP:0003798 (Cognitive impairment, EMG: myotonic runs, Myotonia, EEG abnormality, Abnormality of brainstem morphology, Abnormality of eye movement, Skeletal muscle atrophy, Nemaline bodies)
NotHPOsFreeText: Abnormal metabolic screening, Muscle fiber type grouping
CaseAddInfo: Case is de novo and confirmed via parental testing
CasePreviousTesting: Negative ACTA1 and CRYAB
CaseGenotypingMethod: Based on the Patient 1 results, the same region of TPM3 (Exon 6) was PCR amplified and sequenced in the proband and her parents via bidirectional Sanger sequencing.
Variant: NM_152263.4(TPM3):c.654_656AGA[1] (p.Glu219del)
ClinVar: 235144 https://www.ncbi.nlm.nih.gov/clinvar/variation/235144/
gnomAD: Not in gnomAD
Patient 2
Case2: Female, Birth onset, Germany
CasePresentingHPOs: HP:0003552, HP:0001558, HP:0002375, HP:0002747, HP:0004887, HP:0001385, HP:0001537, HP:0000023, HP:0012418, HP:0000278, HP:0000347, HP:0000470, HP:0001276, HP:0002808, HP:0001376, HP:0002063, HP:0011968, HP:0000975, HP:0003236, HP:0000938, HP:0009803, HP:0030084, HP:0001561, HP:0002828, HP:0005949, HP:0001284, HP:0003198, HP:0003557, HP:0003687, HP:0010602 (Muscle stiffness, Decreased fetal movement, Hypokinesia, Respiratory insufficiency due to muscle weakness, Respiratory failure requiring assisted ventilation, Hip dysplasia, Umbilical hernia, Inguinal hernia, Hypoxemia, Retrognathia, Micrognathia, Short neck, Hypertonia, Kyphosis, Limited joint motion, Rigidity, Feeding difficulties, Profuse sweating, Elevated serum creatine phosphokinase, Osteopenia, Shortened phalanges, Clinodactyly, Polyhydramnios, Multiple joint contractures, Apneic episodes in infancy, Areflexia, Myopathic changes, Increased variability in muscle fiber diameter, Centrally nucleated skeletal muscle fibers, Type 2 muscle fiber predominance)
HPOsFreeText: Tracheostomy performed, Bladder catheter required, Inability to sit or roll, Increased echogenicity on muscle ultrasound, Treatment with carbamazepine, benzodiazepines, and baclofen reportedly provided no substantial benefit, Difficulty sitting due to hyperactivity of hip extensors, Mini rods and z-band broadening were seen in atrophic fibers
CaseNotHPOs: HP:0100543, HP:0003730, HP:0002486, HP:0002353, HP:0002363, HP:0000496, HP:0003202, HP:0003798 (Cognitive impairment, EMG: myotonic runs, Myotonia, EEG abnormality, Abnormality of brainstem morphology, Abnormality of eye movement, Skeletal muscle atrophy, Nemaline bodies)
NotHPOsFreeText: Abnormal metabolic screening, Muscle fiber type grouping
CaseAddInfo: Case is de novo and confirmed via parental testing
CasePreviousTesting: Negative ACTA1 and CRYAB
CaseGenotypingMethod: Based on the Patient 1 results, the same region of TPM3 (Exon 6) was PCR amplified and sequenced in the proband and her parents via bidirectional Sanger sequencing.
Variant: NM_152263.4(TPM3):c.654_656AGA[1] (p.Glu219del)
ClinVar: 235144 https://www.ncbi.nlm.nih.gov/clinvar/variation/235144/
gnomAD: Not in gnomAD
T23159
CaseT23159: Female, 2 days onset
CasePresentingHPOs: HP:0200134, HP:0011167, HP:0010818, HP:0032667, HP:0031475, HP:0032816, HP:0010841, HP:0010845, HP:0006808, HP:0002079, HP:0012753, HP:0002059, HP:0007266, HP:0002273, HP:0011471, HP:0000121, HP:0000141, HP:0000696, HP:0001662, HP:0002045, HP:0000253, HP:0000341, HP:0001525, HP:0001007, HP:0002751, HP:0001371, HP:0001182 (Epileptic encephalopathy, Focal tonic seizure, Generalized tonic seizure, Myoclonic status epilepticus, Nonconvulsive status epilepticus, Neonatal multifocal myoclonic seizure, Multifocal epileptiform discharges, EEG with generalized slow activity, Cerebral hypomyelination, Hypoplasia of the corpus callosum, T2 hypointense basal ganglia, Cerebral atrophy, White matter dysmyelination/demyelination, Tetraparesis, Gastrostomy tube feeding in infancy, Nephrocalcinosis, Amenorrhea, Delayed eruption of permanent teeth, Bradycardia, Hypothermia, Progressive microcephaly, Narrow forehead, Severe failure to thrive, Hirsutism, Kyphoscoliosis, Flexion contracture, Tapered finger)
HPOsFreeText: Thinning of cortical gray matter
CaseNotHPOs: HP:0001272 (Cerebellar atrophy)
NotHPOsFreeText: Hypomyelination of cerebellum and brain stem
CaseAddInfo: Proband confirmed de novo heterozygous by parental sequencing
CasePreviousTesting: Currently on carbamazepime, lamotrigine and lacosamide; previously on pyridoxine, clonazepam, acetazolamide, valproate, phenobarbitone, phenytoin, prednisolone, vigabatrin, topiramate and ketogenic diet
CaseGenotypingMethod: About 10% of the original 290 genes where a single de novo variant had been identified was chosen for targeted sequencing in a new cohort. Most of these individuals had been tested for mutations of known and novel candidate genes as well as pathogenic copy-number variants. These genes were sequenced in the parents and proband to look for de novo variants.
Variant: NM_004171.4(SLC1A2):c.254T>C (p.Leu85Pro)
ClinVar: 254266, https://www.ncbi.nlm.nih.gov/clinvar/variation/254266/
gnomAD: Not in gnomAD
43
Case43: 20 y (at biopsy), Lebanese
Case 43 (Level 2)
CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.1 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1741C>T (p.Arg581Ter)
ClinVar: 554675
CAID: CA364395893
gnomAD: n/a
CaseAddInfo: mut0 type, homozygous mutations.
45
Case45: no age or ethnicity recorded
Case 45 (Level 2)
CasePreviousTesting: same as group. found 1.5 nmol/mg protein/18 h propionate incorporation, 1.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1891delG (p.Ala631GlinfsTer17)
ClinVar: n/a
CAID: CA351288
gnomAD: 0.00002896 (Latino)
CaseAddInfo: mut0 type, homozygous mutations.
42
Case42: 1 y 7 mo (at biopsy), Hmong
Case 42 (Level 2)
CasePreviousTesting: same as group. found 4.5 nmol/mg protein/18 h propionate incorporation, 9.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1663G>A (p.Ala555Thr)
ClinVar: 203850
CAID: CA312769
gnomAD: 0.0003262 (East Asian)
CaseAddInfo: mut- type, homozygous mutations. Additional heterozygous mutations in CUBN gene (Variant 1: NM_001081.3:c.3500G>T, CAID: CA376148913 , gnomAD: 0.00005014, East Asian ) (Variant 2: NM_001081.3:c.6211A>G, CAID: CA5423765 , gnomAD: 0.001003, East Asian )
41
Case41: 6 mo (at biopsy), Pakistani
Case 41 (Level 2)
CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1560G>C (p.Lys520Asn)
ClinVar: n/a
CAID: CA364397073
gnomAD: n/a
CaseAddInfo: mut0 type, homozygous mutations.
40
Case40: Middle Eastern
Case 40 (Level 2)
CasePreviousTesting: same as group. found 1.8 nmol/mg protein/18 h propionate incorporation, 1.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1420C>T (p.Arg474Ter)
ClinVar: 554873
CAID: CA138795916
gnomAD: 0.00003267 (South Asian)
CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.
39
Case39: 1 y (at biopsy), Asian
Case 39 (Level 2)
CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1280G>A (p.Gly427Asp)
ClinVar: 218990
CAID: CA347873
gnomAD: 0.0004011 (East Asian)
CaseAddInfo: mut0 type, homozygous mutations. documented non-consanguinity.
38
Case38: 9 y (at biopsy), German/Polish
Case 38 (Level 2)
CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.1106G>A (p.Arg369His)
ClinVar: 203846
CAID: CA312764
gnomAD: 0.0001504 (East Asian)
CaseAddInfo: mut0 type, homozygous mutations.
37
Case37: 18 mo (at biopsy), Moroccan
Case 37 (Level 2)
CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.5 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.683G>A (p.Arg228Gln)
ClinVar: n/a
CAID: CA3847070
gnomAD: 0.00002905 (Latino)
CaseAddInfo: mut0 type, homozygous mutations.
36
Case36: 14 mo (at biopsy), Hispanic
Case 36 (Level 2)
CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.406G>T (p.Val136Phe)
ClinVar: n/a
CAID: CA364404792
gnomAD: n/a
CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.
35
Case35: 5 y (at biopsy), Hispanic
Case 35 (Level 2)
CasePreviousTesting: same as group. found 0.5 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)
ClinVar: 1887
CAID: CA249732
gnomAD: 0.0008393 (Latino)
CaseAddInfo: mut0 type, homozygous mutations.
33
Case33: 9 mo (at biopsy), Hispanic
Case 33 (Level 2)
CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)
ClinVar: 1887
CAID: CA249732
gnomAD: 0.0008393 (Latino)
CaseAddInfo: mut0 type, homozygous mutations.
32
Case32: 10 y (at biopsy), Arab
Case 32 (Level 2)
CasePreviousTesting: same as group. found 1.0 nmol/mg protein/18 h propionate incorporation, 1.0 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.278G>A (p.Arg93His)
ClinVar: 1880
CAID: CA249728
gnomAD: 0.0004777 (European- Finnish)
CaseAddInfo: mut0 type, homozygous mutations. documented consanguinity.
34
Case34: 3.5 wks (at biopsy), White/Hispanic
Case 34 (Level 2)
CasePreviousTesting: same as group. found 1.6 nmol/mg protein/18 h propionate incorporation, 1.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation
CaseMethod1: same as group
CaseMethod2: same as group
CaseGenotypingMethod: same as group
Variant1: NM_000255.3:c.322C>T (p.Arg108Cys)
ClinVar: 1887
CAID: CA249732
gnomAD: 0.0008393 (Latino)
CaseAddInfo: mut0 type, homozygous mutations.
D
CaseD: Male, French, Quebec
CasePresentingHPOs: HP:0010896, HP:0010897 (Hypersarcosinemia, Hypersarcosinuria)
HPOsFreeText: Elevated blood Sarcosine (229 μmol/l; reference 0-9), Elevated urine Sarcosine (1213 μmol/mmol; reference 0-36)
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
CasePreviousTesting: N/A
CaseGenotypingMethod: DNA was extracted from the probands and immediate family. The whole coding region and the exon-intron boundaries of the SARDH gene was then amplified and sequenced.
Variant: NM_007101.3:c.860C>T (p.Pro287Leu)
ClinVar: 39449 https://www.ncbi.nlm.nih.gov/clinvar/variation/39449/
gnomAD: European (Finnish) 1.692e-4, Overall 1.032e-4 http://gnomad.broadinstitute.org/variant/9-136594942-G-A
GSHSP44 (F)
CaseGSHSP44: Female, 44 yrs onset, Australia/UK
CasePresentingHPOs: HP:0040083, HP:0002317, HP:0002064, HP:0002460, HP:0002395, HP:0007350, HP:0003487, HP:0000012, HP:0012104, HP:0006913, HP:0001761, HP:0031520, HP:0006827 (Toe walking, Unsteady gait, Spastic gait, Distal muscle weakness, Lower limb hyperreflexia, Hyperreflexia in upper limbs, Babinski sign, Urinary urgency, Parietal cortical atrophy, Frontal cortical atrophy, Pes cavus, Groin pain, Atrophy of the spinal cord)
HPOsFreeText: 4/7 disability score, Hip replacement
CaseNotHPOs: HP:0001317, HP:0002464, HP:0100543, HP:0000973, HP:0006938 (Abnormal cerebellum morphology, Spastic dysarthria, Cognitive impairment, Cutis laxa, Impaired vibration sensation at ankles)
NotHPOsFreeText: N/A
CaseGenotypingMethod: Exome sequencing data of 160 index patients with autosomal dominant spastic paraplegia and 275 index patients with autosomal recessive or sporadic spastic paraplegia was examined. 95 patients were screened through panel sequencing. Any determined ALDH18A1 mutations were confirmed by Sanger sequencing.
CasePreviousTesting: N/A
CaseAddInfo: Case is sporadic
Variant reported as c.1949G>T which does not exist in current transcripts
Variant: NM_002860.3:c.1955C>T (p.Ser652Phe)
CAID: CA377700120 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377700120
gnomAD: Not in gnomAD
Patient 3
Case3: Female, 5 yrs report
CasePresentingHPOs: HP:0012072 (Aciduria)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo:
CasePreviousTesting: Partial biotinidase deficiency (19%) was confirmed; Urine AAA (552 mmol/mol creatinine; ref <91) and KAA (251 mmol/mol creatinine) were clearly increased. At 5 years of age, urine AAA and KAA as well as plasma AAA were persistently elevated.
CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.
Variant1: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)
ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/
gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A
Variant2: NM_018706.7(DHTKD1):c.1309G>T (p.Glu437Ter)
ClinVar: 574714 https://www.ncbi.nlm.nih.gov/clinvar/variation/574714/
gnomAD: 0.0001316, https://gnomad.broadinstitute.org/variant/10-12136221-G-T
Proband
CaseF6P: 1 yr report, India
CasePresentingHPOs: HP:0001010, HP:0000750, HP:0001249, HP:0006801, HP:0004923 (Hypopigmentation of the skin, Delayed speech and language development, Intellectual disability, Brisk deep tendon reflexes, Hyperphenylalaninemia)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Family is consanguinous, Predicted to undergo NMD
CasePreviousTesting: Blood phenylalanine before treatment was 1260 μmol/l, Blood tyrosine before treatment was N/A μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.
CaseGenotypingMethod: Genomic DNA was isolated from blood samples of proband and family members. PCR amplification and sequencing was used to screen for mutations. Each mutation was confirmed by bi-directional DNA sequencing.
Variant: NM_000277.3(PAH):c.526C>T (p.Arg176Ter)
ClinVar: 102723 https://www.ncbi.nlm.nih.gov/clinvar/variation/102723/
gnomAD: 0.00008012, http://gnomad.broadinstitute.org/variant/12-103249094-G-A
Patient 1
CaseAL1: Male, 14 yrs report
CasePresentingHPOs: HP:0012120 (Methylmalonic aciduria)
HPOsFreeText: Malonic acidemia/uria
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Born to non-consanguineous Ashkenazi Jewish parents; Proband is confirmed homozygous via parental testing
CasePreviousTesting: Newborn screening identified these probands, with subsequent urine organic acid analysis by gas chromatography mass spectroscopy confirming CMAMMA; Initial urine MMA level was 891 μmol/mmol creatinine; Confirmatory testing showed a urine MMA of 745 μmol/mmol creatinine (normal <25) and MA of 60 μmol/mmol creatinine (normal <6); Plasma MMA level was 18 μmol/l (normal <0.5); No other organic acid abnormality was detected. Carnitine levels, acylcarnitine profiles, plasma amino acids, ammonia, blood gas values, total homocysteine, folate and vitamin B12 levels were all within reference ranges, and the mothers were not vitamin B12 deficient; MCD activity in fibroblasts were within the reference range
CaseGenotypingMethod: Genomic DNA was isolated from fibroblasts and all exons and flanking introns of MLYCD, along with ACSF3, were subject to Sanger sequencing.
Variant: NM_001243279.3:c.1411C>T (p.Arg471Trp)
ClinVar: 31137, https://www.ncbi.nlm.nih.gov/clinvar/variation/31137
gnomAD: 0.007046, https://gnomad.broadinstitute.org/variant/16-89211719-C-T
II.2
CaseBII-2: N/A
CasePresentingHPOs: N/A
HPOsFreeText: Pretreatment phenylalanine level at 270 umol/L
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: N/A
Variant1: NM_000277.3(PAH):c.688G>A (p.Val230Ile)
ClinVar: 102784 https://www.ncbi.nlm.nih.gov/clinvar/variation/102784/
gnomAD: 0.0009025, https://gnomad.broadinstitute.org/variant/12-102855154-C-T?dataset=gnomad_r3
Variant2: NM_000277.3(PAH):c.1241A>G (p.Tyr414Cys)
ClinVar: 593 https://www.ncbi.nlm.nih.gov/clinvar/variation/593/
gnomAD: 0.0005264, https://gnomad.broadinstitute.org/variant/12-102840474-T-C?dataset=gnomad_r3
AC014 II-1
CaseAC014_II-1: Female, 3 yrs report, Lebanon
CasePresentingHPOs: HP:0001992, HP:0025356 (Organic aciduria, Psychomotor retardation)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Parents are consanguineous, Proband is confirmed homozygous for this variant via parental testing, Siblings are healthy
CasePreviousTesting: Identified by the assessment of urinary organic acids by gas chromatography–mass spectrometry; Accumulation of N-acetylated amino acids was much less pronounced than in previously reported patients
CaseGenotypingMethod: Genomic DNA was extracted either from peripheral blood or EBV-transformed lymphocytes. PCR-amplification and bidirectional sequencing of all exons and exon-intron boundaries of ACY1 was performed.
Variant: NM_000666.3(ACY1):c.1132C>T (p.Arg378Trp)
ClinVar: 493363, https://www.ncbi.nlm.nih.gov/clinvar/variation/493363/
gnomAD: 0.00001499 in ExAC, https://gnomad.broadinstitute.org/variant/3-52022996-C-T?dataset=exac
Table 2
Case7: Female, Japan, Asian
CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0003798, HP:0001561, HP:0001558, HP:0000602 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Nemaline bodies, Polyhydramnios, Decreased fetal movements, Ophthalmoplegia)
HPOsFreeText: Atrophic myofibers
CaseNotHPOs: HP:0001627 (Cardiac abnormality)
NotHPOsFreeText: N/A
CaseAddInfo: Severe congenital myopathy, Alive at 1 yr 7 months
CasePreviousTesting: N/A
CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.
Variant1: NM_198271.4:c.349C>T (p.Gln117*)
CAID: CA353477271 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.349C%3ET
gnomAD: Not in gnomAD
Variant2: NM_198271.4:c.1218delA (p.Lys406Asnfs*11)
CAID: CA909806380 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_198271.4%3Ac.1218delA
gnomAD: Not in gnomAD
Table 2
Case11b: Male, Sweden
CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness)
HPOsFreeText: N/A
CaseNotHPOs: HP:0001627 (Cardiac abnormality)
NotHPOsFreeText: N/A
CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period
CasePreviousTesting: N/A
CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.
Variant: NM_198271.4:c.1069G>T (p.Glu357Ter)
ClinVar: 162219 https://www.ncbi.nlm.nih.gov/clinvar/variation/162219/
gnomAD: Not in gnomAD
Table 2
Case1b: Female, Algeria
CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001622 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Preterm delivery)
HPOsFreeText: N/A
CaseNotHPOs: HP:0001627 (Cardiac abnormality)
NotHPOsFreeText: N/A
CaseAddInfo: Severe congenital myopathy, Deceased in neonatal period, Parents are consanguineous
CasePreviousTesting: N/A
CaseGenotypingMethod: Linkage analysis combined with homozygosity mapping was used to identify candidate chromosomal loci. Whole exome sequencing in this family revealed likely pathogenic mutations in LMOD3 which agreed with the aforementioned analysis and was consistent with autosomal recessive inheritance.
Variant: NM_198271.4(LMOD3):c.138dup (p.Ser47Glnfs)
ClinVar: 162215 https://www.ncbi.nlm.nih.gov/clinvar/variation/162215/
gnomAD: European (Non-Finnish) 8.879e-6, Overall 8.049e-6 https://gnomad.broadinstitute.org/variant/3-69171399-T-TG
CaseWG2098: 3 yrs onset
CasePresentingHPOs: HP:0001251, HP:0004302, HP:0001260, HP:0002313, HP:0012120 (Ataxia, Functional motor deficit, Dysarthria, Spastic paraparesis, Methylmalonic aciduria)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Proband has normal 14C-propionate incorporation, suggesting normal MCEE protein activity level; The high gnomAD frequency and homozygotes suggests this is likely a benign polymorphism
CasePreviousTesting: Normal MRI; Propionate Incorporation w/o hydroxycobalamin at 7.0 nmols/mg protein/18hr; Propionate Incorporation with hydroxycobalamin at 8.2 nmols/mg protein/18hr; Adenosylcobalamin synthesis percentage at 12.7%; Elevated methylmalonic values of 621 µmol/mmol creatinine (reference 0.8-5.2 µmol/mmol creatinine)
CaseGenotypingMethod: Genomic DNA was extracted from patient fibroblasts, sequenced, and the three MCEE/thirteen MUT exons were analyzed and amplified. Any reported mutations were resequenced from fresh PCR product.
Variant: NM_032601.4(MCEE):c.178A>C (p.Lys60Gln)
ClinVar: 203812, https://www.ncbi.nlm.nih.gov/clinvar/variation/203812/
gnomAD: 0.01463 (10 homozygotes), https://gnomad.broadinstitute.org/variant/2-71351536-T-G
III-3
CaseDOIII-3: Female, 12 yrs report, White
CasePresentingHPOs: HP:0001531, HP:0002020, HP:0001942, HP:0001944, HP:0002789, HP:0002013, HP:0002014, HP:0002919, HP:0012120 (Failure to thrive in infancy, Gastroesophageal reflux, Metabolic acidosis, Dehydration, Tachypnea, Vomiting, Diarrhea, Ketonuria, Methylmalonic aciduria)
HPOsFreeText: Elevated methylcitric acid
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Parents are first-cousin consanguineous, Son is healthy but second daughter shares phenotypes with the proband and shows clear methylmalonic aciduria, Proband and her sister are confirmed homozygous for this variant via parental testing
CasePreviousTesting: Serum methylmalonic acid was 1314 ng/ml (normal < 32); Vitamin B12 levels were normal (927 pg/ml, normal 200–1100); Vitamin B12 injections improved patient condition; At 12.5 yrs carnitine, plasma AAs, blood counts, and basic metabolic panels are normal but methylmalonic acid remains high at 180–1456 mmol/mol creatinine; Fibroblasts showed normal AdoCbl synthesis, contrary to expected from MMAA or MMAB variants; MUT and MMAB were sequenced with no variation found
CaseGenotypingMethod: Genomic DNA was isolated and PCR-amplified before directly sequencing all exons and flanking intronic sequences of the MCEE gene. Restriction enzyme digest confirmed the phase of the variant in the proband and the parents.
Variant: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)
ClinVar: 2343, https://www.ncbi.nlm.nih.gov/clinvar/variation/2343/
gnomAD: 0.0004884, https://gnomad.broadinstitute.org/variant/2-71351575-G-A
AHN15.1
CaseAHN15.1: Australia, White
CasePresentingHPOs: HP:0008353 (Neutral hyperaminoaciduria)
HPOsFreeText: N/A
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Variants segregate with the disease
CasePreviousTesting: Hartnup aminoaciduria profile was confirmed by ion exchange high performance liquid chromatography;
CaseGenotypingMethod: All SLC6A19 exons and flanking introns were directly amplified and sequenced from genomic DNA.
Variant1: NM_001003841.3(SLC6A19):c.517G>A (p.Asp173Asn)
ClinVar: 2019 https://www.ncbi.nlm.nih.gov/clinvar/variation/2019/
gnomAD: 0.003016, https://gnomad.broadinstitute.org/variant/5-1212453-G-A
Variant2: NM_001003841.3:c.850G>A (p.Gly284Arg)
CAID: CA3182918, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA3182918
gnomAD: 0.00005440, https://gnomad.broadinstitute.org/variant/5-1214143-G-A
3
CaseCA3: Male, 6 months diagnosis
CasePresentingHPOs: HP:0001644, HP:0001875, HP:0001508, HP:0003535, HP:0003756, HP:0030319, HP:0003551 (Dilated cardiomyopathy, Neutropenia, Failure to thrive, 3-Methylglutaconic aciduria, Skeletal myopathy, Facial weakness, Difficulty climbing stairs)
HPOsFreeText: N/A
CaseNotHPOs: HP:0003107 (Abnormal circulating cholesterol concentration)
NotHPOsFreeText: N/A
CaseAddInfo: Cardiac transplant 11 months after presentation; Variant also found in mother and grandmother
CasePreviousTesting: N/A
CaseGenotypingMethod: The TAZ gene was PCR amplified in three fragments and directly sequenced in the mother and proband.
Variant: NM_000116.5(TAZ):c.589G>A (p.Gly197Arg)
ClinVar: 11105, https://www.ncbi.nlm.nih.gov/clinvar/variation/11105/
gnomAD: Not in gnomAD
Subject A
CaseGuA: Male, 6 weeks onset
CasePresentingHPOs: HP:0200134, HP:0020217, HP:0002069, HP:0010852, HP:0012012, HP:0012017, HP:0012018, HP:0010841, HP:0025152, HP:0030211, HP:0008936, HP:0002061, HP:0006986, HP:0002187, HP:0011344, HP:0001344, HP:0012448, HP:0002283, HP:0002079, HP:0012696, HP:0002500, HP:0012751 (Epileptic encephalopathy, Focal aware motor seizure, Bilateral tonic-clonic seizure, EEG with parietal focal spike waves, EEG with parietal focal spikes, EEG with temporal focal spikes, Multifocal epileptiform discharges, Poor visual behavior for age, Slow pupillary light response, Muscular hypotonia of the trunk, Lower limb spasticity, Upper limb spasticity, Profound intellectual disability, Severe global developmental delay, Absent speech, Delayed myelination, Global brain atrophy, Thin corpus callosum, Abnormal thalamic MRI signal intensity, White matter abnormalities, Abnormal basal ganglia MRI signal intensity)
HPOsFreeText: Dyskinetic movements of arms, In ability to sit unsupported, Abnormal MRI signal in putamen and caudate
CaseNotHPOs: N/A
NotHPOsFreeText: N/A
CaseAddInfo: Variant is confirmed heterozygous de novo
CasePreviousTesting: Investigations include electroencephalography (EEG), head MRI, neurometabolic testing, and chromosome microarray; Individuals with self-limiting benign electroclinical syndromes, such as childhood absence epilepsy (onset > 4 years), were excluded; Capture of right arm jerks and chin twitching showed no EEG correlate; Head circumference was 45.1 cm at 8 months (50%), 52 cm at 5 years (50th percentile); Partial response to phenobarbital, levetiracetam, and clobazam; Longest seizure-free period was 16 months
CaseGenotypingMethod: Variants within co-expressed candidate genes in Table S1 were extracted from exome sequencing data. Variants were annotated and were verified with Sanger sequencing of the proband and parents.
Variant: NM_004171.4(SLC1A2):c.244G>A (p.Gly82Arg)
ClinVar: 438736, https://www.ncbi.nlm.nih.gov/clinvar/variation/438736/
gnomAD: Not in gnomAD
Current age 26 years