ABCMdb

PMID: 15371907

Monaghan KG, Highsmith WE, Amos J, Pratt VM, Roa B, Friez M, Pike-Buchanan LL, Buyse IM, Redman JB, Strom CM, Young AL, Sun W
Genotype-phenotype correlation and frequency of the 3199del6 cystic fibrosis mutation among I148T carriers: results from a collaborative study.
Genet Med. 2004 Sep-Oct;6(5):421-5., [PubMed]

Sentences

No. Mutations Sentence Comment

36 ABCC7 p.Ile148Thr Requested testing for 3199del6 was performed using a laboratory-developed direct sequence analysis of exon 17a of the CFTR gene.13 Baylor College of Medicine CF direct mutation analysis was done using a matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry platform (Sequenom), which includes the I148T and 3199del6 mutations. Login to comment 37 ABCC7 p.Ile148Thr Greenwood Genetic Center CF studies for I148T were performed by PCR amplification followed by either laboratory-developed sequencing analysis or oligonucleotide ligation assay (CF OLA v3.0) (Celera Diagnostics/Abbott Diagnostics/Applied Biosystems). Login to comment 39 ABCC7 p.Ile148Thr RESULTS A summary of the 3199del6- and/or I148T-positive patients identified is shown in Table 1. Login to comment 40 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr Data were collected on 662 un- Table 1 Summary of 3199del6 and/or I148T chromosomes identified among 663 individuals undergoing CF DNA testing Indication for DNA testing Race/Ethnicity I148T positive 3199del6 positive Carrier screen Caucasian 71 0 Unspecifieda Caucasian 128 0 Carrier screen Hispanic 8 0 Unspecifieda Hispanic 14 1 Carrier screen Middle Eastern 7 0 Unspecifieda Middle Eastern 6 0 Carrier screen Other 2 0 Carrier screen Asian 5 0 Unspecifieda Asian 14b 0 Carrier screen African American 3 0 Carrier screen Unspecified 47 0 Unspecifieda Other 3 0 Unspecifieda Unspecified 341 3 Subtotal 649 4 (0.6%) Fetus with echogenic bowel Middle Eastern 1 0 Fetus with echogenic bowel Asian 1 0 Male infertility Caucasian 1 0 Male infertility Unspecified 2 0 Rule-out CF Unspecified 6 0 Rule-out CF African American 1 0 Clinical CF Caucasian 1 1 Family history of CF mutation Armenian 1 1 Family history of a CF mutation Caucasian 1 0 Subtotal 15 2 (13.3%) Total 664 6 (0.9%) a The majority of persons undergoing CF DNA testing for an unspecified indication are presumably undergoing carrier screening. Login to comment 41 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr b 12 individuals were heterozygous for I148T, and 1 individual was I148T homozygous. Login to comment 42 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr related I148T heterozygotes and 1 I148T homozygote (total of 663 persons or 664 I148T chromosomes). Login to comment 43 ABCC7 p.Ile148Thr Overall, we identified 6 unrelated individuals positive for both I148T and 3199del6 (0.9%). Login to comment 44 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr With the exception of Case 6 (Table 2), the phase of the I148T/3199del6 was not determined; however, they are presumed in-cis based on previous haplotype studies.9 These studies demonstrated that I148T occurs on a 7T or 9T background, whereas the I148T/3199del6 occurs on a 9T background. Login to comment 45 ABCC7 p.Arg117His Due to ACOG/ACMG recommendations that polyT analysis only be performed as a reflex test for R117H-positive individuals, the polyT status of most of the patients included in this report was not determined. Login to comment 46 ABCC7 p.Ile148Thr Excluding 15 cases referred for CF DNA testing because of a known or suspected diagnosis of CF (including fetal echogenic bowel and male infertility) or a positive family history, 0.6% of I148T carriers were positive for 3199del6. Login to comment 48 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ser1235Arg An unaffected I148T homozygote (Case 1) was detected during routine prenatal screening. Three males (cases 2-4) with congenital bilateral absence of the vas deferens (CBAVD) (I148T/ ⌬F508), obstructive azoospermia (I148T carrier), and infertility (I148T/S1235R) were identified, the latter 2 negative for 5T at the intron 8 polyT locus. Login to comment 49 ABCC7 p.Ile148Thr We cannot exclude the possibility that finding I148T in the heterozygous state in a male with obstructive azoospermia (Case 3) is merely a coincidence. Login to comment 51 ABCC7 p.Ile148Thr Case 5 was a fertile male, compound heterozygous for I148T and ⌬F508, who had a child identified by newborn screening as heterozygous for ⌬F508. Login to comment 53 ABCC7 p.Ile148Thr ABCC7 p.Asp110His Case 6, a female for whom no clinical information is available, was compound heterozygous for D110H and I148T/ 3199del6. Login to comment 54 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr Her son was noted to be positive for I148T/3199del6, confirming the haplotype in this family (assuming that his father is not a carrier for I148T or 3199del6). Login to comment 55 ABCC7 p.Ile148Thr ABCC7 p.Val520Phe Case 7 had a clinical diagnosis of CF and was positive for V520F, a CF mutation associated with pancreatic insufficiency, and I148T/3199del6. Login to comment 56 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr Two fetuses with I148T and echogenic bowel were identified, both before the availability of 3199del6 reflex testing for I148T carriers. Login to comment 60 ABCC7 p.Ile148Thr Parental CF DNA testing identified one parent as a carrier for ⌬F508, and the other had an unusual heteroduplex pattern in exon 4, which was later identified as I148T (before the availability of 3199del6 reflex testing). Login to comment 63 ABCC7 p.Ile148Thr DNA testing performed after delivery was positive for I148T, but negative for ⌬F508. Login to comment 66 ABCC7 p.Ile148Thr ABCC7 p.Asp110His Sex Race Indication Genotype Poly T status Clinical information 1 Female Asian Carrier screening I148Ta /I148Ta12 9T/9T Asymptomatic 2 Male Not provided Infertility I148Ta /⌬F508 Not determined CBAVD 3 Male Not provided Infertility I148Ta heterozygote Negative for 5T Obstructive azoospermia 4 Male Caucasian Infertility I148Ta /S1235R20 7T/9T None available 5 Male Caucasian Family history of CF mutation I148Ta /⌬F508 9T/9T Fertile male who underwent carrier screening after the identification of ⌬F508 in the heterozygous form in his child during newborn screening, child`s mother is negative for 25 mutation ACOG/ACMG CF panel 6 Female Armenian Family history of CF mutation D110H/I148T (3199del6 positive) Not determined Clinical information on this individual is not available, despite multiple attempts to obtain. Login to comment 67 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Val520Phe DNA testing on her son revealed I148T/3199del6 7 Not provided Caucasian Affected with CF V520F/I148T (3199del6 positive) Not determined None available 8 Prenatal test Middle Eastern Fetal echogenic bowel I148Ta carrier Not determined Healthy male reported at age 2 years. Login to comment 68 ABCC7 p.Ile148Thr A subsequent pregnancy of this couple was diagnosed with ⌬F508/I148T (before the availability of 3199del6 reflex testing) and was terminated. Login to comment 69 ABCC7 p.Met82Ile 9 Prenatal test Asian Fetal echogenic bowel I148Ta /M82I Not determined Healthy female last evaluated at age 28 months with no signs or symptoms of CF. Login to comment 71 ABCC7 p.Ile148Thr pregnancy, performed by CVS was positive for ⌬F508 and I148T (again, prior to the availability of 3199del6 reflex testing). Login to comment 72 ABCC7 p.Ile148Thr The parents were counseled regarding the inability to prenatally predict the course of symptoms and severity of CF, though ⌬F508 and I148T were typically associated with pancreatic insufficient (PI) CF. Login to comment 75 ABCC7 p.Ile148Thr In 2003, 3199del6 reflex testing was performed, and the I148T carrier parent was negative for 3199del6. Login to comment 78 ABCC7 p.Ile148Thr One parent was positive for I148T. Login to comment 79 ABCC7 p.Met82Ile A previously unreported variant of unknown clinical significance, M82I (ATG3ATA), was identified in the other parent. Login to comment 80 ABCC7 p.Met82Ile M82I was incidentally detected by heteroduplex analysis of exon 3, which was used by the laboratory to screen for known CF mutations. Login to comment 82 ABCC7 p.Met82Ile It was explained to the couple that M82I was most likely a benign polymorphism because codon 82 is not located in a critical region of the CFTR gene and that the substitution of methionine with isoleucine (both hydrophobic amino acids) in this region of the gene was not likely deleterious (J. Zelienski, personal communication, 2004). Login to comment 83 ABCC7 p.Ile148Thr However, due to the presence of fetal echogenic bowel, one parent a carrier of I148T (classified as a CF mutation at that time), and the other parent a carrier of a variant of unknown clinical significance, prenatal CF testing was performed by amniocentesis. Login to comment 85 ABCC7 p.Ile148Thr ABCC7 p.Met82Ile CF testing was positive for I148T and M82I. Login to comment 94 ABCC7 p.Ile148Thr DISCUSSION I148T results from a T to C substitution at nucleotide 575 in exon 4 of the CFTR gene. Login to comment 95 ABCC7 p.Ile148Thr This sequence change was initially reported to the CF Consortium in 1990.1 I148T is located in the first cytoplasmic loop of the first membrane spanning domain of CFTR14 and results in the substitution of a hydrophobic amino acid, isoleucine, for a polar amino acid, threonine. Login to comment 96 ABCC7 p.Ile148Thr This region is conserved in humans, mouse, and bovine.15 Despite the fact that functional studies revealed normal processing, gating, and conductance of the CFTR,14 I148T was considered to be a severe CF mutation due to its presence in patients with classic CF and a second pathological CF mutation.4,5,7 3199del6, a deletion of ATAGTG from nucleotide 3199, is located in CFTR exon 17a and results in the deletion of isoleucine and valine at codons 1023 to 1024 within the second membrane-spanning domain. Login to comment 97 ABCC7 p.Gly542* ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr 3199del6 was reported to the CF Consortium in 1998 in a pancreatic insufficient CF patient with I148T and 3199del6onthesamechromosomeand⌬F508ontheotherchro- mosome.1 Another study noted a patient with severe CF and 3199del6 and I148T, though it is not noted specifically whether thesemutationsarein-cisorin-trans.16 3199del6alsooccursinthe absence of I148T, as a patient with severe CF has been reported with 3199del6 (negative for I148T) and G542X.17 Recent data suggests that 3199del6 is the deleterious mutation among I148T/3199del6 complex alleles.9 It is puzzling that early reports of patients with classic CF and I148T/⌬F508 did not identify 3199del6, despite the fact that 2 reports described performing mutation analysis of the entire CFTR coding region and splice site junctions either by a screening method (DDGE) or DNA sequencing.5,7 However, a recent report identified 3199del6 in 24 French-Canadian CF patients originally described as compound heterozygous for I148T and a severe CF mutation.11 Though there is little doubt that 3199del6 is a deleterious CF mutation, the clinical significance of I148T in the absence of 3199del6 is unclear, as we have identified this genotype in 3 males with infertility, two of the obstructive type. Login to comment 98 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr In 2001, I148T was included in the ACMG/ACOG CF panel due to its high incidence in the general population.2,3 However, recent data revealed that I148T accounts for Ϸ0.06% of CF chromosomes,9 less than the 0.1% frequency for inclusion in the CF screening panel. Login to comment 99 ABCC7 p.Ile148Thr Therefore, based on its low frequency among CF patients and questions concerning the phenotype associated with I148T, its inclusion in the CF screening panel should be reconsidered. Login to comment 102 ABCC7 p.Ile148Thr In our collaborative study of 663 I148T carriers, 0.9% also had 3199del6. Excluding subjects tested because of a suspected or clinical diagnosis of CF or positive family history, the frequency of 3199del6 decreased to 0.6%. Login to comment 103 ABCC7 p.Ile148Thr We identified 7 unrelated individuals with I148T and a second CF variant, 2 of whom also carried 3199del6. Login to comment 104 ABCC7 p.Val520Phe One patient with a known CF severe mutation, V520F, and I148T(3199del6) had a clinical diagnosis of CF, although no specific clinical information is available. Login to comment 105 ABCC7 p.Asp110His The second individual underwent testing due to the presence of two different CF mutations in her two children and was found to have the genotype D110H/I148T(3199del6). Login to comment 107 ABCC7 p.Ile148Thr One of her sons was subsequently found positive for I148T/3199del6. Login to comment 108 ABCC7 p.Ile148Thr ABCC7 p.Asp110His D110H is a rare CF sequence variant, originally reported in a mildly affected CF patient,18 and recently in homozygous form in an infant with metabolic alkalosis.19 The remaining I148T compound heterozygotes were negative for 3199del6. Login to comment 109 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr Among these include a fertile male with the genotype I148T/⌬F508 who underwent carrier screening due to the presence of a ⌬F508 in his child identified by newborn screening and an asymptomatic female, homozygous for I148T, identified by routine CF prenatal carrier screening. Three males with infertility were I148T positive. Login to comment 110 ABCC7 p.Ile148Thr One with obstructive azoospermia was heterozygous for I148T, but no other mutation (including 5T) was detected. Login to comment 111 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr ABCC7 p.Ser1235Arg A male with unspecified infertility was compound heterozygous for I148T and S1235R (7T/9T)20 and a male with CBAVD was compound heterozygous for I148T and ⌬F508 (polyT status not determined). Login to comment 112 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr Two fetuses with echogenic bowel and I148T were identified, both before the availability of 3199del6 reflex testing; however, both I148T carrier parents were subsequently shown to be negative for 3199del6. Login to comment 113 ABCC7 p.Ile148Thr ABCC7 p.Met82Ile One fetus was compound heterozygous for I148T and M82I, a previously unreported variant of unknown clinical significance. Login to comment 116 ABCC7 p.Ile148Thr One parent was identified as a ⌬F508 heterozygote and the other with an unknown sequence change in exon 4, later identified as I148T. Login to comment 117 ABCC7 p.Ile148Thr Their child was positive for I148T only and at age 2 was reported as healthy. Login to comment 118 ABCC7 p.Ile148Thr This couple underwent prenatal CF testing for a subsequent pregnancy, and the fetus was identified as positive for ⌬F508 and I148T. Login to comment 119 ABCC7 p.Ile148Thr After genetic counseling, which included the inability to prenatally predict the course of symptoms and severity of CF, although ⌬F508 and I148T were typically associated with PI CF, the couple chose to terminate the pregnancy. Login to comment 120 ABCC7 p.Ile148Thr The I148T carrier parent in this relationship is now known to be negative for 3199del6. Login to comment 121 ABCC7 p.Ile148Thr Our data supports previous findings that a small number of individuals with I148T are positive for 3199del6. Login to comment 122 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr The identification of 3 males with infertility and I148T (2 of the obstructive type and 2 who are compound heterozygous for I148Tand another CF mutation) cannot exclude the possibility that I148T alone may be associated with atypical or mild CF. Login to comment 124 ABCC7 p.Ile148Thr ABCC7 p.Ile148Thr Unfortunately, we were unable to obtain detailed information for all patients in whom I148T was identified; therefore, we cannot make reliable predictions on the phenotype of I148T alone. Login to comment 125 ABCC7 p.Ile148Thr Reflex testing for 3199del6 should be considered whenever I148T is identified. Login to comment 126 ABCC7 p.Ile148Thr Such testing is of particular importance in any patient with features of CF or whenever one member of a couple carries a deleterious CF mutation and the other member carries I148T. Login to comment 127 ABCC7 p.Ile148Thr Further studies are necessary to determine if I148T, in the absence of 3199del6, is associated with mild or atypical CF, including male infertility. Login to comment 128 ABCC7 p.Ile148Thr In summary, these data suggest that I148T is not an appropriate mutation for CF screening in the general population. Login to comment 130 ABCC7 p.Ile148Thr We recommend that I148T be deleted from the CF screening panel and that 3199del6 not be added. Login to comment