Researching And Mapping Point Mutations Hemochromatosis

Hemochromatosis>>Task 5: Researching and mapping point mutations

Riddle of the task

Previously on "The Tale of Sir Binfo": Link

After careful thinking you finally decide which Symbol to push and then... nothing...
Did you push the wrong button? What if you're trapped forever? ...But suddendly you hear a loud noise. The sound of stone grinding on stone. A trapdoor opens in the floor and reveals a dusty stairway into the darkness below. As you enter it, magical torches on the walls of a long corridor spring to life and lighten your way. The cobwebs and stale air tell you that this way has been unused for a long time.
After a few minutes the hallway suddenly ends and you stand before a giant door. At least that's what you think it is as you can't find a doorknob or anything else to open it. The only thing you see is a strange circle of runes and a text beside it:

Here we stand. Undefeated, undivided.
We guard this door until united.
Though only one can break us all, for he is King.
It seems like you could move the two outer rings of runes (separately). Maybe some kind of combination lock?

Short task description

Detailed description: Researching and mapping point mutations

In this task we've searched several SNP databases to find SNPs for HFE. These SNPs will then be used in the next assignment.

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

HGMD

The public version of HGMD contains 88745 mutations total (cf. their statistics). Most (50129) of these are missense/nonsense mutations. In contrast to the professional version of HGMD, the public one gets updated with a great delay (2176 additions in the last three years, compared to 34236). The most recent reference for HFE is from 2008, the second most is from 2004. All of HFE's missense/nonsense mutations are supposed to be involved with hemochromatosis or possible side effects thereof (Altered iron status, Diabetes).

SNP statistics for HFE in HGMD (non-professional):

• Missense/nonsense: 24
• Splicing: 3
• Regulatory: 1
• Small deletions: 4
• Small insertions: 1
• Small indels: 0
• Gross deletions: 2
• Gross insertions/duplications: 0
• Complex rearrangements: 1
• Repeat variations: 0
• Total: 36

The alignment between the sequence (NM_000410.3) used by HGMD and the uniprot sequence for Q30201 had 100% identity. Thus the SNP positions don't have to be adjusted.

The missense/nonsense SNPs can be found here.

dbSNP

We searched for silent mutations in the dbSNP and retrieved 9 entries. The search was done using this search options. . We also searched for missense and nonsense mutations, retrieving 34 missense mutations (1 redundant) and 2 nonsense mutations. Tables for the mutations can be found here.

SNPdbe

We've searched SNPdbe with NP_000401 and Q30201 for SNPs in the human genome which listed 35 and 26 results respectively. Some of these hits overlapped though. This resulted in 46 unique SNPs. Both query sequences have an identity of 100% with each other which means that the annotated positions can be used unaltered.
A further search with "HFE" as query yielded another 193 SNPs. This time sequences different from Q30201 were used for the positions. Thus we created a MSA with the T-Coffee Server and adjusted the positions accordingly. This resulted in a final number of 51 unique SNPs for our SNPdbe search.

The SNPs can be found here. For a SNP to be "disease causing" the wild type must have had a conservation of over 40 or hemochromatosis must have been listed as a disease.

OMIM

OMIM lists the following allelic variants for HFE:

• VAL-53-MET
• VAL-59-MET
• HIS-63-ASP
• SER-65-CYS
• GLY-93-ARG
• ILE-105-THR
• GLN-127-HIS
• CYS-282-TYR
• GLN-283-PRO
• ARG-330-MET
• 5569G-A

All of the amino acid mutations have been listed before. The only new information is the single nucleotide polymorphism (5569G-A) in the 4th intron of HFE.

SNPedia

SNPedia lists 14 SNPs for HFE. Two of them are redundant as they have been merged into one entry. All amino acid mutations have already been listed in the dbSNP table. The only exception is Rs9366637 which can't be mapped onto the protein sequence as it is located within the first intron.

Database comparison

<figure id="overlap">

Figure 1: Overlap between the SNPs annotated by HGMD, SNPdbe, and dbSNP.

</figure>

The Venn diagram in <xr id="overlap"/> shows that only 15 out of all 66 SNPs are common to HGMD, SNPdbe, and dbSNP. SNPdbe has the most database unique SNPs (15) while missing only 15 SNPs total. dbSNP contributes the second most SNPs (43, with 9 unique to dbSNP). The two most significant mutations for hemochromatosis (Cys-282-Tyr and His-63-Asp) are shared among all databases.

SNPs contained in all databases:

• Arg-6-Ser
• Val-53-Met
• Val-59-Met
• His-63-Asp
• Ser-65-Cys
• Gly-93-Arg
• Ile-105-Thr
• Gln-127-His
• Glu-168-Gln
• Arg-224-Gln
• Glu-277-Lys
• Cys-282-Tyr
• Gln-283-Pro
• Val-295-Ala
• Arg-330-Met

Mapping