Lab journal Task 7

HGMD

The HFE accession number in HGMD is NM_000410.3 (transcript variant 1 http://www.ncbi.nlm.nih.gov/nuccore/NM_000410.3). the nucleotide sequence was downloaded in fasta format and then translated to the protein sequence with http://molbiol.ru/eng/scripts/01_13.html using the first reading frame.

dbSNP

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 and also because this isoform is used in HGMD. The corresponding mRNA sequence for this protein is the transcript variant 1 (http://www.ncbi.nlm.nih.gov/nuccore/NM_000410.3).

The dbSNP webserver was search for "SNP" and the following query was used: "synonymous-codon"[Function_Class] AND HFE[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS]. We used the graphic summary display of the results. Under the sequence line of each hit are several links, among others a link to the "Gene view". All different types of SNPs in the HFE gene can be listed in the geneView. This table was used to used to extract all mutations for the protein NP_000401 and especially the synonymous ones. and to extract the numbers of the different SNPs in the HFE gene.

SNPdbe

SNPdbe was searched for the protein "NP_000401". The results were downloaded as textfile and analysed with R.

OMIM

Omim was searched for "HFE". The first result links to the page of " * 613609. HFE GENE; HFE". It contains a section "Allelic variants" containing several publicated mutations that can also be viewed as a table (http://omim.org/allelicVariant/613609). We only included results for the protein sequence of "NP_000401" that was also used for SNPdbe.

Mutation map

The reference sequence for the HFE protein in all four databases is the same, because we only collected mutations from one mRNA transcript. Therefore, we did not have to map the codon numbers of different databases. The two domains were selected using the SCOP annotation: MHC antigen-recognition domain (4-181) and Immunglobulin domain (182-275). Since the reference sequence contains 22 residues before the start of the pdb structure sequence (1A6Z,A), 22 was added to positions of the domains to get the corresponding indices for the reference sequence.

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<figtable id="hgmd">

Table 1: Summary of all 71 found mutations.

accession	codon position	aa change	disease association	mutation type
rs149342416, CM032270	6	Arg -> Ser	hemochromatosis	missense
rs114758821	7	Pro -> Pro	N/A	synonymous
rs368895240	10	Leu -> Leu	N/A	synonymous
rs201657128	14	Leu -> Val	N/A	missense
rs143662783	17	Thr -> Ile	N/A	missense
rs148161858	23	Arg -> His	N/A	missense
rs2242956	35	Met -> Thr	N/A	missense
rs377254261	37	Ala -> Val	N/A	missense
CM091838	46	Leu -> Trp	hemochromatosis	missense
rs28934889, CM994469	53	Val -> Met	hemochromatosis	missense
rs147297176	58	Phe -> Phe	N/A	synonymous
rs28934890, rs111033557, CM994470	59	Val -> Met	hemochromatosis	missense
rs1799945, CM960827	63	His -> Asp	In hereditary haemochromatosis (HH) (PMD)	missense
rs147426902, HM971246,	63	His -> His	N/A	synonymous
rs1800730, CM990718	65	Ser -> Cys	hemochromatosis	missense
CM033969	66	Arg -> Cys	hemochromatosis	missense
rs139523708	67	Arg -> His	N/A	missense
CM020721	71	Arg -> Term	hemochromatosis	nonsense
rs62625342	76	Ser -> Ser	N/A	synonymous
rs28934597, CM990719	93	Gly -> Arg	hemochromatosis (SwissVar). In hemochromatosis (PMD)	missense
rs376650371	97	Met -> Ile	N/A	missense
rs28934596, CM990720	105	Ile -> Thr	hemochromatosis (SwissVar). In hemochromatosis (PMD)	missense
rs199988202	106	Met -> Thr	N/A	missense
rs28934595, CM990721	127	Gln -> His	hemochromatosis (SwissVar). In variegate porphyria (VP) (PMD)	missense
rs200706856, CM091839	129	Asp -> Asn	hemochromatosis	missense
rs201885016	130	Asn -> Ser	N/A	missense
rs369790080	132	Thr -> Thr	N/A	synonymous
CM091840	138	Tyr -> Term	hemochromatosis	nonsense
rs372789940	141	Asp -> Asn	N/A	missense
rs199879669	157	Ala -> Pro	N/A	missense
rs149662565	160	Pro -> Thr	N/A	missense
rs145475682	162	Ala -> Ser	N/A	missense
rs148480830	162	Ala -> Ala	N/A	synonymous
rs144170531	166	Lys -> Glu	N/A	missense
rs146519482, CM004810	168	Glu - > Gln	hemochromatosis	missense
CM004106	168	Glu -> Term	hemochromatosis	nonsense
CM004107	169	Trp -> Term	hemochromatosis	nonsense
CM015326	176	Ala -> Val	hemochromatosis	missense
rs199916850, CM081301	183	Leu -> Pro	hemochromatosis	missense
rs140957442	192	Gln -> Term	N/A	nonsense
rs4986950	217	Thr -> Ile	N/A	missense
rs144797937	224	Arg -> Trp	N/A	missense
rs62625346, CM034097	224	Arg -> Gln	hemochromatosis	missense
CM101181	233	Gln -> Term	hemochromatosis	nonsense
rs140515012	245	Pro -> Ala	N/A	missense
rs150402693	251	Phe -> Leu	N/A	missense
rs138176635	252	E -> G	N/A	missense
rs182920795	253	Pro -> Pro	N/A	synonymous
rs202068193	256	Val -> Ile	N/A	missense
rs143846467	259	Asn -> Ser	N/A	missense
CM024530	272	Val -> Leu	hemochromatosis	missense
rs140080192, CM994771	277	Glu -> Lys	hemochromatosis	missense
rs369354634	281	Thr -> Thr	N/A	synonymous
rs1800562, CM960828	282	Cys -> Tyr	hemochromatosis	missense
CM004391	282	Cys -> Ser	hemochromatosis	missense
rs111033563, CM032271	283	Gln-Pro	hemochromatosis (SwissVar)	missense
rs201310322	292	Pro -> Pro	N/A	synonymous
rs143175221, HM030028	295	Val -> Ala	hemochromatosis (SwissVar)	missense
rs114038675	298	Glu -> Glu	N/A	synonymous
rs372856303	301	Pro -> Pro	N/A	synonymous
rs147519426	315	Val -> Gly	N/A	missense
rs148632352	315	Val -> Val	N/A	synonymous
rs371192232	317	Val -> Val	N/A	synonymous
rs141229562	318	Val -> Ile	N/A	missense
rs150716212	322	Ile -> Thr	N/A	missense
rs138993448	327	Ile -> Thr	N/A	missense
rs111033558, CM990722	330	Arg -> Met	hemochromatosis (SwissVar). In hereditary haemochromatosis (HH) (PMD)	missense
rs368122334	340	Gly -> Ala	N/A	missense
rs35201683	342	Tyr -> Tyr	N/A	synonymous
rs370285936	343	Val -> Asp	N/A	missense
rs146508927	347	Arg -> His	N/A	missense

</figtable>

The gene view was created with the following R script

<source lang="rsplus"> data <- read.table("/home/kathi/Dokumente/SS13/masterPractical/task7/task7_table_all_filtered.txt", header=TRUE, sep="\t")

xmax = 348

n <- data[data$association!=" N/A",] d <- data[data$association==" N/A",]

1. MHC antigen-recognition domain: 4-181
2. immunglobulin: 182-275
3. pdb structure is shorter: +22
4. -> 22+4 - 22+181
5. --> 22+182 - 22+275

png("/home/kathi/Dokumente/SS13/masterPractical/task7/mutation_map.png", width=2000, height=500 )

oldpar <- par()

par( mfrow=c(3,1), mar=c(0.1, 12.1, 0.1, 0.1), oma=c(10, 0.1, 7, 0.1), mgp=c(0,2,0) )

plot(-1,-1, xlim =c(0,xmax) , ylim=c(0,1), axes = FALSE, xlab=NA, ylab=NA) segments(x0=n$codon.pos, y0=rep(0, length(n$codon.pos)), x1=n$codon.pos, y1=rep(1, length(n$codon.pos)), col="darkblue", lwd=2) mtext("non dc\nmutations", side=2, line=-0.5 , cex=2.1, las=1)

plot(-1,-1, xlim =c(0,xmax) , ylim=c(0,1), axes = FALSE, , xlab=NA, ylab = NA) segments(x0=d$codon.pos, y0=rep(0, length(d$codon.pos)), x1=d$codon.pos,y1=rep(1, length(d$codon.pos)), col="firebrick2", lwd=2) mtext("dc\nmutations", side=2, line=-0.2 , cex=2.1, las=1)

plot(-1,-1, xlim =c(0,xmax) , ylim=c(0,1), axes = FALSE, xlab = NA, ylab = NA, cex=1.5) axis(1, at=seq(0, xmax, 20), line=0.7, lwd=3, lwd.ticks=3, cex.axis=3 ) rect(0,0,xmax,1, col="lavender") rect(22+4,0,22+181,1, col="palegreen3") rect(22+182,0,22+275,1, col="steelblue3") text(22+4+70, 0.5, "MHC antigen-recognition domain", cex=3.7, col="white") text(22+182+50, 0.5, "Immunoglobulin domain", cex=3.7, col="white") mtext("protein\ndomains", side=2, line=-0.2 , cex=2.1, las=1)

mtext("mutation map for HFE", side=3, line=2, cex=3, outer=TRUE, adj=0.5) mtext("codon position", side=1, line=6.4, cex=2.5, outer=TRUE)

par <- oldpar dev.off() </source>