Case30 Female, 24yo diagnosis (Family 25)

CasePresentingHPOs HP:0001083, HP:0001256, HP:0001263, HP:0002625, HP:0002204

(Lens dislocation, Mild intellectual disability, Developmental delay, Deep vein thrombosis, Pulmonary embolism)

HPOsFreeText Presented with a pulmonary embolus at 23yo after birth of son, presumably secondary to deep vein thrombosis. Patient's plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine.

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Diagnosed by family screen and deep vein thrombosis.

Variant 1. NM_000071.2(CBS):c.536_553del18 (p.Asp179_Leu184del), 2. NM_000071.2(CBS):c.1105C>T (p.Arg369Cys), comp het

ClinVar 1. 198388, 2. 212860

gnomAD 1. MAF=0.00002683(European(non-Finnish), no homozygotes, 2. MAF= 0.006796(Ashkenazi Jewish), 5 homozygotes

CaseAddInfo mother of patient 29

CasePMIDs n/a

Case12 4yo diagnosis, Anglo-Celtic

CasePresentingHPOs n/a

HPOsFreeText Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

CaseNotHPOs HP:0001249, HP:0001083

(Intellectual disability, Lens dislocation)

NotHPOsFreeText no other sequelae

CasePreviousTesting Diagnosis was based on family screen. Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.430G>A (p.Glu144Lys), 2. NM_000071.2(CBS):c.146C>T (p.Pro49Leu), compound heterozygous

ClinVar 1. 122, 2. 212872

gnomAD 1. MAF=0.00009799(South Asian), no homozygotes, 2. MAF=0.0003116(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case33 41yo diagnosis, South African

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Diagnosis was based on dislocated lens and skeletal deformities. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.494G>A (p.Cys165Tyr), 2. NM_000071.2:c.1622dup (p.Asn541LysfsTer?), comp het

ClinVar 1. 495531

CAID 2. register

gnomAD 1. MAF=0.00001308(European(non-Finnish)), no homozygotes, 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case26 2yo diagnosis, Australia, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0010864, HP:0000939, HP:0001263

(Lens dislocation, Severe intellectual disability, Osteoporosis, Developmental delay)

HPOsFreeText Patient had severe osteoporosis and was diagnosed on the basis of developmental delay and osteogenesis impefecta type IV. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs n/a

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided. (PMID:9156316): Urinary homocysteine was 42μmol/l before and 14μmol/l after treatment with betaine, folic acid, and aspirin.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS. (PMID:9156316): c.992C>A variant was also confirmed with HinfI restriction digest. A G mismatch was introduced to the 3' end of the antisense primer used to amplify the region in order to create the Hinfl restriction site as c.992C>A does not do so on its own. While the father and control sample had only an uncleaved 105bp band, both a 73bp and 32bp fragment were detected on HinfI restriction digestion analysis of the mother and proband.

Variant 1. NM_000071.2(CBS):c.992C>A (p.Ala331Glu), 2. NM_000071.2:c.444dup, comp het

ClinVar 1. 212857

CAID 2. register

gnomAD 1. MAF=0.000008824(European(non-Finnish), no homozygotes, 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs 9156316

Case20 7yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0002650

(Lens dislocation, Scoliosis)

HPOsFreeText Diagnosis based on lens dislocation. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.919G>A (p.Gly307Ser), 2. NM_000071.2(CBS):c.494G>A (p.Cys165Tyr), comp het

ClinVar 1. 117, 2. 495531

gnomAD 1. MAF=0.00041539(Other), no homozygotes, 2. MAF= 0.00001308(European(non-Finnish)), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case9 11yo diagnosis, Anglo-Celtic

CasePresentingHPOs n/a

HPOsFreeText Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

CaseNotHPOs HP:0001249, HP:0001083

(Intellectual disability, Lens dislocation)

NotHPOsFreeText no other sequelae

CasePreviousTesting Diagnosis was based on family screen. Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.1221delC (p.Trp408Glyfs), compound heterozygous

ClinVar 1. 120, 2. 495530

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.000008802(European(non-Finnish), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case14 29yo diagnosis, Australia, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0002751, HP:0000939

(Lens dislocation, Kyphoscoliosis, Osteoporosis)

HPOsFreeText Diagnosis was based on dislocated lens and skeletal deformity. Patient has severe kyphoscoliosis. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient had a partial response to the treatment. Homocystine levels were sharply reduced on pyridoxine and folate treatment, but levels did not fall below 20μmol (nv <60μmol) on this treatment alone. (PMID:9156316:): In this study, patient was found to have mild intellectual disability and osteoporosis at 50yo.

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided. (PMID:9156316): Serum homocysteine was 100μmol/l and methionine was 18μmol/l after five years of treatment. Addition of betaine(3g twice per day) lowered homocysteine to 18μmol/l which remained <50μmol for years.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.1058C>T (p.Thr353Met), comp het

ClinVar 1. 120, 2. 131

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.0002916(African), no homozygotes

CaseAddInfo Patient carries a common 68bp insertion, 88ins68, variant that does not cause hyperhomocysteinemia. (PMID:9156316): Additionally is heterozygous for a c.699C>T(Y233Y) synonymous variant as well as homozygous c.1080T>C(A360A) synonymous variants.

CasePMIDs 9156316

Case24 6yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Patient had marfanoid features and was diagnosed on the basis of dislocated lenses. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.904G>A (p.Glu302Lys), 2. NM_000071.2(CBS):c.430G>A (p.Glu144Lys); 3. NM_000071.2(CBS):c.1316G>A (p.Arg439Gln), comp het, 2&3 in cis

ClinVar 1. 496864, 2. 122; 3. 189088

gnomAD 1. MAF=0.00006153(African), no homozygotes 2. MAF=0.00009799(South Asian), no homozygotes, 3. MAF=0.00005341(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

Case14 29yo diagnosis, Australia, Anglo-Celtic

CasePresentingHPOs HP:0001083, HP:0002751, HP:0000939

(Lens dislocation, Kyphoscoliosis, Osteoporosis)

HPOsFreeText Diagnosis was based on dislocated lens and skeletal deformity. Patient has severe kyphoscoliosis. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. This patient had a partial response to the treatment. Homocystine levels were sharply reduced on pyridoxine and folate treatment, but levels did not fall below 20μmol (nv <60μmol) on this treatment alone. (PMID:9156316:): In this study, patient was found to have mild intellectual disability and osteoporosis at 50yo.

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided. (PMID:9156316): Serum homocysteine was 100μmol/l and methionine was 18μmol/l after five years of treatment. Addition of betaine(3g twice per day) lowered homocysteine to 18μmol/l which remained <50μmol for years.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. NM_000071.2(CBS):c.1058C>T (p.Thr353Met), comp het

ClinVar 1. 120, 2. 131

gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. MAF=0.0002916(African), no homozygotes

CaseAddInfo Patient carries a common 68bp insertion, 88ins68, variant that does not cause hyperhomocysteinemia. (PMID:9156316): Additionally is heterozygous for a c.699C>T(Y233Y) synonymous variant as well as homozygous c.1080T>C(A360A) synonymous variants.

CasePMIDs 9156316

Case24 6yo diagnosis, Anglo-Celtic

CasePresentingHPOs HP:0001083

(Lens dislocation)

HPOsFreeText Patient had marfanoid features and was diagnosed on the basis of dislocated lenses. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Patient was not responsive to the treatment, plasma homocysteine levels went unchanged. Patient was given additional oral betaine(3g twice per day) with a low protein diet

CaseNotHPOs HP:0001249

(Intellectual disability)

NotHPOsFreeText n/a

CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

CaseMethod1 PCR

CaseMethod2 Sanger

CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

Variant 1. NM_000071.2(CBS):c.904G>A (p.Glu302Lys), 2. NM_000071.2(CBS):c.430G>A (p.Glu144Lys); 3. NM_000071.2(CBS):c.1316G>A (p.Arg439Gln), comp het, 2&3 in cis

ClinVar 1. 496864, 2. 122; 3. 189088

gnomAD 1. MAF=0.00006153(African), no homozygotes 2. MAF=0.00009799(South Asian), no homozygotes, 3. MAF=0.00005341(African), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

FamilyLabel HCU-220

Family#PresentingHPOs HP:0001249, HP:0001083, HP:0002970, HP:0001010, HP:0000924, HP:0001263

(Intellectual disability, Ectopia lentis, Genu varum, Hypopigmentation, Skeletal abnormality, cognitive delay)

HPOsFreeText CBS deficiency diagnosis, skeletal abnormality/elongated long bones, cognitive delay was apparent as early as 2yo

FamilyNotHPOs HP:0000501

(Glaucoma)

CountryOrigin Iran

Ethnicity Sistani

Race n/a

Family#PreviousTesting no other CBS variants were observed after Sanger sequencing

FamilyMethod1 Linkage analysis or Homozygosity mapping (genome-wide)

FamilyMethod2 Sanger

FamilyGenotypingMethod Genome-wide SNP genotyping and whole genome linkage analysis using MERLIN to analyze DNA of the parents and 7 siblings. Homoygosity mapping of the homozygous regions common to the three affected individuals and absent in unaffected individuals then narrowed the homozygous region to a locus including 296 protein coding genes. CBS, being one of those genes, was considered since intellectual disability accompanies homocysteinuria. The 15 coding exons and flanking intronic sequences of the CBS gene were PCR amplified then Sanger sequenced.

ProbandLabel HCU-220-5

Variant NM_000071.2(CBS):c.346G>A (p.Gly116Arg), homozygous

ClinVar 188787

gnomAD MAF=0.00002892(Latino), no homozygotes

FamilyAddInfo family from a remote village in the province of Sistan and Baluchestan. consanguinity-first cousin parents, several heterozygous family members (both parents and 2 siblings) had cardiac disorders such as mitral regurgitation or mitral valve prolapse, but were generally negative for the phenotypes of the affected individuals. Heterozygous sibling HCU-220-3 is the only individual who presented in this study with glaucoma and mitral valve prolapse.

FamilyPMIDs n/a

FamilyLabel Family 1

Family1PresentingHPOs HP:0003235

(Increased blood methionine)

HPOsFreeText increased pre-treatment blood homocysteine and post-treatment total homocysteine, affected individuals were treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

FamilyNotHPOs n/a

NotHPOsFreeText Marfan syndrome, vascular occlusion

CountryOrigin Korea

Ethnicity n/a

Race n/a

Family1PreviousTesting tested plasma homocysteine and methionine in both siblings, both metabolites were elevated

FamilyMethod1 PCR

FamilyMethod2 Sanger

FamilyGenotypingMethod PCR amplified all 16 coding exons of CBS gene, then direct sequenced. Deletion variant sequenced after cloning into pGEM T easy vector.

ProbandLabel Case 2

Variant 1. NM_001178008.1:c.700_702del(p.Asp234del), NM_000071.2(CBS):c.770C>T (p.Thr257Met), compound heterozygous

ClinVar 1. n/a, 2. 188927

CAID 1. register link

gnomAD 1. not in gnomAD, 2. MAF=0.0001396(Other), no homozygotes

FamilyAddInfo D234del inherited from father, T257M inherited from mother

FamilyPMIDs n/a

FamilyLabel Family 1

Family1PresentingHPOs HP:0003235

(Increased blood methionine)

HPOsFreeText increased pre-treatment blood homocysteine and post-treatment total homocysteine, affected individuals were treated with low-methionine diet, vitamin B6, folate, vitamin B12, and betaine after diagnosis

FamilyNotHPOs n/a

NotHPOsFreeText Marfan syndrome, vascular occlusion

CountryOrigin Korea

Ethnicity n/a

Race n/a

Family1PreviousTesting tested plasma homocysteine and methionine in both siblings, both metabolites were elevated

FamilyMethod1 PCR

FamilyMethod2 Sanger

FamilyGenotypingMethod PCR amplified all 16 coding exons of CBS gene, then direct sequenced. Deletion variant sequenced after cloning into pGEM T easy vector.

ProbandLabel Case 2

Variant 1. NM_001178008.1:c.700_702del(p.Asp234del), NM_000071.2(CBS):c.770C>T (p.Thr257Met), compound heterozygous

ClinVar 1. n/a, 2. 188927

CAID 1. register link

gnomAD 1. not in gnomAD, 2. MAF=0.0001396(Other), no homozygotes

FamilyAddInfo D234del inherited from father, T257M inherited from mother

FamilyPMIDs n/a