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View Full Version : What is the difference between M412 and P310?



fieldrat
03-20-2017, 09:25 PM
I am (for perhaps obvious personal reasons) trying to figure out if the variants R-M412 and R-P310 on the Y chromosome are different variants or not.

I looked at genetichomeland.com and it says that the difference is a SNP at location 18907236 on the Y chromosome. Yet, if you look at this, it says that the ancestral and derived (Ref and Alt) variants are both "C". And if I look at my downloaded data from 23andme, they don't report any data for this offset.

It seems very strange that the "Ref" and "Alt" should be the same nucleotide, and it seems very strange that if this is standard variant, that 23andme would not test for it.

Is 23andme not giving me the complete picture, or is there something about the R-M412/R-P310 split that is somehow strange (like a SNP was reported at this location, but the report was faulty in some way)?

Thanks for any insight you can give.

MacUalraig
03-20-2017, 09:35 PM
I am (for perhaps obvious personal reasons) trying to figure out if the variants R-M412 and R-P310 on the Y chromosome are different variants or not.

I looked at genetichomeland.com and it says that the difference is a SNP at location 18907236 on the Y chromosome. Yet, if you look at this, it says that the ancestral and derived (Ref and Alt) variants are both "C". And if I look at my downloaded data from 23andme, they don't report any data for this offset.

It seems very strange that the "Ref" and "Alt" should be the same nucleotide, and it seems very strange that if this is standard variant, that 23andme would not test for it.

Is 23andme not giving me the complete picture, or is there something about the R-M412/R-P310 split that is somehow strange (like a SNP was reported at this location, but the report was faulty in some way)?

Thanks for any insight you can give.

P310 is an A->C mutation. Ancestry report a positive as C,C - this is quite standard reporting for a Y call on these generic chip tests. If you are negative you should get A,A. Don't have a 23andme file for comparison.

rs9786283 24 18907236 C C

M412 is a different SNP, different location and a G->A mutation.
Not sure if this answers your question?

fieldrat
03-20-2017, 09:44 PM
Thanks, MacUalraig. That answers my question about what differentiates P310.

This is what my download of 23andme data looks like:

# Each line corresponds to a single SNP. For each SNP, we provide its identifier
# (an rsid or an internal id), its location on the reference human genome, and the
# genotype call oriented with respect to the plus strand on the human reference sequence.
# We are using reference human assembly build 37 (also known as Annotation Release 104).

# rsid chromosome position genotype
rs35667440 Y 18903669 --
rs17249854 Y 18914441 T

They are listed in numerical order, which makes me believe that 23andme didn't test at this offset, which seems strange.

Thanks for the insight.

MacUalraig
03-20-2017, 09:49 PM
Also (not wanting to complicate things too much) the human reference is derived for P310 - if you look in a genome browser it shows C as the 'ref' but this is because most of the reference sequence was a hg R male.

This is why genetichomeland report it like this

SNP Y 18907236 P310 PF6546 S129 C C ISOGG 2014 Corrected Ref A to HG19 FASTA c

but Thomas Krahn's browser has it as
Name: P310
Type: snp
Source: point
Position: ChrY:18907236..18907236 (+ strand)
Length: 1
allele_anc: A
allele_der: C
comment: aka rs9786283

fieldrat
03-20-2017, 10:03 PM
Thanks. I think that the answer to my question is that 23andme did not test at this location, so I can't tell whether I have M412 (ancestral) or P310 (derived) variant.

ArmandoR1b
03-21-2017, 12:20 AM
Thanks. I think that the answer to my question is that 23andme did not test at this location, so I can't tell whether I have M412 (ancestral) or P310 (derived) variant.
M412 is a synonym for L51 which is at position 8502236 and is identified in 23andme as rs9786140 and the mutation is G to A. G is ancestral and A is derived. As far as I know that SNP was tested in v2 through v4. It shows up in the new experience at https://you.23andme.com/tools/data/?query=rs9786140

L51/M412 is upstream of P310. P310 is a phylogenetic equivalent of L151. Neither P310 or L151 were tested by v4. P312 was tested by v2 but not by v3 or v4.

You can check the YFull tree (https://www.yfull.com/tree/R-L51/) or the ISOGG tree (https://isogg.org/tree/ISOGG_HapgrpR.html) for phylogenetic equivalents and synonyms. The forward slash / separates synonyms. You can check the Ybrowse csv file (http://ybrowse.org/gbrowse2/gff/snps_hg19.csv) for the position of each SNP and it's mutation, and the 23andme mutation mapper (https://www.23andme.com/you/labs/haplogroup_tree_mut_mapper/results/?lineage_type=paternal&haplogroup=R1b1b2a1a) for the RSID , shorthand name, mutation, and 2009 longhand name. Another reference is the ISOGG SNP Index (https://isogg.org/tree/ISOGG_YDNA_SNP_Index.html)