Task 7: Research SNPs

Lab journal Task 7

<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; width: 60%; }

.colBasic2 th,td { padding: 3px; border: 1px solid black; }

.colBasic2 td { text-align:left; }

/* for orange try #ff7f00 and #ffaa56 for blue try #005fbf and #aad4ff

maria's style blue: #adceff grey: #efefef

• /

.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;}

[edit] </css>

HGMD (The Human Gene Mutation Database)

The results for the HFE gene contain the following types of mutations:

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

• total in public 40
• non public 49

missense, nonsens mutations for HFE

accession number	codon change	aa change	codon 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
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

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)			99869
dbSNP	26.06.2012	Build 137			192,678,553	10	41	10	162	213
SNPdbe	05.03.2012	-			967879