Task 7: Research SNPs

Lab journal Task 7

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HGMD (The Human Gene Mutation Database)

The search results for the HFE gene contain the different types of mutations that are specified in <xr id="hgmd"/>:

<figtable id="hgmd">

Table 1: Table of the different mutation types that were found for HFE in the HGMD.

mutation type	definition	number
missense, nonsense	mutation that leads to a change of amino acid or a stop codon	28
splicing	mutation that affects mRNA splicing	3
regulatory	substitiution causing abnormal regulation	1
small deletion	micro deletion (<= 20 bp)	4
small insertion	micro insertions (<= 20 bp)	1
small indel	micro indels (<= 20 bp)	0
gross deletion	delition > 20 bp	2
gross insertions/duplications	insertion > 20bp	0
complex rearrangments	rearrangements of stretches of the DNA sequence	1
repeat variations	differences in repeat length	0

</figtable>

In total, we found 40 mutation in the public version of the database and 49 in the non-public version.

<figtable id="hgmd missense">

Table 2: 28 missense and nonsense mutations for HFE from the HGMD.

accession number	codon change	aa change	codon number
CM032270	AGGc-AGC	Arg-Ser	6
CM091838	TTG-TGG	Leu-Trp	46
CM994469	cGTG-ATG	Val-Met	53
CM994470	cGTG-ATG	Val-Met	59
HM971246	CATg-CAC	His-His	63
CM960827	tCAT-GAT	His-Asp	63
CM990718	gAGT-TGT	Ser-Cys	65
CM033969	tCGC-TGC	Arg-Cys	66
CM020721	cCGA-TGA	Arg-Term	71
CM990719	aGGG-CGG	Gly-Arg	93== HGMD == dbSNP We wanted to look for silent (synonymous) mutations in dbSNP. A silent mutation does not lead to a change in the amino acid sequence of the protein. There are several different isoforms for the HFE protein. We decided to look at isoform 1 precursor (http://www.ncbi.nlm.nih.gov/protein/NP_000401.1) because there is the most data for this isoform. transcript variant 1 (NM_000410.3). The dbSNP webserver was search for SNP and the following query: "synonymous-codon"[Function_Class] AND HFE[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS]. All different types of SNPs in the HFE gene can be listed in the geneView. This table was used to extract the number of different SNPs in the HFE gene. SNPdbe Mutation map
CM990720	ATT-ACT	Ile-Thr	105
CM990721	CAAg-CAC	Gln-His	127
CM091839	aGAC-AAC	Asp-Asn	129
CM091840	TACg-TAG	Tyr-Term	138
CM004810	gGAG-CAG	Glu-Gln	168
CM004106	gGAG-TAG	Glu-Term	168
CM004107	TGG-TAG	Trp-Term	169
CM015326	GCC-GTC	Ala-Val	176
CM081301	CTG-CCG	Leu-Pro	183
CM034097	CGG-CAG	Arg-Gln	224
CM101181	cCAG-TAG	Gln-Term	233
CM024530	tGTA-TTA	Val-Leu	272
CM994771	aGAG-AAG	Glu-Lys	277
CM960828	TGC-TAC	Cys-Tyr	282
CM004391	TGC-TCC	Cys-Ser	282
CM032271	CAG-CCG	Gln-Pro	283
HM030028	GTG-GCG	Val-Ala	295
CM990722	AGG-ATG	Arg-Met	330

</figtable>

The 28 missense and nonsense mutations for HFE are listed in <xr id="hgmd missense"/> together with the amino acid (aa) change and the codon number.

dbSNP

Results

synonymous SNPS in coding region of isoform 1 human and transcript variant 1

cluster ID	MAF	SNP allel	residue	codon position	aa position
rs114758821	9E-4	G -> A	Pro	3	7
rs147297176	5E-4	C -> T	Phe	3	58
rs147426902	3.2E-3	T -> C	His	3	63
rs62625342	5E-4	C -> T	Ser	3	76
rs148480830	-	C -> G	Ala	3	162
rs182920795	5E-4	T -> A	Pro	3	253
rs201310322	-	C -> T	Pro	3	292
rs114038675	5E-4	G -> A	Glu	3	298
rs148632352	-	T -> C	Val	3	315
rs35201683	6.4E-3	C -> T	Tyr	3	342

Comparison of databases

database	last update	version	what information	where from	# entries homo sapiens	# s SNPs	# ns SNPs	# disease causing SNPs	# SNPs in UTR	total
HGMD	spring 2013	public 2013.1 (mainly 3 year old data)	Collection of published gene lesions in the human genome that cause inherited diseases.	Only from publications. Journals are searched manually and by computational means each week.	99869
dbSNP	26.06.2012	Build 137	Short nucleotide sequence variations in different organisms (common and rare)	Submissions from laboratories but also private research companies.	192,678,553	10	41	10	162	213
SNPdbe	05.03.2012	-	Annotations for single amino acid substitutions (SAASs), e.g. functional effect (experimental, predicted), associated disease, evol. conservation,...	Based on entries from SwissProt, dbSNP, 1000 Genomes, PMD	967879

References

Stenson et al (2009), The Human Gene Mutation Database (HGMD®): 2008 Update. Genome Med 1(1):13
http://www.ncbi.nlm.nih.gov/books/NBK3848/
ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_SNP.pdf
https://www.rostlab.org/services/snpdbe/