Biallelic

Case#: Patient 2, male, 5 years (report), Turkish

CaseHPOs: HP:0003235, HP:0002240 (hypermethioninemia, hepatomegaly)

CaseHPOsFreeText: Identified by newborn screening.

CaseNotHPOsFreeText: No signs of hepatic failure, no clinical symptoms.

CasePreviousTesting: On day of life 3, elevated methionine concentration in blood of 390 µmol/L (normal 20–40). Total homocysteine in plasma was 59 µmol/L (normal 5–15). At later age (not specified), plasma methionine ranged from 1000 to 2070 µmol/L, while total homocysteine in plasma ranged from 30 to 55 µmol/L.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

Variant: c.125T>C (p.Leu42Pro) (homozygous)

ClinVar: N/A

CAID: CA377363776

gnomAD: The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population.

VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to ~10 and ~20% of wild type respectively (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

Points: 0.5

Biallelic

Case#: Patient 1, female, 25 years (report), German

CaseHPOs: HP:0003235 (hypermethioninemia)

CaseHPOsFreeText: Identified by newborn screening.

CaseNotHPOsFreeText: Hepatic, vascular or neurological symptoms have never been noted, and cranial MRI was normal at the age of 20 years

CasePreviousTesting: Over a period of 25 years, methionine concentrations ranged from 850 to 1100 µmol/L (normal 20–40), and fasting total plasma homocysteine was 30–45 µmol/L (normal 5–15).

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

Variant: c.65C>T (p.Ser22Leu) (homozygous)

ClinVar: N/A

CAID: CA377364910

gnomAD: The highest population minor allele frequency in gnomAD is 0.00002891 (Latino)

VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to <50% of wild type (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

CaseAddInfo: Parents are reported to be unrelated

Points: 0.5

Biallelic

Case#: Hazelwood case, 43 yrs (report), male

CaseHPOs: HP:0003235, HP:0012185 (hypermethioninemia, carpal tunnel)

CaseHPOsFreeText: Elevated urine methionine; Halitosis due to elevated breath dimethylsulphide; mild aortic insufficiency “attributable to rheumatic fever”, Gilbert disease (based on transient hyperbilirubinemia)

CaseNotHPOsFreeText: Normal brain MRI with no evidence of demyelination (age 43 years). Developmentally, physically, and mentally normal. Liver histology was normal (age 31 years). Normal neurologic exam. Normal electrolytes and blood chemistry, normal cholesterol, normal AST, ALT, and LDH, normal testosterone.

CasePreviousTesting: 25–30-fold elevation of plasma methionine (716-941 uM; controls 15-40, mean 26). Normal plasma tyrosine, normal homocysteine. Urine methionine 352-578 umol/day (controls 39-225, mean 99). Urine transamination metabolites 174-254 mmol/mol creatinine (controls ~1.8); breath dimethylsulfide 2.52-5.86 nmol/L (controls 0.13-0.65, mean 0.34); 7% normal activity of hepatic methionine adenosyltransferase in liver; hepatic activities of cystathionine-beta-synthase, gamma-cystathionase, and betaine homocysteine methyltransferase were normal.

CaseMethod1: SSCP

CaseMethod2: Sequencing

CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

Variant: c.539insTG (homozygous)

ClinVar: NA

CAID: CA210326818

gnomAD: The highest population minor allele frequency = 0.00001759 (non-Finnish); no homozygotes in any population.

CaseAddInfo: Both parents are heterozygous for the variant. Possible consanguinity - the patient’s father’s maternal grandfather and his mother’s paternal grandmother shared the same name and had lived their entire lives in an isolated West Virginia community.

CasePMIDs: 3812486, 3339126

Points: 1.5 points. This individual is homozygous for a frameshift variant in MAT1A. The highest population minor allele frequency = 0.00001759 (non-Finnish); no homozygotes in any population. The score is reduced because only some, but not all, causes of hypermethioninemia have been ruled out.

Biallelic

Case#: Patient 10, male, 5.9 years (report)

CaseHPOs: HP:0003235 (hypermethioninemia)

CaseHPOsFreeText: Identified by newborn screening

CaseNotHPOsTest: Normal neurologic and/or muscular status, IQ 111

CasePreviousTesting: Plasma methionine 484-742; transamination products in plasma 5.01-6.21 uM (normal 0.2-0.54) and in urine 45.2-75.6 mmol/mol creatinine (normal 1.2-4.6), urine dimethylsuphide 10 nM (normal – trace-2 nM).

Variant: p.Arg199Cys (homozygous)

ClinVar: N/A

CAID: CA5576749

gnomAD: The highest population minor allele frequency in gnomAD is 0.0001735 (Latino); no homozygotes in any population.

VariantEvidence: When the variant was expressed in bacteria, the amount of MAT1A protein was reduced on Western blot, and MAT1A activity was 11% of normal.

CasePMIDs: 7573050

Points: 1 point. This individual is homozygous for a missense change, p.Arg199Cys, in MAT1A. When the variant was expressed in bacteria, the amount of MAT1A protein was reduced on Western blot, and MAT1A activity was 11% of normal. The highest population minor allele frequency in gnomAD is 0.0001735 (Latino); no homozygotes in any population.

Biallelic

Case#: Patient 8, female, 14 years (report)

CaseHPOs: HP:0003235, HP:0001249, HP:0001332 (Hypermethioninemia, Intellectual disability, dystonia)

CaseHPOsFreeText: demyelination

CasePreviousTesting: Plasma methionine 1114–1629; transamination products in plasma 41.2 uM (normal 0.2-0.54) and in urine 992 mmol/mol creatinine (normal 1.2-4.6), urine dimethylsuphide 535 nM (normal – trace-2 nM).

Variant: c.1043_1044delTG (homozygous)

ClinVar: NA

CAID: CA594460387

gnomAD: The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population

VariantEvidence: When the variant was expressed in bacteria, the amount and size of the protein was reduced on Western blot, and there was no detectable MAT1A activity.

CasePMIDs: 7573050 Points: 1 point. This individual is homozygous for a frameshift variant in MAT1A. When the variant was expressed in bacteria, there was no detectable MAT. The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population. The score is reduced because other causes of hypermethioninemia have not been ruled out.

Case: Patient C, 11 years, female CaseHPOs: HP:0003235, HP:0011098, Hypermethioninemia, speech dyspraxia

CaseHPOsFreeText: “pronounced hypermethioninaemia on neonatal screening”, cleft lip and palate; Hypermethioninaemia has persisted; unpleasant odor with high blood concentrations of mercaptans; fine nystagmus, dysdiadochokinesis, and increased tendon reflexes led to brain MRI and CT at age 11 years which showed demyelination, calcification of basal ganglia, IQ 87; normal myelination and all symptoms resolved after 12 months treatment with S-adenosylmethionine toluene sulphonate.

CaseNotHPOs: Homocystine was not detected in plasma or urine,normal liver function tests.

CasePreviousTesting: Plasma methionine 600–1,400 umol/L; otherwise normal amino acids. 5-methyl tetrahydrofolate 329, 232 nmol/L (normal 23-170, mean 85+/-41), normalized after 12 months on S-adenosylmethionine toluene sulphonate; S-adenosylmethionine 70, 87 nmol/L (normal 172-450, mean 255 +/-69), improved but still low after 12 months on S-adenosylmethionine toluene sulphonate.

Variant: c.826dupG (homozygous)

ClinVar: N/A

CAID: CA5576692

gnomAD: The highest population minor allele frequency in gnomAD is 0.00003298 (S. Asian); no homozygotes in any population.

VariantEvidence: When the variant was expressed in bacteria, the amount and size of the protein was reduced on Western blot, and there was no detectable MAT1A activity.

CaseAddInfo: The mother is heterozygous for the variant; DNA testing results for the father are not available.

CasePMIDs: 1683972

Points: 2 points. This patient is homozygous for a frameshift variant in MAT1A. When the variant was expressed in bacteria, there was no detectable MAT activity. The highest population minor allele frequency in gnomAD is 0.00003298 (S. Asian); no homozygotes in any population.

Biallelic

Case#:15, 5 months (report), Korean, female

CaseHPOs: HP:0003235, (hypermethioninemia)

CaseNotHPOsFreeText: No neurologic problems or developmental delay; no treatment or special diet.

CaseNotHPOs:

CasePreviousTesting: At 5 months and 25 months, respectively, plasma methionine 300.2, 87.7 umol (normal <50), plasma homocysteine 14.4, 5.4 umol (<15 umol)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: All nine MAT1A exons (exon I to IX) and exon–intron boundaries were amplified by polymerase chain reaction (PCR) and directly sequenced.

Variant: c.487C>T (p.Arg163Trp) (homozygous)

ClinVar: N/A

CAID: CA5576782

gnomAD: The highest population minor allele frequency in gnomAD is 0.00006152 (African); no homozygoutes in any population.

VariantEvidence: None.

CaseAddInfo: The mother is heterozygous, the father had only the wild type allele in leukocyte DNA. Biparental inheritance was proven by microsatellite analysis suggesting that either the father is mosaic or this is a de novo variant.

CasePMIDs:

Points: 0.25 points. This individual is homozygous for a missense variant in MAT1A. The highest population minor allele frequency in gnomAD is 0.00006152 (African); no homozygotes in any population. The score is reduced because no functional evidence is available to support the deleterious impact of this variant.

Biallelic

Case#: 14, Korean, female, 58 months (report)

CaseHPOs: HP:0003235, (hypermethioninemia)

CaseNotHPOsFreeText: No neurologic problems or developmental delay; no treatment or special diet.

CasePreviousTesting: At 20 days and 58 months, respectively, Plasma methionine 1352.6, 815.2 umol (normal <50), plasma homocysteine 21.1, 19.06 umol (<15 umol)

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: All nine MAT1A exons (exon I to IX) and exon–intron boundaries were amplified by polymerase chain reaction (PCR) and directly sequenced.

Variant: 1) c.895C>T (p.Arg299Cys); 2) c.1005C>G (p.Tyr335X)

ClinVar: 1) 418870 2) N/A

CAID: 2) CA377360418

gnomAD: The highest population minor allele frequency in gnomAD for c.895C>T (p.Arg299Cys) is 0.0001431 (East Asian). c.1005C>G (p.Tyr335X) is not in gnomAD

VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to ~15% and ~20% of wild type respectively (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

CaseAddInfo: The mother is heterozygous for the nonsense variant, methionine levels are not available.

Points: 1 point. This individual and her sister, who also has hypermethioninemia, are compound heterozygous for a missense variant, p.Arg299Cys, and a nonsense variant in MAT1A (p.Tyr335X). While the nonsense variant occurs in the second to last exon of it is further than 50 bp from the 3’ end of the exon (~80 bp), and therefore should be identified by nonsense-mediated decay. The highest population minor allele frequency in gnomAD for c.895C>T (p.Arg299Cys) is 0.0001431 (East Asian). c.1005C>G (p.Tyr335X) is not in gnomAD. The score is reduced because other causes of hypermethioninemia have not been ruled out.

Monoallelic, AD

Case#: Muriello case

CaseHPOs: HP:0003235 (hypermethioninemia)

CaseHPOsFreeText: Elevated methionine on newborn screen. Intermottent elevations of ALT (66 and 88 U/L) with normal AST, alkaline phosphatase and total bilirubin.

CaseNotHPOsFreeText: Normal plasma homocysteine

CasePreviousTesting: Plasma methionine 0.81 mg/dL (54 μmol/L) at 1 day, 1.08 mg/dL (73 μmol/L) at 16 days (normal < 0.8 mg/dL). Methionine concentration was 175, 185, 192, 136, 75 μmol/L (reference range 9–43 μmol/L) at ages 3.5 weeks, 2 months, 3 months, 5 months, and 12 months, respectively. Normal plasma homocysteine, normal tyrosine. Normal S-adenosylmethionine, and S-adenosylhomocysteine.

CaseGenotypingMethod: WES

Variant: NM_000429.2:c.776C>T (p.Ala259Val) (heterozygous)

ClinVar: 279845

gnomAD: The highest population minor allele frequency in gnomAD is 0.00006437 (African)

VariantEvidence: In the dimerization domain, like p.R264H. 80% reduction of the MAT activity

CaseAddInfo: The variant is maternally inherited. The mother had a mild elevation of methionine of 50 μmol/L (normal range 10–42) at 27 years of age; this was normal on repeat at 28 years old (33 umol/L) Transaminases were normal on both occasions, but she had a history of elevated liver enzymes as a child including a hepatitis-like illness, which lasted months.

CasePMIDs:

Points: 0.5 This patient and her mother are heterozygous for a missense variant in MAT1A. The highest population minor allele frequency in gnomAD is 0.00006437 (African). The Ala259 residue is located in the dimerization interface of the protein and is predicted to act in a dominant negative fashion by interfering with the dimerization (MAT III) or tetramerization (MAT I) of the enzyme.