ABCC7 p.Ser686Tyr
| CF databases: |
c.2057C>A
,
p.Ser686Tyr
(CFTR1)
?
,
|
| Predicted by SNAP2: | A: N (72%), C: N (57%), D: N (66%), E: N (78%), F: D (59%), G: N (78%), H: N (57%), I: D (59%), K: N (66%), L: D (59%), M: D (53%), N: N (82%), P: D (59%), Q: N (82%), R: D (53%), T: N (82%), V: D (53%), W: D (63%), Y: N (61%), |
| Predicted by PROVEAN: | A: N, C: N, D: N, E: N, F: N, G: N, H: N, I: N, K: N, L: N, M: N, N: N, P: N, Q: N, R: N, T: N, V: N, W: D, Y: N, |
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[hide] Increased prevalence of CFTR mutations and variant... Hum Genet. 2003 Aug;113(3):286-92. Epub 2003 Jun 3. Sheth S, Shea JC, Bishop MD, Chopra S, Regan MM, Malmberg E, Walker C, Ricci R, Tsui LC, Durie PR, Zielenski J, Freedman SD
Increased prevalence of CFTR mutations and variants and decreased chloride secretion in primary sclerosing cholangitis.
Hum Genet. 2003 Aug;113(3):286-92. Epub 2003 Jun 3., [PMID:12783301]
Abstract [show]
Primary sclerosing cholangitis (PSC) and cystic fibrosis (CF) are both slowly progressive cholestatic liver diseases characterized by fibro-obliterative inflammation of the biliary tract. We hypothesized that dysfunction of the CF gene product, cystic fibrosis transmembrane conductance regulator (CFTR), may explain why a subset of patients with inflammatory bowel disease develop PSC. We prospectively evaluated CFTR genotype and phenotype in patients with PSC ( n=19) compared with patients with inflammatory bowel disease and no liver disease ( n=18), primary biliary cirrhosis ( n=17), CF ( n=81), and healthy controls ( n=51). Genetic analysis of the CFTR gene in PSC patients compared with disease controls (primary biliary cirrhosis and inflammatory bowel disease) demonstrated a significantly increased number of mutations/variants in the PSC group (37% vs 8.6% of disease controls, P=0.02). None of the PSC patients carried two mutations/variants. Of PSC patients, 89% carried the 1540G-variant-containing genotypes (resulting in decreased functional CFTR) compared with 57% of disease controls ( P=0.03). Only one of 19 PSC patients had neither a CFTR mutation nor the 1540G variant. CFTR chloride channel function assessed by nasal potential difference testing demonstrated a reduced median isoproterenol response of 14 mV in PSC patients compared with 19 mV in disease controls ( P=0.04) and 21 mV in healthy controls ( P=0.003). These data indicate that there is an increased prevalence of CFTR abnormalities in PSC as demonstrated by molecular and functional analyses and that these abnormalities may contribute to the development of PSC in a subset of patients with inflammatory bowel disease.
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No. Sentence Comment
83 S686Y and I1366F are novel potentially disease-causing variants that have not been reported from screening thousands of CF and healthy patients (http://www.genet.sickkids.on.ca/cftr/).
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ABCC7 p.Ser686Tyr 12783301:83:0
status: NEW109 The remaining three PSC patients had potentially disease-causing mutations (S686Y, I1366F, R75Q), which may contribute to CF-like phenotypes.
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ABCC7 p.Ser686Tyr 12783301:109:76
status: NEW115 For example, S686Y, which results in a change of serine to tyrosine, is a potentially disease-causing mutation because it would abolish the consensus phosphorylation site for both PKA and PKC protein kinases.
X
ABCC7 p.Ser686Tyr 12783301:115:13
status: NEW[hide] Lack of association of common cystic fibrosis tran... Am J Gastroenterol. 2005 Apr;100(4):874-8. Gallegos-Orozco JF, E Yurk C, Wang N, Rakela J, Charlton MR, Cutting GR, Balan V
Lack of association of common cystic fibrosis transmembrane conductance regulator gene mutations with primary sclerosing cholangitis.
Am J Gastroenterol. 2005 Apr;100(4):874-8., [PMID:15784035]
Abstract [show]
BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic progressive cholestatic liver disease of uncertain etiology. However, the histologic features of PSC liver disease can resemble those in cystic fibrosis (CF), an inherited disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. We sought to determine if PSC patients have a higher frequency of common CF alleles than disease controls. METHODS: DNA was extracted from peripheral lymphocytes of patients with end-stage liver disease. Samples were obtained before liver transplantation from 59 PSC patients and from three groups of control patients (20 each with primary biliary cirrhosis, autoimmune hepatitis, or hepatitis C). DNA samples were genotyped for 32 common CF mutations, the intron 8 T tract variants, and the M470V variant. RESULTS: One of 59 PSC patients (1.7%) had the common CF mutation (DeltaF508) in one CFTR gene. Two controls (3.3%) carried a single CF mutation (DeltaF508 in one primary biliary cirrhosis patient; W1282X in one hepatitis C patient). These rates do not differ from expected in the general population. The frequency of CFTR variants (5T and M470V) was also similar between PSC patients and controls. CONCLUSIONS: Despite anatomical similarities between CF liver disease and PSC, we could not confirm that PSC patients carried common CF mutations or common CFTR variants in higher than expected frequencies. These data suggest that CFTR dysfunction does not influence the pathogenesis of PSC.
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No. Sentence Comment
104 The remaining four mutations included two novel variants S686Y and I1366F of unknown functional and phenotypic effect, a Table 4.
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ABCC7 p.Ser686Tyr 15784035:104:57
status: NEW106 of Classic CF Nonclassic CFTR Mutations Reference PSC Patients Mutations CF Mutations IVS8-5T of Unknown Effect McGill (1996) (21) 19 1 (G551D) 1 (R117H) NA NA Girodon (2002)(19) 29 0 3 (L997F, S1235R, D1270N) 2 1 (N782K) Sheth (2003)* (18) 19 0 3 (2752-26A→G, 3849 + 10kbC→T, I1139V) 1 3 (S686Y, I1366F, R75Q) Gallegos-Orozco (2004) 59 1 ( F508) 0 2 NA Total, no.
X
ABCC7 p.Ser686Tyr 15784035:106:304
status: NEW[hide] Symmetric snapback primers for scanning and genoty... Clin Chem. 2013 Jul;59(7):1052-61. doi: 10.1373/clinchem.2013.202689. Epub 2013 Mar 15. Zhou L, Palais RA, Ye F, Chen J, Montgomery JL, Wittwer CT
Symmetric snapback primers for scanning and genotyping of the cystic fibrosis transmembrane conductance regulator gene.
Clin Chem. 2013 Jul;59(7):1052-61. doi: 10.1373/clinchem.2013.202689. Epub 2013 Mar 15., [PMID:23503723]
Abstract [show]
BACKGROUND: High-resolution melting of PCR products is an efficient and analytically sensitive method to scan for sequence variation, but detected variants must still be identified. Snapback primer genotyping uses a 5' primer tail complementary to its own extension product to genotype the resulting hairpin via melting. If the 2 methods were combined to analyze the same PCR product, the residual sequencing burden could be reduced or even eliminated. METHODS: The 27 exons and neighboring splice sites of the CFTR [cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)] gene were amplified by the PCR in 39 fragments. Primers included snapback tails for genotyping 7 common variants and the 23 CFTR mutations recommended for screening by the American College of Medical Genetics. After symmetric PCR, the amplicons were analyzed by high-resolution melting to scan for variants. Then, a 5-fold excess of H2O was added to each reaction to produce intramolecular hairpins for snapback genotyping by melting. Each melting step required <10 min. Of the 133 DNA samples analyzed, 51 were from CFTR patient samples or cell lines. RESULTS: As expected, the analytical sensitivity of heterozygote detection in blinded studies was 100%. Snapback genotyping reduced the need for sequencing from 7.9% to 0.5% of PCR products; only 1 amplicon every 5 patients required sequencing to identify nonanticipated rare variants. We identified 2 previously unreported variants: c.3945A>G and c.4243-5C>T. CONCLUSIONS: CFTR analysis by sequential scanning and genotyping with snapback primers is a good match for targeted clinical genetics, for which high analytical accuracy and rapid turnaround times are important.
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126 d One sample had 2 rare variants (R668C and S686Y) that required sequencing but were in the same amplicon.
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ABCC7 p.Ser686Tyr 23503723:126:44
status: NEW174 Such was the case in the current study with p.S686Y in exon 14, which is 4 bases away from the ACMG CFTR mutation c.2052delA.
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ABCC7 p.Ser686Tyr 23503723:174:46
status: NEW