gene sequence

3gr8kids

New member
We got my daughtor's gene sequence back and we know she is a carrier for R1162L and also she carries two mutations that says in the classification that they are benign and i am a little confused about this.....How do they know they are benign??? being that they are benign why do they even list them??? have they been studied before?
 

3gr8kids

New member
We got my daughtor's gene sequence back and we know she is a carrier for R1162L and also she carries two mutations that says in the classification that they are benign and i am a little confused about this.....How do they know they are benign??? being that they are benign why do they even list them??? have they been studied before?
 

3gr8kids

New member
We got my daughtor's gene sequence back and we know she is a carrier for R1162L and also she carries two mutations that says in the classification that they are benign and i am a little confused about this.....How do they know they are benign??? being that they are benign why do they even list them??? have they been studied before?
 

3gr8kids

New member
We got my daughtor's gene sequence back and we know she is a carrier for R1162L and also she carries two mutations that says in the classification that they are benign and i am a little confused about this.....How do they know they are benign??? being that they are benign why do they even list them??? have they been studied before?
 

3gr8kids

New member
We got my daughtor's gene sequence back and we know she is a carrier for R1162L and also she carries two mutations that says in the classification that they are benign and i am a little confused about this.....How do they know they are benign??? being that they are benign why do they even list them??? have they been studied before?
 

CFHockeyMom

New member
If your daughter has CF then, yes, she definitely has two mutations (R1162L being one and the other???). As far as classifications go, there are five classes, "benign" isn't one of them.

Class I mutations lead to defects in the synthesis of stable CFTR mRNA transcripts resulting in absence of the CFTR protein. About half of all mutations in CFTR (encompassing premature termination, exon skipping, aberrant mRNA splicing, and frameshifts) are thought to fall into this class and result in complete loss of CFTR protein/function.

Class II mutations complete protein translation but produce an abnormal protein that fails to escape the endoplasmic reticulum. Little or no CFTR reaches the plasma membrane, and the absence of all surface CFTR results in a severe phenotype. It is being increasingly recognized that mutations in unrelated genes can create defective proteins, which fail to traffic properly through the cell. Classically, missense mutations creating an abnormal protein were thought to be relatively benign or less consequential than nonsense mutations (null) or large deletions. This is no longer strictly the case because examples from CF and other inherited disorders demonstrate that a synthesized protein that fails to mature along the normal biosynthetic pathway often becomes quite destructive.

Class III mutations disrupt activation and regulation of CFTR at the plasma membrane. Thus biosynthesis, trafficking, and processing are undisturbed, but the channel may be defective with respect to ATP binding and hydrolysis, or phosphorylation.

Class IV mutations affect chloride conductance or channel gating and thus result in reduced chloride current.

Class V mutations reduce the level of normal CFTR protein by alterations in the promoter or by altering splicing. Currently it is thought that a reduction in mRNA to less than 10% of normal results in disease in CF.

I tried to find some info on the R1162L with regard to what class it may fall in. So far, the only thing I've found is the "definition" which is, the replacement of arginine at codon 1162 (CGA) by leucine (CTA) [Arg1162Leu (R1162L)]. I believe this is a Class IV type mutation but your best bet is to check with Steve under the Ambry Genetics thread/sticky in the families section.

Also note that the class of the second gene is important. Class interactions do play a part in clinical outcome along with environment, compliance, quality of care, and luck. If you know the other gene, I may be able to provide you with input on that as well.
 

CFHockeyMom

New member
If your daughter has CF then, yes, she definitely has two mutations (R1162L being one and the other???). As far as classifications go, there are five classes, "benign" isn't one of them.

Class I mutations lead to defects in the synthesis of stable CFTR mRNA transcripts resulting in absence of the CFTR protein. About half of all mutations in CFTR (encompassing premature termination, exon skipping, aberrant mRNA splicing, and frameshifts) are thought to fall into this class and result in complete loss of CFTR protein/function.

Class II mutations complete protein translation but produce an abnormal protein that fails to escape the endoplasmic reticulum. Little or no CFTR reaches the plasma membrane, and the absence of all surface CFTR results in a severe phenotype. It is being increasingly recognized that mutations in unrelated genes can create defective proteins, which fail to traffic properly through the cell. Classically, missense mutations creating an abnormal protein were thought to be relatively benign or less consequential than nonsense mutations (null) or large deletions. This is no longer strictly the case because examples from CF and other inherited disorders demonstrate that a synthesized protein that fails to mature along the normal biosynthetic pathway often becomes quite destructive.

Class III mutations disrupt activation and regulation of CFTR at the plasma membrane. Thus biosynthesis, trafficking, and processing are undisturbed, but the channel may be defective with respect to ATP binding and hydrolysis, or phosphorylation.

Class IV mutations affect chloride conductance or channel gating and thus result in reduced chloride current.

Class V mutations reduce the level of normal CFTR protein by alterations in the promoter or by altering splicing. Currently it is thought that a reduction in mRNA to less than 10% of normal results in disease in CF.

I tried to find some info on the R1162L with regard to what class it may fall in. So far, the only thing I've found is the "definition" which is, the replacement of arginine at codon 1162 (CGA) by leucine (CTA) [Arg1162Leu (R1162L)]. I believe this is a Class IV type mutation but your best bet is to check with Steve under the Ambry Genetics thread/sticky in the families section.

Also note that the class of the second gene is important. Class interactions do play a part in clinical outcome along with environment, compliance, quality of care, and luck. If you know the other gene, I may be able to provide you with input on that as well.
 

CFHockeyMom

New member
If your daughter has CF then, yes, she definitely has two mutations (R1162L being one and the other???). As far as classifications go, there are five classes, "benign" isn't one of them.

Class I mutations lead to defects in the synthesis of stable CFTR mRNA transcripts resulting in absence of the CFTR protein. About half of all mutations in CFTR (encompassing premature termination, exon skipping, aberrant mRNA splicing, and frameshifts) are thought to fall into this class and result in complete loss of CFTR protein/function.

Class II mutations complete protein translation but produce an abnormal protein that fails to escape the endoplasmic reticulum. Little or no CFTR reaches the plasma membrane, and the absence of all surface CFTR results in a severe phenotype. It is being increasingly recognized that mutations in unrelated genes can create defective proteins, which fail to traffic properly through the cell. Classically, missense mutations creating an abnormal protein were thought to be relatively benign or less consequential than nonsense mutations (null) or large deletions. This is no longer strictly the case because examples from CF and other inherited disorders demonstrate that a synthesized protein that fails to mature along the normal biosynthetic pathway often becomes quite destructive.

Class III mutations disrupt activation and regulation of CFTR at the plasma membrane. Thus biosynthesis, trafficking, and processing are undisturbed, but the channel may be defective with respect to ATP binding and hydrolysis, or phosphorylation.

Class IV mutations affect chloride conductance or channel gating and thus result in reduced chloride current.

Class V mutations reduce the level of normal CFTR protein by alterations in the promoter or by altering splicing. Currently it is thought that a reduction in mRNA to less than 10% of normal results in disease in CF.

I tried to find some info on the R1162L with regard to what class it may fall in. So far, the only thing I've found is the "definition" which is, the replacement of arginine at codon 1162 (CGA) by leucine (CTA) [Arg1162Leu (R1162L)]. I believe this is a Class IV type mutation but your best bet is to check with Steve under the Ambry Genetics thread/sticky in the families section.

Also note that the class of the second gene is important. Class interactions do play a part in clinical outcome along with environment, compliance, quality of care, and luck. If you know the other gene, I may be able to provide you with input on that as well.
 

CFHockeyMom

New member
If your daughter has CF then, yes, she definitely has two mutations (R1162L being one and the other???). As far as classifications go, there are five classes, "benign" isn't one of them.

Class I mutations lead to defects in the synthesis of stable CFTR mRNA transcripts resulting in absence of the CFTR protein. About half of all mutations in CFTR (encompassing premature termination, exon skipping, aberrant mRNA splicing, and frameshifts) are thought to fall into this class and result in complete loss of CFTR protein/function.

Class II mutations complete protein translation but produce an abnormal protein that fails to escape the endoplasmic reticulum. Little or no CFTR reaches the plasma membrane, and the absence of all surface CFTR results in a severe phenotype. It is being increasingly recognized that mutations in unrelated genes can create defective proteins, which fail to traffic properly through the cell. Classically, missense mutations creating an abnormal protein were thought to be relatively benign or less consequential than nonsense mutations (null) or large deletions. This is no longer strictly the case because examples from CF and other inherited disorders demonstrate that a synthesized protein that fails to mature along the normal biosynthetic pathway often becomes quite destructive.

Class III mutations disrupt activation and regulation of CFTR at the plasma membrane. Thus biosynthesis, trafficking, and processing are undisturbed, but the channel may be defective with respect to ATP binding and hydrolysis, or phosphorylation.

Class IV mutations affect chloride conductance or channel gating and thus result in reduced chloride current.

Class V mutations reduce the level of normal CFTR protein by alterations in the promoter or by altering splicing. Currently it is thought that a reduction in mRNA to less than 10% of normal results in disease in CF.

I tried to find some info on the R1162L with regard to what class it may fall in. So far, the only thing I've found is the "definition" which is, the replacement of arginine at codon 1162 (CGA) by leucine (CTA) [Arg1162Leu (R1162L)]. I believe this is a Class IV type mutation but your best bet is to check with Steve under the Ambry Genetics thread/sticky in the families section.

Also note that the class of the second gene is important. Class interactions do play a part in clinical outcome along with environment, compliance, quality of care, and luck. If you know the other gene, I may be able to provide you with input on that as well.
 

CFHockeyMom

New member
If your daughter has CF then, yes, she definitely has two mutations (R1162L being one and the other???). As far as classifications go, there are five classes, "benign" isn't one of them.

Class I mutations lead to defects in the synthesis of stable CFTR mRNA transcripts resulting in absence of the CFTR protein. About half of all mutations in CFTR (encompassing premature termination, exon skipping, aberrant mRNA splicing, and frameshifts) are thought to fall into this class and result in complete loss of CFTR protein/function.

Class II mutations complete protein translation but produce an abnormal protein that fails to escape the endoplasmic reticulum. Little or no CFTR reaches the plasma membrane, and the absence of all surface CFTR results in a severe phenotype. It is being increasingly recognized that mutations in unrelated genes can create defective proteins, which fail to traffic properly through the cell. Classically, missense mutations creating an abnormal protein were thought to be relatively benign or less consequential than nonsense mutations (null) or large deletions. This is no longer strictly the case because examples from CF and other inherited disorders demonstrate that a synthesized protein that fails to mature along the normal biosynthetic pathway often becomes quite destructive.

Class III mutations disrupt activation and regulation of CFTR at the plasma membrane. Thus biosynthesis, trafficking, and processing are undisturbed, but the channel may be defective with respect to ATP binding and hydrolysis, or phosphorylation.

Class IV mutations affect chloride conductance or channel gating and thus result in reduced chloride current.

Class V mutations reduce the level of normal CFTR protein by alterations in the promoter or by altering splicing. Currently it is thought that a reduction in mRNA to less than 10% of normal results in disease in CF.

I tried to find some info on the R1162L with regard to what class it may fall in. So far, the only thing I've found is the "definition" which is, the replacement of arginine at codon 1162 (CGA) by leucine (CTA) [Arg1162Leu (R1162L)]. I believe this is a Class IV type mutation but your best bet is to check with Steve under the Ambry Genetics thread/sticky in the families section.

Also note that the class of the second gene is important. Class interactions do play a part in clinical outcome along with environment, compliance, quality of care, and luck. If you know the other gene, I may be able to provide you with input on that as well.
 

3gr8kids

New member
thx so much for your response! this is the babys sequence....My other 2 children are carriers of delta f508 and R1162L....but the doctor was trying to explain the seq to me for the baby saying that she is just a carrier but to me she has more symptoms than my other two....Both of my girls have low sweat tests 16 and 6 for the baby...but the baby only gained 1 lb in 6 months...has horrible stools and is on the low end for absorbtion....it may be something else but it is just so confusing when this paper says the dna sequence change and the classifications....the R1162L says likely clinically significant and the other two that are on here T854T and Q1463Q the classification says Benign.....
 

3gr8kids

New member
thx so much for your response! this is the babys sequence....My other 2 children are carriers of delta f508 and R1162L....but the doctor was trying to explain the seq to me for the baby saying that she is just a carrier but to me she has more symptoms than my other two....Both of my girls have low sweat tests 16 and 6 for the baby...but the baby only gained 1 lb in 6 months...has horrible stools and is on the low end for absorbtion....it may be something else but it is just so confusing when this paper says the dna sequence change and the classifications....the R1162L says likely clinically significant and the other two that are on here T854T and Q1463Q the classification says Benign.....
 

3gr8kids

New member
thx so much for your response! this is the babys sequence....My other 2 children are carriers of delta f508 and R1162L....but the doctor was trying to explain the seq to me for the baby saying that she is just a carrier but to me she has more symptoms than my other two....Both of my girls have low sweat tests 16 and 6 for the baby...but the baby only gained 1 lb in 6 months...has horrible stools and is on the low end for absorbtion....it may be something else but it is just so confusing when this paper says the dna sequence change and the classifications....the R1162L says likely clinically significant and the other two that are on here T854T and Q1463Q the classification says Benign.....
 

3gr8kids

New member
thx so much for your response! this is the babys sequence....My other 2 children are carriers of delta f508 and R1162L....but the doctor was trying to explain the seq to me for the baby saying that she is just a carrier but to me she has more symptoms than my other two....Both of my girls have low sweat tests 16 and 6 for the baby...but the baby only gained 1 lb in 6 months...has horrible stools and is on the low end for absorbtion....it may be something else but it is just so confusing when this paper says the dna sequence change and the classifications....the R1162L says likely clinically significant and the other two that are on here T854T and Q1463Q the classification says Benign.....
 

3gr8kids

New member
thx so much for your response! this is the babys sequence....My other 2 children are carriers of delta f508 and R1162L....but the doctor was trying to explain the seq to me for the baby saying that she is just a carrier but to me she has more symptoms than my other two....Both of my girls have low sweat tests 16 and 6 for the baby...but the baby only gained 1 lb in 6 months...has horrible stools and is on the low end for absorbtion....it may be something else but it is just so confusing when this paper says the dna sequence change and the classifications....the R1162L says likely clinically significant and the other two that are on here T854T and Q1463Q the classification says Benign.....
 

CFHockeyMom

New member
This is a good question for Steven but here's what I've gathered...

Your children's CF genes are DF508 (Class II) and R1622L (Class IV?). The T845T and the Q1463Q have to do with gene sequence/location also know as alleles. So, it sounds as if your baby is simply a carrier of the R1622L gene.
 

CFHockeyMom

New member
This is a good question for Steven but here's what I've gathered...

Your children's CF genes are DF508 (Class II) and R1622L (Class IV?). The T845T and the Q1463Q have to do with gene sequence/location also know as alleles. So, it sounds as if your baby is simply a carrier of the R1622L gene.
 

CFHockeyMom

New member
This is a good question for Steven but here's what I've gathered...

Your children's CF genes are DF508 (Class II) and R1622L (Class IV?). The T845T and the Q1463Q have to do with gene sequence/location also know as alleles. So, it sounds as if your baby is simply a carrier of the R1622L gene.
 

CFHockeyMom

New member
This is a good question for Steven but here's what I've gathered...

Your children's CF genes are DF508 (Class II) and R1622L (Class IV?). The T845T and the Q1463Q have to do with gene sequence/location also know as alleles. So, it sounds as if your baby is simply a carrier of the R1622L gene.
 

CFHockeyMom

New member
This is a good question for Steven but here's what I've gathered...

Your children's CF genes are DF508 (Class II) and R1622L (Class IV?). The T845T and the Q1463Q have to do with gene sequence/location also know as alleles. So, it sounds as if your baby is simply a carrier of the R1622L gene.
 
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