CasePU7: Female, 8 months report, White

CasePresentingHPOs: HP:0012120, HP:0003193, HP:0004322, HP:0000964 (Methylmalonic aciduria, Allergic rhinitis, Short stature, Eczema)

HPOsFreeText: Malonic aciduria

CaseNotHPOs: HP:0003353 (Propionyl-CoA carboxylase deficiency)

NotHPOsFreeText: N/A

CaseAddInfo: Proband cannot be confirmed in-trans due to lack of parental testing

CasePreviousTesting: 6.3 propionate incorporation (nmol/mg protein/18 h); Plasma homocysteine and plasma amino acid levels were within the reference range; MMA levels responded partially to cobalamin treatment

CaseGenotypingMethod: Genomic DNA was extracted from fibroblasts. Next-generation sequencing was performed with 24 genes being sequenced including all coding exons and 20 bp of their flanking intronic regions.

CasePMIDs: PMID:30740739 as Case 5

Variant1: NM_001243279.3:c.1239+2T>G

CAID: CA397142431, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397142431

gnomAD: Not in gnomAD

Variant2: NM_001243279.3(ACSF3):c.1672C>T (p.Arg558Trp)

ClinVar: 31134, https://www.ncbi.nlm.nih.gov/clinvar/variation/31134/

gnomAD: 0.004790, https://gnomad.broadinstitute.org/variant/16-89220556-C-T

CaseLE19: Male, 16 yrs report

CasePresentingHPOs: HP:0000964, HP:0002650, HP:0000501, HP:0000518, HP:0000750, HP:0010862, HP:0002572 (Eczema, Scoliosis, Glaucoma, Cataract, Delayed speech and language development, Delayed fine motor development, Episodic vomiting)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants not confirmed in-trans due to lack of parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2; Congenital unilateral persistent hyperplastic primary vitreous (PHPV), causing glaucoma and cataract

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3(ACSF3):c.1075G>A (p.Glu359Lys)

ClinVar: 31136, https://www.ncbi.nlm.nih.gov/clinvar/variation/31136/

gnomAD: 0.001054, https://gnomad.broadinstitute.org/variant/16-89180844-G-A

Variant2: NM_001243279.3:c.1239+2T>G

CAID: CA397142431, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397142431

gnomAD: Not in gnomAD

CaseLE12: Female, 23 yrs report

CasePresentingHPOs: HP:0002725 (Systemic lupus erythematosus)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variant 1 homozygous, with variant 2 in-cis with one copy confirmed via parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3:c.1553C>A (p.Ala518Asp)

CAID: CA8238286, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8238286

gnomAD: 0.00006153, https://gnomad.broadinstitute.org/variant/16-89212397-C-A

Variant2: NM_001243279.3:c.473C>T (p.Pro158Leu)

CAID: CA8237662, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA8237662

gnomAD: 0.0002823, https://gnomad.broadinstitute.org/variant/16-89167562-C-T

CaseLE25: Male, 7 yrs report

CasePresentingHPOs: HP:0000639 (Nystagmus)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants confirmed in-trans via parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3:c.634G>A (p.Val212Met)

CAID: CA397135749, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397135749

gnomAD: 0.00004778, https://gnomad.broadinstitute.org/variant/16-89167723-G-A

Variant2: NM_001243279.3(ACSF3):c.1470G>C (p.Glu490Asp)

ClinVar: 377432, https://www.ncbi.nlm.nih.gov/clinvar/variation/377432/

gnomAD: 0.001502, https://gnomad.broadinstitute.org/variant/16-89211778-G-C

CaseLE17: Male, 7 yrs report

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Variants not confirmed in-trans due to lack of parental testing

CasePreviousTesting: Specific plasma MMA levels, urine MMA levels, urine MA levels, and MMA/MA ratio available in Table 2

CaseGenotypingMethod: See Group

Variant1: NM_001243279.3:c.774_775del (p.Trp259Glyfs*10)

CAID: CA1139532418, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA1139532418

gnomAD: Not in gnomAD

Variant2: NM_001243279.3(ACSF3):c.1672C>T (p.Arg558Trp)

ClinVar: 31134, https://www.ncbi.nlm.nih.gov/clinvar/variation/31134/

gnomAD: 0.004790, https://gnomad.broadinstitute.org/variant/16-89220556-C-T

CaseREU3: Male, 6 yrs report, United Kingdom

CasePresentingHPOs: HP:0001337, HP:0001263, HP:0000717, HP:0001382, HP:0012120 (Tremor, Global developmental delay, Autism, Joint hypermobility, Methylmalonic aciduria)

HPOsFreeText: Malonic aciduria

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this variant

CasePreviousTesting: All participants had undergone multiple standard and specialized biochemical tests, invasive procedures (e.g. muscle and/or skin biopsy, lumbar puncture) and targeted gene testing; MRI head not performed

CaseGenotypingMethod: 16 broad classes of IEM was target enriched and sequenced. Any suspected pathogenic variants were confirmed with Sanger sequencing.

Variant: NM_001243279.3:c.1453A>C (p.Ser485Arg)

CAID: CA397148172, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397148172

gnomAD: Not in gnomAD

FamilySVDV: N/A

FamilyPresentingHPOs: HP:0001298, HP:0002179, HP:0010553, HP:0003487, HP:0002300, HP:0012120 (Encephalopathy, Opisthotonus, Oculogyric crisis, Babinski sign, Mutism, Methylmalonic aciduria)

HPOsFreeText: Diffusely increased T2 signal in the white matter, Malonic acidemia/uria

FamilyNotHPOs: N/A

NotHPOsFreeText: N/A

FamilyGenotypingMethod: Diagnostic exome sequencing was performed and identified compound heterozygous missense mutations in ACSF3.

FamilyPreviousTesting: Both patients improved clinically after treatment with lorazepram; MMA concentrations were consistently elevated in urine as well as plasma; The range of urine MA excretion was 15–201 and 13–226 μmol/mmol creatinine in patient A and patient B, respectively; Control values vailable in Fig 2 and 3

FamilyAddInfo: N/A

Variant1: NM_001243279.3(ACSF3):c.1075G>A (p.Glu359Lys)

ClinVar: 31136, https://www.ncbi.nlm.nih.gov/clinvar/variation/31136/

gnomAD: 0.001054, https://gnomad.broadinstitute.org/variant/16-89180844-G-A

Variant2: NM_001243279.3:c.311A>T (p.Asn104Ile)

CAID: CA397133842, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397133842

gnomAD: 0, https://gnomad.broadinstitute.org/variant/16-89167400-A-T

Affected: 2

Unaffected: 0

Segregations: N/A

AddSegregationInfo: Parents are unrelated; Not enough info

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