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Download for Rare SNP Analysis

Discussion in 'Genetic Testing and SNPs' started by Valentijn, Aug 29, 2013.

  1. MimiLoves

    MimiLoves

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    Hi Valentijn,

    Yes I was a little surprised about the Cohen's marker. I have a feeling that it may have been what a great great uncle of mine in the late 1800's had. Judging by photographs and the information passed down. The albinism of course, I have had since birth (I know you cannot tell by my picture since I wear make up and stuff, but look at my arm) I am actually in an albinism study at the NIH in Bethesda, Maryland and I am the first person to start a trial drug called nitisinone (Orfadin) to cure albinism. More so because of vision problems and not just for vanity. People with albinism have HORRIBLE vision because of the lack of pigment. The Fuchs Corneal dystrophy I definitely have due to the appearance of gutatta on my corneas and I found out about that before 23andme. I did find a marker in my genome that was thought to be connected. Although I am sure that you know that many conditions, particularly ones dealing with connective tissue are still in the early stages of research and discovery. I was diagnosed with EDS before 23andme as well, but I haven't found a solid indication of it. Long QT, I had seen the rare marker on KCNE2 for it but thought nothing of it. When I was at the NIH, they said that my EKG showed a slightly elongated QT interval, and I said "Oh yeah, I found a genetic marker for that in my genome." Later, I told my dad and he said that he was diagnosed with Long QT in 1989 but never mentioned it because he didn't think it was a big deal. And the Cystic Fibrosis, I knew that I was a carrier since a few years ago when my husband and I went for a fertility work up and I had a little genetic panel done to see if I carried any common conditions. I have had numerous other relatives with CF so I wasn't surprised. As you mentioned, some carriers present with mild symptoms of the condition, and my DeltaF508 mutation for CF is one of those. I have chronic bronchitis and sinus issues. Johns Hopkins Hospital did a research study on that and found that it is true, although it is difficult for me to convince doctors that this is the cause of my issues. I think it is because of the misconception of how genes and cells actually work. I get a lot of respect and props from the doctors at the NIH because of my knowledge of genetics (which I know is still very feeble compared to doctors there) but my knowledge of genetics and how they work is still higher than most doctors practicing in our neighborhoods and not involved in research. My doctors at the NIH are some of the top in their field and specialties and have taken the time to also answer questions for me and help me learn even more about genetics. it really is very complex. The more that I learn, the more that I realize how much that I do not know and understand yet. I must be a true nerd at heart because I find it fascinating enough to stay up late nights on end, reading medical and genetic research documents on my ipad in bed, instead of sleeping, like its a thrilling novel or something, haha.
     
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  2. MRESTIVO

    MRESTIVO

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    Here are my results. Is there anything I should look out for?

    rs17365584 1 T 0.010 CT
    rs1057624 1 C 0.010 CT
    rs35737219 1 A 0.010 AG
    rs11573142 1 G 0.010 AG r
    s17442970 1 A 0.010 AC
    rs17559902 1 G 0.010 AG
    rs11548275 1 T 0.010 CT
    rs11572262 1 T 0.010 CT
    rs7537934 1 T 0.010 GT
    rs17017651 1 C 0.010 CT
    rs10305710 1 T 0.010 CT
    rs11465212 1 A 0.010 AG
    rs8177971 1 A 0.010 AC
    rs11578472 1 T 0.010 GT
    rs35012521 1 A 0.003 AT
    rs45500891 1 T 0.010 CT
    rs2234698 1 C 0.010 CT
    i5008907 2 G 0.003 AG Renamed rs61743502
    rs1396835 2 T 0.010 CT
    rs12997487 2 A 0.010 AG
    rs7594370 2 T 0.010 CT
    rs17776702 2 G 0.010 AG
    rs13400424 2 A 0.010 AG
    rs16859473 2 G 0.010 AG
    rs10178538 2 C 0.010 CT
    rs10206109 2 T 0.010 CT
    i5004956 2 A 0.010 AT Renamed rs121908120
    rs13032621 2 A 0.010 AA Homozygous
    rs2041 3 T 0.010 CT
    rs1025568 3 A 0.010 AC
    rs3844057 3 C 0.010 CT
    rs34231037 4 G 0.010 AG
    rs28913916 4 G 0.010 AG
    rs17393302 4 T 0.010 CT
    rs17597712 4 C 0.010 CT
    i5004911 5 T 0.002 CT Renamed rs121909362
    rs1048957 5 G 0.010 GT
    rs34006513 5 A 0.010 AG
    rs12195092 6 A 0.010 AG
    rs9501680 6 G 0.010 AG
    rs17875388 6 C 0.010 CT
    rs28399993 6 A 0.010 AG
    i5900163 6 T 0.010 CT Renamed rs143589474
    rs11751895 6 C 0.010 CT
    rs17856332 6 G 0.010 AG
    rs205353 6 T 0.010 CT
    rs13203014 6 C 0.010 CT
    rs7743462 6 C 0.010 CT
    rs4535615 7 G 0.010 AG
    rs17777652 7 C 0.010 CT
    rs17132152 7 A 0.010 AC
    rs17132196 7 G 0.010 AG
    rs17092911 7 T 0.010 CT
     
  3. MRESTIVO

    MRESTIVO

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    rs17132201 7 G 0.010 AG
    rs17132206 7 G 0.010 AG
    rs17132208 7 G 0.010 GT
    rs2235063 7 C 0.010 CT
    rs11765354 7 T 0.010 CT
    rs17249588 7 C 0.010 CT
    rs39326 7 A 0.010 AG
    rs16872818 7 A 0.010 AG
    rs7790704 7 G 0.010 GT
    rs11765511 7 T 0.010 CT
    rs17747688 8 T 0.010 CT
    rs7814768 8 G 0.010 AG
    rs4647904 8 A 0.010 AG
    rs17365305 8 A 0.010 AG
    rs9942821 8 A 0.010 AG
    rs13279146 8 A 0.010 AG
    rs4741289 9 T 0.010 CT
    rs10972206 9 G 0.010 AG
    rs11145055 9 A 0.010 AG
    rs35142681 9 T 0.010 CT
    rs11572142 10 G 0.010 AG
    rs12780429 10 G 0.010 AG
    rs12293349 11 T 0.005 CT
    rs4647760 11 A 0.010 AC
    rs11231164 11 C 0.004 CT
    rs17825668 11 G 0.010 AG
    rs17245810 11 G 0.010 AG
    rs12277797 11 C 0.010 CT
    rs10492162 12 A 0.010 AG
    rs1805555 12 A 0.010 AG
    rs35303786 12 C 0.010 CT
    rs10507168 12 C 0.010 CT
    rs3135641 13 A 0.010 AG
    rs7993202 13 T 0.010 CT
    rs11617392 13 T 0.010 GT
    rs4646231 13 C 0.010 CT
    rs7322352 13 T 0.010 CT
    rs4907646 13 G 0.010 GT
    rs34457782 14 A 0.010 AG
    rs17393098 14 T 0.010 CT
    rs12878498 14 T 0.010 GT
    rs17363343 15 A 0.004 AG
    rs2470168 15 A 0.010 AC
    rs4775085 15 A 0.010 AG
    rs13379935 15 C 0.010 CT
    rs17601226 15 C 0.010 CT
    rs8176928 16 G 0.004 GG Homozygous
    rs669561 16 T 0.010 CT
    rs611704 16 A 0.010 AG
    rs9282774 16 T 0.010 CT
    rs4312323 16 T 0.010 CT
    rs5743271 16 G 0.010 AG
    rs7198865 16 A 0.010 AG
     
  4. MRESTIVO

    MRESTIVO

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    rs2232229 16 A 0.010 AG
    rs12920868 16 T 0.010 CT
    rs11653054 17 T 0.010 CT
    rs34399035 17 T 0.004 CT
    rs12325826 17 A 0.010 AG
    rs2090019 17 T 0.010 CT
    rs11466310 19 T 0.010 CT
    rs34462078 19 T 0.010 CT
    rs13040764 20 G 0.010 AG
    rs34716589 20 G 0.010 AG
    rs17275984 21 T 0.010 CT
    rs8130161 21 T 0.010 CT
    rs9975011 21 A 0.010 AG
    rs17179966 21 A 0.010 AG
    rs8142331 22 A 0.010 AA Homozygous
    rs4988443 22 T 0.010 CT
     
  5. Valentijn

    Valentijn Senior Member

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    @MRESTIVO - The ones which are "renamed" are often the more interesting ones, since 23andMe uses their proprietary numbering system to hide pathogenic SNP results.
    This is a rare missense mutation on the APOB gene, suspected of causing very high levels of cholesterol. Mutations in the gene act in an autosomal dominant manner, meaning being heterozygous for it is sufficient to cause disease. But there's not much data, just this study of familial hypercholesterolemia patients finding it in one patient and the mutation being in a vulnerable location on the gene: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4587402/

    Another rare missense mutation, this time on the WNT10A. When homozygous it causes problems with some teeth not growing in. When heterozygous, sometimes there are missing teeth, but sometimes teeth are normal. I don't have this mutation, but myself, my aunt, and my cousin all had a molar which never grew in, so we probably have a different mutation on the same gene :D More data for your mutation is at http://www.omim.org/entry/606268#0003

    This is on the GHR (growth hormone receptor) gene, and can result in being a bit short when heterozygous, about 1 standard deviation below the mean based on a very small study. It's discussed a little bit in http://www.nejm.org/doi/full/10.1056/NEJM199510263331701#t=article

    Sometimes homozygous results are interesting, but yours aren't on genes, and one is an error from 23andMe.

    There's also some additional files on the download site at https://sourceforge.net/projects/analyzemygenes/files/Databases/ . If you download and unzip "remarks.zip" to the same folder as the program files, it'll label results with known missense and pathogenic mutations, etc. This makes the ten_percent.zip file in the same folder more useful as well, as it can efficiently sort through the results, and it's possible to look for compound heterozygous results.
     
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  6. MRESTIVO

    MRESTIVO

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    Thank You so much! Marty
     
  7. Jenny TipsforME

    Jenny TipsforME Senior Member

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    @Valentijn (and anyone else) what do you make of these? (Can't make it look like a table sorry). I have ME/CFS and POTS diagnoses.
    (tabs=)SNP CHRM RARE PERCENT GENOTYPE Rename Mutation Blosum Clinsig Genes Homozygous =Notes web
    • rs5388 17 T 0.003 CT V96I 3 GH1 =can't find
    • rs55778349 19 C 0.003 CG P194R -2 Likely pathogenic JAK3 =Severe combined immunodeficiency https://www.snpedia.com/index.php/Rs55778349
    • i5002979 9 G 0.001 AG rs75391579 Q12R 1 Pathogenic GALT/? =The RARS2 gene encodes mitochondrial arginine-tRNA synthetase, pontocerebellar hypoplasia
    • rs11555096 15 T 0.01 CT R341W -3 Pathogenic FAH =This variant shows pseudodeficiency for production of FAH protein which is connected with hereditary tyrosinemia type I.
    • rs28370127 1 C 0.005 CG E521Q 2 CAPN2 =missense location Chromosome 1:223761612
    • rs35910969 17 G 0.01 CG L110V 1 Pathogenic SLC9A3R1/MIR3615 =NHERF1 is a cytoplasmic adaptor protein that recruits various signaling proteins, cellular receptors, ion transporters, and other proteins to the plasma membrane of epithelia and other cell types http://www.omim.org/entry/604990?search=L110V&highlight=l110v
    • rs1801158 1 T 0.01 CT S534N 1 untested DPYD =(to do with response to cancer drug) The variant was implicated in dihydropyrimidine dehydrogenase deficiency when present as a compound heterozygote with M166V
    I have others I haven't looked up and a homo missense I've discussed before with @Valentijn
     
  8. Valentijn

    Valentijn Senior Member

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    This one is marked as "benign" and involves an amino acid being replaced with one which is nearly identical. So it probably doesn't have any impact.


    This one has been found in a patient with SCID in a few studies. But it's an autosomal recessive disease, so someone would have to be homozygous for it to be a problem.

    According to a paper cited at http://www.omim.org/entry/606999#0006, being heterozygous results in enzyme activity being reduced to 15% (or maybe it's a calculated 32.5%). But it's a recessive disease, so that still might be enough to function pretty normally.

    There's also another not-too-uncommon GALT silent substitution (L218L, T allele at rs2070075) which basically fixes the problem, and enzyme activity is normal or even above normal, despite having one of the pathogenic GALT mutations. It's thought to have that effect by upregulating production of the enzyme, which compensates for the reduced functionality of the enzyme.

    This allele is associated with "pseudodeficiency" (a general genetic term). Basically it alters the protein, maybe in an essential manner, but doesn't cause disease. It might be similar to the GALT situation above, where there can be decreased functionality but increased levels to compensate.

    This one hasn't been studied, but it sounds like computer models predict it doesn't have any effect.

    When heterozygous, this causes "NEPHROLITHIASIS/OSTEOPOROSIS, HYPOPHOSPHATEMIC, (Type) 2". Or slightly more comprehensibly, "impaired renal phosphate absorption resulting in calcium nephrolithiasis and decreased BMD (bone mineral density". http://www.omim.org/entry/604990#0001

    It sounds like being heterozygous can't cause a proper DPYD deficiency, but it can result in one cancer drug (Fluorouracil) being toxic.
     
  9. Jenny TipsforME

    Jenny TipsforME Senior Member

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    Oh the SCID one is very interesting. I'm not convinced I actually have Severe combined immunodeficiency (though not impossible, I had low immunity from early on eg constant ear infections and glue ear) but look how relevant the general problem sounds to ME:

    "Severe combined immunodeficiency, SCID, also known asalymphocytosis, Glanzmann–Riniker syndrome, severe mixed immunodeficiency syndrome, and thymic alymphoplasia,[1] is a genetic disorder characterized by the disturbed development of functional T cells and B cells caused by numerous genetic mutations that result in heterogeneous clinical presentations.[2] SCID involves defective antibody response due to either direct involvement with B lymphocytes or through improper B lymphocyte activation due to non-functional T-helper cells.[3]Consequently, both "arms" (B cells and T cells) of the adaptive immune system are impaired due to a defect in one of several possible genes. SCID is the most severe form of primary immunodeficiencies," https://en.wikipedia.org/wiki/Severe_combined_immunodeficiency#Treatment

    @Valentijn has anyone else had rs55778349 mutation? It is super rare (0.003) so if it isn't relevant I doubt anyone else on here has it.

    SCID treatment is bone marrow transplant (or living in a protective bubble!). I think I probably wouldn't have made it to 38 years without treatment, if I'm reading it right. Also all those routine "healthy" blood tests would have shown it up I think. These disease links are just associations though, presumably there could be different clinical presentation of the expressed SNP that hasn't yet been studied? eg ME related?

    Looking on LiveWello, I also have some other risks for SCID

    SEVERE COMBINED IMMUNODEFICIENCY
    SNP
    rsID Minor Allele Genotype Phenotype
    IL7R rs1494555 G GG +/+
    IL7R rs1494558 T TT +/+


    DCLRE1C -(23 AND ME) PARTIAL TO SEVERE COMBINED:
    SNP rsID Minor Allele Genotype Phenotype
    COLEC10 rs5005859 C - NG
    DCLRE1C rs11259405 C CT +/-
    DCLRE1C rs11517377 T GT +/-

    DCLRE1C rs11593133 A GG -/-
    DCLRE1C rs12245497 G AA -/-
    DCLRE1C rs12572872 A GG -/-
    DCLRE1C rs12768894 C TT -/-
    DCLRE1C rs35441642 C GG -/-
    DCLRE1C rs41299724 G AG +/-
    DCLRE1C rs7916726 G AG +/-

    GNAS rs6026555 T - NG
    LOC105372537 rs6042016 T - NG
    LOC105372537 rs6042019 T - NG
    SNP? rs5005860 A - NG
    SNP? rs6042018 T TT +/+
    SNP? rs6057088 G - NG

    No spoons to actually look those ones up today.
     
  10. Valentijn

    Valentijn Senior Member

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    Nope, it's not showing up in anyone's rare results nor the compiled results of 31 patients.
     
  11. Jenny TipsforME

    Jenny TipsforME Senior Member

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    Posts crossed over before @Valentijn

    Is that definite? So not relevant. It's an interesting condition in relation to ME though. Could it be that ME is not an autosomal recessive disease? ie it's not possible for me to have SCID but it is possible to have something up with my B cells due to this mutation?

    According to a paper cited at http://www.omim.org/entry/606999#0006, being heterozygous results in enzyme activity being reduced to 15% (or maybe it's a calculated 32.5%). But it's a recessive disease, so that still might be enough to function pretty normally.

    There's also another not-too-uncommon GALT silent substitution (L218L, T allele at rs2070075) which basically fixes the problem, and enzyme activity is normal or even above normal, despite having one of the pathogenic GALT mutations. It's thought to have that effect by upregulating production of the enzyme, which compensates for the reduced functionality of the enzyme.

    "Jenny H’s genotype for GALT rs2070075 is CC" so I don't have that fix

    This allele is associated with "pseudodeficiency" (a general genetic term). Basically it alters the protein, maybe in an essential manner, but doesn't cause disease. It might be similar to the GALT situation above, where there can be decreased functionality but increased levels to compensate.

    OK
    This one hasn't been studied, but it sounds like computer models predict it doesn't have any effect.

    OK

    When heterozygous, this causes "NEPHROLITHIASIS/OSTEOPOROSIS, HYPOPHOSPHATEMIC, (Type) 2". Or slightly more comprehensibly, "impaired renal phosphate absorption resulting in calcium nephrolithiasis and decreased BMD (bone mineral density". http://www.omim.org/entry/604990#0001

    Kidney stones?

    It sounds like being heterozygous can't cause a proper DPYD deficiency, but it can result in one cancer drug (Fluorouracil) being toxic.[/QUOTE]
    Hopefully that won't be relevant
     
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  12. Jenny TipsforME

    Jenny TipsforME Senior Member

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    @Valentijn oh my comments look like they're part of your quote. Think I may need to switch off the computer...
     
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  13. Jenny TipsforME

    Jenny TipsforME Senior Member

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    Just closing down a multitude of internet tabs related to genetic stuff
    @Valentijn how do you interpret this quote re SCID and related issues:

    "Combined immunodeficiency syndromes are a heterogeneous group of disorders arising from a disturbance in the development and function of both T and B cells (cellular and humoral immunity) (figure 1 and table 1 and table 2) [1]. These disorders are termed "severe" (eg, severe combined immune deficiency [SCID]) when they lead to early death from overwhelming infection, typically in the first year of life. Mutations of a particular gene may lead to SCID or to milder immunodeficiency, depending upon whether the defect is complete or partial. Gene defects that lead to partial function of the gene product are called "hypomorphic", whereas complete defects are called "null" or "amorphic." from http://www.uptodate.com/contents/severe-combined-immunodeficiency-scid-specific-defects which I can't access any more of.

    Would this still rely on homozygous mutation or by "partial function of the gene" do they mean heterozygous?
    If it is a thing hetero wise, is this the sort of thing which would have shown up in standard FBC tests?
    I feel immunodeficient (I catch viruses easily) but my standard blood tests are OK, only immune related thing ever picked up was EBV. Of course NHS tests usually quite basic, when they have gone off the beaten path it is my experience that positive results turn up (in my case high creatine kinase, inner ear lesion, POTS and nearly constant tachycardia).

    If it seems likely relevant I will take to my doctor, but after so long with ME I have a natural aversion to raising anything that might undermine my credibility as an informed patient.

     
  14. Valentijn

    Valentijn Senior Member

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    No, they're not referring to homozygous versus heterozygous. That would typically be in the context of "recessive" versus "dominant", with a milder effect from heterozygous mutations having "incomplete dominance".

    What they're talking about in the bit you quoted is how much of an impact a mutation has. "Hypomorphic" is a down-regulation resulting in less activity from the gene product, whereas a null or amorphic mutation mean that there is no functional gene product.

    Down-regulations can be very mild and cause no real problems, but the complete lack of the enzyme created by a gene usually is a problem. Though sometimes there is another gene performing an identical function or getting the same job done via a different pathway.
     
  15. Jenny TipsforME

    Jenny TipsforME Senior Member

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    @Valentijn so are they still talking about people with homozygous mutations, but some of them have a severe effect from it and for some the impact is mild? Not sure I quite understand.

    I guess what I need to know is if I mention this to my doctor is that a waste of time and likely to make me look silly, because I'm heterozygous and can't have this problem anyway?

    Thanks for all your help, it must get a little frustrating when we don't get these things.
     
  16. Jenny TipsforME

    Jenny TipsforME Senior Member

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    Having said that I am actually homo for 3 of the related SNPs, just not the rare one

    Probably worth looking those up
     
  17. Jenny TipsforME

    Jenny TipsforME Senior Member

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    If anyone else is interested, this thread discusses other pwme and SCID related mutations
    http://forums.prohealth.com/forums/...ith-cfs-who-have-done-23andme-testing.264689/

    I haven't finished reading but I'm confused about this person's interpretation. They mention that mutations need to be homo (they're hetero) and yet doctors appear to take it on board.

    Later they say they're compound heterogeneous on two related SNPs which can have effect similar to homo on one. I'm not sure that sounds right if the condition is recessive. Wouldn't the dominant allele on each just cancel out the recessive ones? Wondering if I'm misunderstanding some basics here. @Valentijn ?
     
    Last edited: Jul 12, 2016
  18. Valentijn

    Valentijn Senior Member

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    Yes. That specific disease, when it arises from that specific gene, is recessive. But depending on the specific mutation on the gene, the gene product might be very functional, or barely functional, or not functional at all, or something in between. It depends on the location of the mutation, and the new amino acid which is replacing the normal amino acid.

    If the mutation is near the beginning of the gene, a premature stop to the enzyme will probably make it completely nonfunctional, but a premature stop near the end of the gene might leave all the essential parts intact. And some amino acids are extremely similar to each other (in size, charge, etc), so typically don't cause problems when replacing each other, but an amino acid with very different properties might make its links to its neighbors break down faster or slower at normal body temperatures. Additionally, if a mutation is at a critical position in the enzyme, it might cause the enzyme to have the wrong shape, or interfere with the ability of the enzyme to us that section to connect with other substances in the body.

    Based on your 23andMe results, there's no indication that you have SCID. But 23andMe testing is very scattered and incomplete. Generally it's testing dozens or less of the SNPs on a gene which has hundreds or thousands of potentially pathogenic SNPs. So a rare heterozygous result might be a reason to take a look at the rest of the gene much more closely, by sequencing the entire gene (or just its exons), or by running the lab tests which can be used to diagnose the disease.

    So your 23andMe data isn't diagnostic for you having the disease, but it could be an indication that it's a reasonable direction to take a closer look.

    These are marked as pathogenic, but it's based on the results of a single patient with SCID. But on average, 14% of people around the world are homozygous for those, and up to 40% in Asian populations. Due to the very high prevalence rate in the general population, it almost certainly was not causing SCID in that patient. The prevalence rates between the two SNPs are very similar overall, and identical in some European groups, so they are probably inherited together and not rarer or having any extra effect if both are present instead of just one.

    This isn't close enough to the IL7R gene, and either allele is extremely common (near 50%).

    I don't have sufficient understanding to go into a detailed explanation, but basically two pathogenic compound heterozygous mutations on a gene is equivalent to having a pathogenic homozygous mutation.

    From what I recall, both strands are used to attempt to create the gene product (an enzyme). If one is faulty (heterozygous for recessive disease), the good strand can keep things functional by producing the normal enzyme as well. But if each strand has a fault, neither is producing the enzyme properly. But the different strands don't merge and correct each others' faults.

    And for mutations to be compound heterozygous, this is why they must be on different strands. Multiple mutations on a single strand won't be a problem in a recessive disease, so long as the other strand lacks pathogenic mutations.
     
    Last edited: Jul 12, 2016
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  19. Jenny TipsforME

    Jenny TipsforME Senior Member

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    Thanks @Valentijn. How do you know so much about genetics? Was it your pre-ME world?
     
  20. Valentijn

    Valentijn Senior Member

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    No, I was a lawyer. I nearly flunked high school biology :p

    Mostly I learned by taking a few basic genetics classes on Coursera. And with the basics in place, it's easier to read papers about genetics, and understand other informational sources (such as wikipedia, OMIM, books, etc). I'd like to take more courses, but my brain isn't up for it currently, even if I ignore deadlines and don't worry about the assignments that I can't handle.
     
    Last edited: Jul 12, 2016
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