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
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
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

dbSNP was searched to silent (synonymous) mutations of the HFE gene. Silent mutations are mutations in the nucleotide sequence that do not lead to a change in the amino acid sequence of the protein.

<figtable id="dbSNP silent">

Table 3: Synonymous SNPS in the coding regin of the isoform 1 human and the transcript variant 1 of the HFE gene.

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

</figtable>

All found synonymous SNPS in coding region of the isoform 1 human and the transcript variant 1 of the HFE gene are listed in <xr id="dbSNP silent"/>.

SNPdbe

35 mutations that are associated with the human HFE protein were found in SNPdbe.

<figtable id="exp evidence">

Table 4: Types of experimental evidence and their occurence among the 35 mutations associated with HFE.

exp. evidence	count
1000Genome,freq,cluster	6
by cluster	6
by cluster,freq	2
Not validated	13
by freq	8

</figtable>

Not all mutations have experimental evidence, over one third is not validated, see <xr id="exp evidence"/>.

<figtable id="snpdbe">

Table 4: Mutations in the HFE protein from SNPdbe.

dbSNP	Mutation	Disease association	Experimental evidence
rs1799945	H63D	In hereditary haemochromatosis (HH) (PMD)	1000Genome,freq,cluster
rs1800562	C282Y	hemochromatosis (SwissVar)	1000Genome,freq,cluster
rs1800730	S65C	hemochromatosis (SwissVar). In hereditary hemochromatosis patient who had resulted positive to screening for iron overload (PMD)	1000Genome,freq,cluster
rs2242956	M35T	N/A	by cluster
rs4986950	T217I	N/A	by cluster,freq
rs28934595	Q127H	hemochromatosis (SwissVar). In variegate porphyria (VP) (PMD)	by cluster
rs28934596	I105T	hemochromatosis (SwissVar). In hemochromatosis (PMD)	by cluster
rs28934597	G93R	hemochromatosis (SwissVar). In hemochromatosis (PMD)	by cluster
rs28934889	V53M	N/A	1000Genome,freq,cluster
rs62625346	R224Q	N/A	by cluster,freq
rs28934890	V59M	N/A	Not validated
rs111033558	R330M	hemochromatosis (SwissVar). In hereditary haemochromatosis (HH) (PMD)	by cluster
rs111033563	Q283P	hemochromatosis (SwissVar)	by cluster
rs149342416	R6S	hemochromatosis (SwissVar)	by freq
rs140080192	E277K	N/A	1000Genome,freq,cluster
rs143175221	V295A	hemochromatosis (SwissVar)	by freq
rs148161858	R23H	N/A	1000Genome,freq,cluster
N/A	M106T	N/A	Not validated
rs146519482	E168Q	N/A	Not validated
N/A	L183P	N/A	Not validated
rs138176635	E252G	N/A	Not validated
rs138993448	I327T	N/A	Not validated
rs139523708	R67H	N/A	Not validated
rs140515012	P245A	N/A	Not validated
rs141229562	V318I	N/A	Not validated
rs143662783	T17I	N/A	by freq
rs143846467	N259S	N/A	Not validated
rs144170531	K166E	N/A	by freq
rs144797937	R224W	N/A	by freq
rs145475682	A162S	N/A	by freq
rs146508927	R347H	N/A	by freq
rs147519426	V315G	N/A	by freq
rs149662565	P160T	N/A	Not validated
rs150402693	F251L	N/A	Not validated
rs150716212	I322T	N/A	Not validated

</figtable>

A list of the 35 mutations and their experimental evidence can be found in <xr id="snpdbe/>.

OMIM

OMIM (Online Mendelian Inheritance in Man) also contains information about HFE, but only a small amount of all known mutations can be found.

<figtable id="omim">

Table 5: Mutations from OMIM that are associated with the HFE protein .

dbSNP accession	Phenotype	Mutation
rs1799945	HEMOCHROMATOSIS	HIS63ASP
rs1800730	HEMOCHROMATOSIS	SER65CYS
rs28934889	HFE POLYMORPHISM	VAL53MET
rs111033557	HFE POLYMORPHISM	VAL59MET
rs28934595	HEMOCHROMATOSIS	GLN127HIS
rs111033558	HEMOCHROMATOSIS	ARG330MET
rs28934596	HEMOCHROMATOSIS	ILE105THR
rs28934597	HEMOCHROMATOSIS	GLY93ARG
rs111033563	HEMOCHROMATOSIS	GLN283PRO

</figtable>

A complete list of the mutations can be found in <xr id="omim"/>.

Databases comparison

<figtable id="comparison">

Table 6: .

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
OMIM

</figtable>

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/