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Lab Manual for UCSF Clinical Laboratories

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Inherited Biochemical Disorders

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Biochemical Services
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Congenital Bilateral Absence of the Vas Deferencs (CBAVD)

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The splice acceptor site for exon 9 contains a series of T nucleotides that are polymorphic and occur commonly as 3 alleles. 5T, 7T and 9T. The 7T allele is the most common allele and occurs on 83% of non-CF chromosomes. The variability of the number of T's at the acceptor site affects the efficiency of exon 9 splicing, such that 5T allele transcripts largely but not always miss exon 9 due to alternate splicing. Transcripts that lack exon 9 result in a non or partly functional CFTR protein. When the 5T allele is associated with another CF mutation, the amount of intact mRNA for the normal CFTR protein is drastically reduced and limited to the efficiency of normal splicing from the 5T allele, thus causing CBAVD without the entire phenotype of cystic fibrosis. The severity of the CF phenotype is related to the amount of normal CFTR protein produced. Generally, CFTR levels above 10% are adequate. However, levels between 5% and 10% can lead to CBAVD. Homozygosity for the 5T allele (which is present at 5% in the general population) without any CF mutation, is not associated with any phenotype as the CFTR levels are above the 10% threshold level.

This polyT variant assay will detect the 5T, 7T or 9T alleles. The interpretation of the test requires CFTR genotyping as the variants are also present in the general population.

One purple top tube of whole blood is required and is adequate for genotyping of both the polyT variant and the most common CF mutations. The polyT variant and CF tests can be ordered either separately or simultaneously.

Cystic Fibrosis

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Our test will detect the 31 most common CF mutations as well as the F508C polymorphism by PCR and reverse dot blot hybridization. The mutations are shown below and approximately cover 88-90% of CF chromosomes from North American Caucasians, 97% in Ashkenazi Jews, 65% in Hispanics, and 45% in African Americans:

  1. ∆F508
  2. G542X
  3. G551D
  4. R553X
  5. W1282X
  6. N1303K
  7. 3905insT
  8. R117H
  9. G85E
  10. R347P
  11. A455E
  12. 1898+1
  13. 2184delA
  14. 711+1
  15. 2789+5
  16. Y1092X
  1. ∆I507
  2. 3120+1
  3. 621+1
  4. R1162X
  5. 1717-1
  6. 3659delC
  7. R560T
  8. E60X
  9. I148T
  10. R334W
  11. R347H
  12. Q493X
  13. 1078 del T
  14. S549N
  15. 3849+10 kb
  16. 508C polymorphism


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83% of Hereditary Hemochromatosis are caused by a G to A substitution at nucleotide 845 of the HLA-H gene. The carrier frequency among Europeans is 10%. Thus, one in 400 individuals will be homozygous for this mutation and may be affected with hemochromatosis.

Medium Chain of acylCoA deficiency (MCAD)

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MCAD deficiency is an inherited defect in fatty acid metabolism which can cause a Reyes'-like syndrome in children and has been weakly associated with the sudden infant death syndrome (SIDS). This PCR test detects the G985 mutation found in 90% of MCAD chromosomes.

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