Inquiry

[Laith Moushib]

Hello 

I am a PhD student working on primary immunodeficiency.  I am groping my way in molecular genetics and I have some technical questions .

We have done WGS (using hg19 genome build) on some patients and I found two interesting  variants:

1-KMT2D: chr12_49426905_TTGC_T  ; c.11580_11582delGCA ; p.Gln3863del

2-FLG: chr1-152285861_G_A;  c.1501C>T; p.Arg501*

When I search NCBI  for gene (cDNA) sequence in order to design primers, I do not see the nucleotide sequence in the DNA sequence on NCBI database for the bespoken genes ( that is, I do not see GCA in location 11580 to 11582  for KMT2D  and I do not see either  C  in location 1501 for FLG). Why i that ? is the genome build for these genes on NCBI on hg38 ? How to solve this issue? 

In addition, when I design primers should I use  cDNA  or gene sequence containing introns and exons ?

Looking forward for your guidance on this issue 

Thanks in advance 

Laith