CAM 162

Testing of Homocysteine Metabolism-Related Conditions

Category:Laboratory   Last Reviewed:January 2019
Department(s):Medical Affairs   Next Review:January 2020
Original Date:March 2017    

Classical homocystinuria, also known as cystathionine beta synthase deficiency or CBS deficiency, is an inherited disorder of the metabolism of the amino acid methionine, often involving cystathionine beta synthase. 

There are multiple forms of homocystinuria, which are distinguished by their signs and symptoms and genetic cause. The most common form of homocystinuria is characterized by nearsightedness (myopia), dislocation of the lens at the front of the eye, an increased risk of abnormal blood clotting and brittle bones that are prone to fracture (osteoporosis) or other skeletal abnormalities. Some affected individuals also have developmental delay and learning problems. 

Less common forms of homocystinuria can cause intellectual disability, failure to grow and gain weight at the expected  rate (failure to thrive), seizures,  problems with movement and a blood disorder called megaloblastic anemia. Megaloblastic anemia occurs when a person has a low number of red blood cells (anemia), and the remaining red blood cells are larger than normal (megaloblastic). 

The most common form of homocystinuria affects at least 1 in 200,000 to 335,000 people worldwide. The disorder appears to be more common in some countries, such as Ireland (1 in 65,000), Germany (1 in 17,800), Norway (1 in 6,400) and Qatar (1 in 1,800). The rarer forms of homocystinuria each have a small number of cases reported in the scientific literature (Picker & Levy, 2014).

Clinical characteristics of Homocyatinuria
Homocystinuria caused by cystathionine β-synthase (CBS) deficiency is characterized by developmental delay/intellectual disability, ectopia lentis and/or severe myopia, skeletal abnormalities (excessive height and length of the limbs) and thromboembolism. Expressivity is variable for all of the clinical signs. Two phenotypic variants are recognized:

  1. BG-responsive homocystinuria and
  2. BG-non-responsive homocystinuria.

BG-responsive homocystinuria  is typically, but not always, milder than the non-responsive variant. In the majority of untreated affected individuals, ectopia lentis occurs by age eight years. Individuals are often tall and slender with an asthenic ("marfanoid") habitus and are prone to osteoporosis. Thromboembolism is the major cause of early death and morbidity. IQ in individuals with untreated homocystinuria ranges widely, from 10 to 138. In BG-responsive individuals the mean IQ is 79, versus 57 for those who are BG non-responsive. Other features that may occur include: seizures, psychiatric problems, extrapyramidal signs (e.g., dystonia), hypopigmentation, malar flush, Jivedo reticularis and pancreatitis.

The signs and symptoms of homocystinuria typically develop within the first year of life, although some mildly affected people may not develop features until later in childhood or adulthood (Genetic Home Reference, 2016). 

The major clinical findings in classic homocystinuria:

  • Developmental delayIintellectual disability
  • Ectopia lentis (dislocation of the ocular lens) and/or severe myopia
  • Skeletal abnormalities, such as excessive height and limb length
  • Vascular abnormalities characterized by thromboembolism
  • Clinical suggestion of Marfan syndrome (although often joint flexibility is decreased in homocystinuria) 

Genetic Changes
Based on scientific publications and references, mutations in the CBS, MTHFR, MTR, MTRR and M MADHC genes cause homocystinuria.

  • Mutations in the CBS gene cause the most common form of homocystinuria. The CBS gene provides instructions for producing an enzyme called cystathionine beta-synthase. This enzyme acts in a chemical pathway and is responsible for converting the amino acid homocysteine to a molecule called cystathionine. As a result of this pathway, other amino acids, including methionine, are produced. Mutations in the CBS gene disrupt the function of cystathionine beta-synthase, preventing homocysteine from being used properly. As a result, this amino acid and toxic byproducts build up in the blood. Some of the excess homocysteine is excreted in urine. 
  • Rarely, homocystinuria can be caused by mutations in several other genes. The enzymes made by the MTHFR, MTR, MTRR and MMADHC genes play roles in converting homocysteine to methionine. Mutations in any of these genes prevent the enzymes from functioning properly, which leads to a buildup of homocysteine in the body. Researchers have not determined how excess homocysteine and related compounds lead to the signs and symptoms of homocystinuria.

Inheritance Pattern
The condition Homocystinuria  is inherited in an autosomal recessive pattern, which means both copies of the gene in each cell have mutations. Most often, the parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but do not show signs and symptoms of the condition.

Although people who carry one mutated copy and one normal copy of the CBS gene do not have homocystinuria, they are more likely than people without a CBS mutation to have shortages (deficiencies) of vitamin B12 and folic acid. 

Diagnosis/testing (Picker & Levy, 2014)
The cardinal biochemical features of homocystinuria  are: markedly increased concentrations of plasma  homocystine, total homocysteine,  homocysteine-cysteine-mixed disulfide and methionine; increased  concentration of urine homocystine; and reduced cystathionine of P­ synthase (CBS) enzyme activity. The diagnosis can be substantiated by detection of biallelic pathogenic variants in CBS, the gene encoding cystathionine P-synthase.

Classic homocystinuria is caused by deficiency of cystathionine P-synthase (CBS), a pyridoxine (vitamin Bo)-dependent enzyme. Because homocysteine is at the branch point between transculturation and methionine remethylation in the methionine metabolic cycle, a block at CBS limits transsulfuration and results in both increased homocysteine and increased methionine, the latter caused by enhanced remethylatlon.

The diagnosis of homocystinuria caused by CBS deficiency is suspected in newborns with an abnormal  newborn screen and individuals with clinical findings that  range from  multiple organ disease beginning in infancy or early childhood to thromboembolism only, expressed in early to middle  adult years. 

Newborn Screening
Classic homocystinuria can be detected in some (not all) affected individuals by screening the newborn blood spot specimen for hypermethioninemia. 

If the initial screening test result exceeds the cutoff level of methionine, follow-up testing is required. This may be:

  1. a repeat dried blood specimen submitted to the newborn screening program or
  2. a quantitative plasma amino acid analysis and analysis of plasma total homocysteine as recommended in the methionine ACMG ACT Sheet and ACMG Algorithm of the American College of Medical Genetics. 

According to the American College of Medical Genetics (2009):
Diagnostic Evaluation: Quantitative plasma amino acids will show increased homocystine and methionine in classical homocystinuria but only increased methionine in the other disorders. Plasma homocysteine analysis will show markedly increased homocysteine in classical homocystinuria and normal or only slightly increased homocysteine in the other disorders. Urine homocysteine is markedly increased in classical homocystinuria.

Clinical Considerations:  Homocystinuria  is usually asymptomatic  in the neonate. If untreated, these children eventually develop mental retardation, ectopia  lentis, a marfanoid appearance including arachnodactyly,  osteoporosis, other  skeletal deformities  and thromboembolism.   MAT I/Ill deficiency may be benign. Adenosylhomocysteine  hydrolase deficiency has been associated with developmental delay and hypotonia, and both this disorder and GNMT deficiency can cause liver  abnormalities. 

Note: The choice between the dried blood specimen and the plasn1a analyses is based on the recommendation of the screening program, which usually depends on the degree of the methionine increase in the initial screen. 

If 1 above is selected (i.e., a second test sent to the newborn screening program) and if the result confirms hypermethioninemia, quantitative plasma amino acid testing with attention to concentrations of methionine, homocystine and homocysteine-cysteine mixed disulfide, as well as a specific plasma total homocysteine analysis, are performed to confirm or exclude the diagnosis of homocystinuria.

  • At least one newborn screening program performs second-tier testing for homocysteine on all newborn specimens with elevated methionine in order to reduce the frequency of false­ positive results (Matern et al., 2007). 
  • Newborn screening is for methionine and not for homocystine or homocysteine. Thus, other causes of elevated total homocysteine, such as disorders of remethyation (e.g., methylenetetrahydrofolate reductase deficiency and the cobanomin defects are not detected because the methionine level in these disorders is reduced (or normal). 
  • Virtually all infants with homocystinurio detected by newborn screening programs have had pyridoxine (vitamin 86) non-responsive homocystinuria. It is likely that infants who are pyridoxine responsive rarely have increased methionine during the first two to three days of life, when the newborn screening specimen is obtained. 

Establishing the Diagnosis
The diagnosis of classic homocystinuria in a proband can be established by measurement of amino acids in plasma and urine, assay of cystathionine-synthase (CBS) enzyme activity or molecular genetic testing of CBS (encoding cystathionine β-synthase). 

Plasma and Urine Amino Acids
Plasma homocysteine concentration must be determined in the absence of pyridoxine supplementation (including a multivitamin) for two weeks.

The cardinal biochemical features, summarized in the table below are:

  • Markedly increased concentrations of plasma homocystine, total homocysteine, homocysteine-cysteine mixed disulfide and methionine
  • Increased concentration of urine homocystine

Cardinal Biochemical Findings that Establish the Diagnosis of Homocystinuria

Analyte Specimen Expected Findings
Neonate with Homocystinuria Untreated Older Individual with Homocystinuria Control
Homocystine Plasma 10-45µmol/L >100µmol/L Undetectable
  (0-1.2mg/dl) (>3mg/dl)
Total homocysteine 1 (Hey) Plasma 50-100µmol/L >100µmol/L <15µmol/L
Methionine Plasma 200-1500µmol/L >SOµmol/L 10-40µmol/L
  (3-23mg/dl) (>0.7mg/dl) (0.2-0.6mg/dl)
Homocystine Urine Detectable Detectable Undetectable

Testing Following Establishment of the Diagnosis
Pyridoxine (B6) challenge test. The two phenotypic variants of classic homocystinuria -- B6-responsive and B6-non-responsive homocystinuria -- have differing natural history and management. Once the diagnosis of homocystinuria caused by deficiency of cystathionine β-synthase (CBS) is established, a pyridoxine challenge to measure vitamin B6­ responsiveness is used to determine which phenotype is present.

  • While continuing a normal diet, plasma is obtained for baseline measurements of amino acids, the affected individual is given 100 mg pyridoxine orally and the concentrations of plasma amino acids are again measured 24 hours later. A reduction of 30% or more in plasma homocystine or homocysteine and/or plasma methionine concentration suggests 86 responsiveness.
  • If no significant change occurs, 200 mg pyridoxine is given orally and the amino acid analysis repeated in 24 hours.
  • If still no change has occurred, 500 mg of pyridoxine is given orally to a child or adult but no more than 300 mg to an infant. If plasma homocystine or homocysteine and methionine concentrations are not significantly decreased after the last dose of pyridoxine, it is concluded that the individual is BG-non-responsive.

Note: Infants should not receive more than 300 mg of pyridoxine. Several infants given daily doses of 500 mg pyridoxine developed respiratory failure and required ventilatory support. The respiratory symptoms resolved on withdrawal of pyridoxine. 

Molecular Genetic Testing of CBS
Identification of biallelic CBS pathogenic variants substantiates the diagnosis. Most individuals worldwide are compound heterozygotes for novel pathogenic variants. 

Summary of Molecular Genetic Testing Used in Homocystinuria Caused by Cystathionine Beta­ Synthase Deficiency (Pagon, 2016)

Gene Test Method Proportion of Probands with a Pathogenic Variant Detectable by This Medthod
CBS Targeted analysis for pathogenic variants two most common CBS pathogenic variants, p.lle278Thr and p.Gly307Ser, are found in exon 8
Sequence analysis >95%
Deletion/duplicatin analysis Nine individuals with deletions or duplications involving 25 or more nucleotides have been  reported  to date (Picker & Levy, 2014)


  1. Genetic Counseling is considered MEDICALLY NECESSARY and is recommended prior to genetic testing for Homocystinuria.
  2. Molecular genetic testing of CBS (encoding cystathionine β-synthase) gene is considered MEDICALLY NECESSARY for diagnosis and/or confirmation of Homocystinuria.
  3. Genetic testing for MTR, MTRR, and MMADHC genes is considered INVESTIGATIONAL.
  4. Newborn screening for homocysteine-related conditions is considered MEDICALLY NECESSARY in the following situations:
    • For classic homocystinuria due to CBS deficiency by performing quantitative plasma amino acids analysis and/or plasma or urine total homocysteine analysis
    • Testing for homocystinuria in dried blood spots.
    • Testing for hypemethioninemia in dried blood spots.
  5. A repeat dried blood specimen submitted to the newborn screening program, or a quantitative plasma amino acid analysis and analysis of plasma total homocysteine is considered MEDICALLY NECESSARY if the initial screening test result exceeds the cut-off level of methionine.
  6. Pyridoxine (B6) Challenge test is considered MEDICALLY NECESSARY to diagnose phenotype variants of classic homocystinuria due to cystathionine β-synthase (CBS) deficiency. 
  7. Total homocysteine testing in plasma and dried blood spots is considered MEDICALLY NECESSARY in patients with suspected CBS deficiency and for monitoring therapy.
  8. Plasma free homocysteine testing is considered NOT MEDICALLY NECESSARY.
  9. For symptomatic patients (i.e., having elevated urine and/or serum homocysteine levels) that test negative for CBS classic homocystinuria OR for patients with a first-degree relative positive for known variants of MTHFR that cause homocystinuria genetic test for known variants of MTHFR is considered MEDICALLY NECESSARY.


  1. American College of Medical Genetics and Genomics (ACMG). 2009. Methionine elevated or decreased. Accessed from­ methionine.pdf
  2. American College of Medical Genetics. 2010. Newborn screening ACT sheet {Increased methionine) Homocystinuria (CBS deficiency). 2010. Accessed Nov 29, 2016: link 
  3. MaternD,TortorelliS,OglesbeeD,GavrilovD,RinaldoP.Reductionofthefalse-positive rate in newborn screening by implementation of MS/MS based second-tier tests: TheMayo Clinic Experience (2004-2007). J Inherit Metab Dis. 2007; 30: 585-92. 
  4. National Institute of Health. 2016.  Homocystinuria. Accessed Nov 29, 2016  from
  5. Pagon RA, Adam MP, Ardinger HH, et al; GeneReviews; 1993-2016
  6. Picker, J.D.,Levy, H.L. 2014. Homocytinuria caused by cystathionine beta-synthase deficiency. Accessed January 12, 2017, from<1 524/ 

Coding Section 

Codes Number Description
CPT  82136 Amino acids, 2 to 5 amino acids, quantitative, each specimen
  82139 Amino acids, 6 or more amino acids, quantitative, each specimen
  83090  Homocysteine 
  84207 Pyridoxal phosphate (Vitamin B-6)
  96040  Medical genetics and genetic counseling services, each 30 minutes face-to-face with patient/family 
  S0265  Genetic counseling, under physician supervision, each 15 minutes 
ICD-10 Diagnoses Codes  E34.4  Disproportionate tall stature 
  E72.11 Homcystinuria
  E72.19 Other disorders of sulfur-bearing amino-acid metabolism
  E72.9  Abnormality of amino acid metabolism 
  E88.09  Other disorders of plasma-protein metabolism, not elsewhere classified 
  E88.9  Other specified metabolic disorders 
  F73, R78, F79  Intellectual disability 
  G12.22  Pseudobulbar palsy 
  G40.801-G40.824, G40.89 Seizures 
  G81 codes  Hemiplegia 
  H27.1 codes, Q12.1 Ectopia lentis 
  H44 codes, H52 codes  Myopia
  I25 codes  Coronary artery disease 
  I25.10  Premature Atherosclerosis 
  I26.99 Pulmonary embolism 
  I67.82  Cerebralischemia 
  I74.2  Arterial thrombosis 
  I82 codes  Venous thrombosis 
  M26.31  Dental crowding 
  M81.0  Osteoporosis 
  M84.40XA-M84.48XS  Recurrent fractures 
  Q87.43  Arachnodactyly 
  R27.0  Ataxia 
  R47.01  Aphasia 
  R79.9  Abnormal finding of blood chemistry, unspecified 
  Z00.01  Encounter for general adult medical examination with abnormal findings 
  Z05.43 Obs & eval of newborn for suspected immunologic condition ruled out
  Z05.8  Observation and evaluation of newborn for other specified suspected condition ruled out 
  Z13.228  Encounter for screening for other metabolic disorders 
  Z13.71  Encounter for nonprocreative screening for genetic disease carrier status 
  Z13.79 Encounter for other screening for genetic and chromosmal anomailies
  Z15.89  Genetic susceptibility to other disease 
  Z33.1-Z33.3  Pregnant state 
  Z34.00-Z34.93  Encounter for supervision of normal pregnancy 
  Z51.81  Encounter for therapeutic drug monitoring

Procedure and diagnosis codes on Medical Policy documents are included only as a general reference tool for each Policy. They may not be all-inclusive. 

This medical policy was developed through consideration of peer-reviewed medical literature generally recognized by the relevant medical community, U.S. FDA approval status, nationally accepted standards of medical practice and accepted standards of medical practice in this community, Blue Cross and Blue Shield Association technology assessment program (TEC) and other non-affiliated technology evaluation centers, reference to federal regulations, other plan medical policies and accredited national guidelines.

"Current Procedural Terminology© American Medical Association.  All Rights Reserved" 

History From 2017 Forward     


Annual review, adding medical necessity statement regarding newborn testing for hypermethioninemia in dried blood spots. Also adding limited coverage for 81291/ MTHFR testing. Updating coding. 


Interim Review. Updated diagnosis coding. No other changes made 


Annual review, expanding medical necessity coverage for some newborn issues. Adding criteria for pyridoxine challenge testing. Adding criteria for testing for suspected CBS deficiency. No other changes. 


Interim review to align with Avalon quarterly schedule. Updated category to Laboratory 


Corrected formatting  in policy statement. 


New Policy


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