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    Created in 2008, Phoenix Rising is the largest and oldest forum dedicated to furthering the understanding of and finding treatments for complex chronic illnesses such as chronic fatigue syndrome (ME/CFS), fibromyalgia (FM), long COVID, postural orthostatic tachycardia syndrome (POTS), mast cell activation syndrome (MCAS), and allied diseases.

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Download for Rare SNP Analysis

Messages
17
Thumbs up @Valentijn , I am a step further in my investigations.
On my old XP , I had following happening :
- Before downloading the comment file, the safe as PDF gave an completely empty file.
- But the text file was OK
- After adding the comments file the save as PDF suddenly worked.
- The sorting by first collumn works on the PDF file , but not on the TXT file.
And now ? Learn how to lookup .... and not panic when I find a scary one :)
From
i3000469 2 T 0.060 CT Mutation T105I (-1) Clinsig is other Genes HNMT Renamed rs11558538
i3003198 15 T 0.010 CT Genes LIPC Renamed rs35511894
i5008401 1 A 0.001 AG Mutation P20L (-3) Clinsig is Patho Genes NPHS2 Renamed rs74315344
i5900152 5 C 0.050 CT Genes PDE6A Renamed rs112771183
I find only info about 74315344
 
Messages
15,786
- Before downloading the comment file, the safe as PDF gave an completely empty file.
Ah, that makes sense. We only added the pdf file option recently I think, at the same time the "remarks" database was added. We still need to repackage the latest versions of the files so everything that goes together gets downloaded together :p

- The sorting by first collumn works on the PDF file , but not on the TXT file.
With the text file, the best approach is to open it from Excel. Then each field will be in a sortable column.

And now ? Learn how to lookup .... and not panic when I find a scary one :)
You can look them up by rsID (rs11558538, etc) at www.ncbi.nlm.nih.gov/projects/SNP/ . That will often link to any pathogenic info, or you can directly look up a gene at OMIM.org.

There are usually multiple different positions given for missense mutations, as more info about the protein created is uncovered, so positions given in the report can be wrong. But the amino acid abbreviations are always the same. So the report might say the mutation is "T105I" but it's reported elsewhere as "T71I". So on OMIM and similar, it can be important to look for nearby numbers with the same amino acids.

So for HNMT T105I, there's no link to pathogenic info about it, though you can see links to all the research if you hover over the cyan box in the map view. But at OMIM that SNP is listed at http://omim.org/entry/605238#0001 and the research is summarized. Some says its a risk factor for asthma, some says it isn't. So it's not pathogenic, and might or might not mean asthma is more likely.

Your NPHS2 mutation is more interesting. http://www.omim.org/entry/604766#0006 shows that it's pathogenic when autosomal recessive (homozygous or compound heterozygous) but also indicates that people heterozygous for this mutation can have a milder form of Nephrotic Syndrome which is sometimes responsive to steroids. Though as it says in the summary on OMIM, it can't be ruled out that there's another heterozygous mutation on the same gene which causes them to be compound heterozygous. 0.4% of the general population is heterozygous for that mutation, so it's quite rare.
 

Moof

Senior Member
Messages
778
Location
UK
Somewhat behind the curve, as usual, I've just gone through this fascinating thread this evening. @Valentijn, are you still collecting 23andMe data from confirmed M.E. patients? Happy to send mine if you are...been ill with it for more than 40 years, so will contribute to any project that may yield interesting results! (No worries if you've long since left it behind.) And happy new year, all!
 
Messages
6
Hello, thank you for you deciphering skills. I tried the Analyze my Data site, but did not get very far lol. Could u please summarize my methylation analysis results and detox? Thank you~

comt v158m aa ++
comt h62h tt ++
vdr taq aa ++
mthfr a1298c gg ++
cbs c699t ag +-

cyp1b1 L432v CG +-
cyp2c19*17 CT +-
cyp2e1*1b 9896c>g CG +-
gstp1 I105v AG +-
sod2 a16v AG +-
nat2 I114T CT +-
nat2 R197Q AG +-
nat2 K268R AG +-