Friday, 10 February 2012

Location for variants, and more on genes

Before I undertook my trawl of the different variants of HSP, I had in my mind that I would be able to find a "translation" between the detailed results of genetic tests and the variant of the condition. I thought it would be quite a simple exercise - listing the known genetic variations by SPG number and making something clear which I thought wasn't too clear when I got my test results.

Of course, now I realise that there are over 270 genetic variants for SPG4 and over 70 for SPG 11 I realise that this would be a mammoth table, so not something that is easily undertaken. So, a much simpler question to ask is "which genes are affected" - It would seem that each SPG variant affects a different gene, so there are 48 answers to that question. A brief trawl of the internet identifies that the more commonly occurring variants have had their genes named:

SPG4 Spastin
SPG11 Spastacin
SPG3A Alastin
SPG7 Paraplegin
SPG17 Seipin
A more detailed trawl (for another day) may get further down this line.

Which leads me to perhaps an even more basic question - which chromosomes are affected. I know the Spast gene is on Chromosome 2, but are all the SPG variants? - Quick answer: No.

This made me realise that I had described my genetic test result, and looked at the chromosomal location for other SPGs without really explaining to myself what was going on. There were various references to 'p's and 'q's, but I didn't really understand. So, here goes:

There are 23 pairs of chromosomes in the human body. The first 22 pairs are the same, whereas the last pair is different - and identifies your sex. The chromosomes are numbered by length, with number 1 being the longest and 22 being the shortest. Each chromosome has two arms either side of a narrowing (or centromere). These are the 'p' and the 'q' arms, the 'p' arm is the shortest arm (coming from the French petit - small).  Starting at the centromere the locations on the gene are numbered sequentially, with the first location being given 1, the second 2 etc. etc.

So SPG4 is 2p24-2p21, meaning its on the short arm of the 2nd chromosome, between the 21st and 24th location away from the centromere.

This allows me to do a quick set of stats on my trawl of SPG variants - number of variants on each chromosome:
Chromosome Number
1 4
2 4
3 3
4 1
5 0
6 1
7 1
8 3
9 2
10 4
11 2
12 3
13 2
14 4
15 3
16 2
17 0
18 1
19 3
20 0
21 0
22 0
x 5
Unspec 2
Total 50

This more or less ties up with this search. Perhaps I'll look into the differences at some point!

I have 39 'q's and 13'p's - four variants including both.

Various links that helped me find out more are here:

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