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Old 11-18-2014, 09:53 AM   #1
leontp587
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Default Understand clinvar genotype

Looking at the SNP's in Clinvar, for example http://www.ncbi.nlm.nih.gov/clinvar/variation/11/, I see that the SNP NM_000410.3(HFE):c.193A>T (p.Ser65Cys) (also known as rs1800730) corresponds to the disease hemochromatosis. Since we have 2 alleles, that means the genotype possibilities are AA, AT, or TT. From the ClinVar data, is it possible to see which genotype are associated with the disease? I assume that since we have a A to T mutation, then T must be the pathogenic allele. So, does this mean TT is worse than AT which is worse than AA?

Last edited by leontp587; 11-18-2014 at 01:37 PM.
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Old 06-21-2018, 01:50 AM   #2
juhuvn
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Quote:
Originally Posted by leontp587 View Post
Looking at the SNP's in Clinvar, for example http://www.ncbi.nlm.nih.gov/clinvar/variation/11/, I see that the SNP NM_000410.3(HFE):c.193A>T (p.Ser65Cys) (also known as rs1800730) corresponds to the disease hemochromatosis. Since we have 2 alleles, that means the genotype possibilities are AA, AT, or TT. From the ClinVar data, is it possible to see which genotype are associated with the disease? I assume that since we have a A to T mutation, then T must be the pathogenic allele. So, does this mean TT is worse than AT which is worse than AA?
I have the same question. Could anyone can explain?
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Old 06-25-2018, 11:57 PM   #3
finswimmer
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Hello,

whether AT or TT is needed to be pathogenic depends on the mode of inheritance. Is it dominant than it is enough if one allele has T, if it is recessive you need TT (or a second mutation in the gene on the other allele).

In clinvar you find under "Condition(s)" links to OMIM, where you can read about the inheritance.

fin swimmer
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Old 06-26-2018, 11:10 AM   #4
r.rosati
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You may also want to expand the text in "Summary evidence" (on the Illumina and Invitae rows).
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