Difference between revisions of "Mapping SNPs GLA"

From Bioinformatikpedia
(HGMD)
(Databases)
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=Databases=
 
=Databases=
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Two databases have been used to do research about SNPs in our protein: [http://www.hgmd.org/ HGMD] and [http://www.ncbi.nlm.nih.gov/projects/SNP/ DbSNP].
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==HGMD==
 
==HGMD==
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Human Gene Mutation Database (HGMD) is a database maintained by the Institute of Medical Genetics in Cardiff. <!--[http://www.hgmd.cf.ac.uk/docs/new_back.html]-->
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The table below shows the different types of mutations that are listed in HGMD:
 
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! Describtion
 
! Describtion
 
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|Missense/nonsense ||344 ||
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|Missense/nonsense ||344 ||different amino acid/stop codon
 
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|Splicing ||26 ||
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|Splicing ||26 ||different splice site
 
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|Regulatory ||1 ||
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|Regulatory ||1 ||substitutions cause regulatory abnormalities
 
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|Small deletions ||69 ||
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|Small deletions ||69 ||micro-deletions (20 bp or less)
 
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|Small insertions ||28 ||
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|Small insertions ||28 ||micro-insertions (20 bp or less)
 
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|Small indels ||8 ||
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|Small indels ||8 ||micro-indels (20 bp or less)
 
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|Gross deletions ||14 ||
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|Gross deletions ||14 ||deletions in regions of data with variable quality
 
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|Gross insertions/duplications ||1 ||
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|Gross insertions/duplications ||1 ||insertions/duplications in regions of data with variable quality
 
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|Complex rearrangements ||3 ||
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|Complex rearrangements ||3 ||sequence is not continuous
 
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|Repeat variations ||0||
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|Repeat variations ||0|| variations of the sequence are repeated
 
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missense/nonsense: codon codes for a different amino acid/premature stop codon
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splicing: a mutation that causes splicing
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regulatory: mutation affecting the regulation of gene expression
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small/gross deletions: mutation that deletes residues
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small/gross insertions: mutation that inserts residues
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small indels: insertion or deletion (maybe not recognizable)
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duplications: duplicated sequence pieces
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complex rearrangements: part of the sequence is placed somewhere else
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repeat variations: repeated varied parts of the sequence are placed somewhere else
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!Position
 
!Position

Revision as of 00:03, 21 June 2011

by Benjamin Drexler and Fabian Grandke

Introduction

Databases

Two databases have been used to do research about SNPs in our protein: HGMD and DbSNP.

HGMD

Human Gene Mutation Database (HGMD) is a database maintained by the Institute of Medical Genetics in Cardiff.

The table below shows the different types of mutations that are listed in HGMD:

Mutation Type Number of Mutations Describtion
Missense/nonsense 344 different amino acid/stop codon
Splicing 26 different splice site
Regulatory 1 substitutions cause regulatory abnormalities
Small deletions 69 micro-deletions (20 bp or less)
Small insertions 28 micro-insertions (20 bp or less)
Small indels 8 micro-indels (20 bp or less)
Gross deletions 14 deletions in regions of data with variable quality
Gross insertions/duplications 1 insertions/duplications in regions of data with variable quality
Complex rearrangements 3 sequence is not continuous
Repeat variations 0 variations of the sequence are repeated
   missense/nonsense: codon codes for a different amino acid/premature stop codon
   splicing: a mutation that causes splicing
   regulatory: mutation affecting the regulation of gene expression
   small/gross deletions: mutation that deletes residues
   small/gross insertions: mutation that inserts residues
   small indels: insertion or deletion (maybe not recognizable)
   duplications: duplicated sequence pieces
   complex rearrangements: part of the sequence is placed somewhere else
   repeat variations: repeated varied parts of the sequence are placed somewhere else 



Position Amino Acids Codons
1 Met->Thr ATG-ACG
1 Met->Arg ATG-AGG
1 Met->Ile ATGc-ATA
14 Leu->Pro CTT-CCT
16 Leu->Pro CTT-CCT
18 Phe->Ser TTC-TCC
19 Leu->Pro CTG-CCG
20 Ala->Pro gGCC-CCC
31 Ala->Val GCA-GTA
32 Leu->Pro CTG-CCG
34 Asn->Ser AAT-AGT
34 Asn->Lys AATg-AAG
35 Gly->Arg tGGA-AGA
40 Pro->Leu CCT-CTT
40 Pro->Ser gCCT-TCT
41 Thr->Ile ACC-ATC
42 Met->Thr ATG-ACG
42 Met->Leu cATG-CTG
42 Met->Val cATG-GTG
43 Gly->Asp GGC-GAC
43 Gly->Val GGC-GTC
43 Gly->Arg gGGC-CGC
44 Trp->Ter TGG-TAG
46 His->Arg CAC-CGC
46 His->Tyr gCAC-TAC
47 Trp->Gly cTGG-GGG
47 Trp->Leu TGG-TTG
48 Glu->Lys gGAG-AAG
49 Arg->Pro CGC-CCC
49 Arg->Leu CGC-CTC
49 Arg->Ser gCGC-AGC
49 Arg->Gly gCGC-GGC
50 Phe->Cys TTC-TGC
51 Met->Lys ATG-AAG
51 Met->Ile ATGt-ATA
52 Cys->Arg gTGC-CGC
52 Cys->Ser TGC-TCC
52 Cys->Ter TGCa-TGA
54 Leu->Pro CTT-CCT
56 Cys->Gly cTGC-GGC
56 Cys->Tyr TGC-TAC
56 Cys->Phe TGC-TTC
56 Cys->Ter TGCc-TGA
59 Glu->Lys aGAG-AAG
63 Cys->Tyr TGC-TAC
66 Glu->Gly GAG-GGG
66 Glu->Lys tGAG-AAG
66 Glu->Gln tGAG-CAG
68 Leu->Phe gCTC-TTC
72 Met->Arg ATG-AGG
72 Met->Ile ATGg-ATA
72 Met->Val gATG-GTG
73 Ala->Val GCA-GTA
76 Met->Thr ATG-ACG
78 Ser->Ter TCA-TGA
79 Glu->Ter aGAA-TAA
81 Trp->Ter TGG-TAG
81 Trp->Ser TGG-TCG
85 Gly->Asp GGT-GAT
86 Tyr->Cys TAT-TGT
86 Tyr->Ter TATg-TAG
88 Tyr->Asp gTAC-GAC
89 Leu->Pro CTC-CCC
89 Leu->Arg CTC-CGC
91 Ile->Thr ATT-ACT
92 Asp->Asn tGAT-AAT
92 Asp->His tGAT-CAT
92 Asp->Tyr tGAT-TAT
93 Asp->Gly GAC-GGC
93 Asp->Val GAC-GTC
93 Asp->Asn tGAC-AAC
94 Cys->Tyr TGT-TAT
94 Cys->Ser TGT-TCT
95 Trp->Ter TGG-TAG
95 Trp->Ser TGG-TCG
97 Ala->Val GCT-GTT
97 Ala->Pro gGCT-CCT
99 Gln->Ter cCAA-TAA
100 Arg->Lys AGA-AAA
100 Arg->Thr AGA-ACA
102 Ser->Ter TCA-TGA
103 Glu->Gln aGAA-CAA
106 Leu->Arg CTT-CGT
107 Gln->Ter tCAG-TAG
112 Arg->His CGC-CAC
112 Arg->Ser gCGC-AGC
112 Arg->Cys gCGC-TGC
113 Phe->Leu cTTT-CTT
113 Phe->Ser TTT-TCT
118 Arg->Cys tCGC-TGC
119 Gln->Ter cCAG-TAG
121 Ala->Pro aGCT-CCT
125 His->Pro CAC-CCC
126 Ser->Gly cAGC-GGC
127 Lys->Ter cAAA-TAA
128 Gly->Glu GGA-GAA
129 Leu->Pro CTG-CCG
131 Leu->Pro CTA-CCA
132 Gly->Arg aGGG-AGG
134 Tyr->Ser TAT-TCT
134 Tyr->Ter TATg-TAG
135 Ala->Val GCA-GTA
136 Asp->His aGAT-CAT
138 Gly->Glu GGA-GAA
138 Gly->Arg tGGA-AGA
141 Thr->Ile ACC-ATC
142 Cys->Arg cTGC-CGC
142 Cys->Tyr TGC-TAC
142 Cys->Ter TGCg-TGA
142 Cys->Trp TGCg-TGG
143 Ala->Thr cGCA-ACA
143 Ala->Pro cGCA-CCA
144 Gly->Val GGC-GTC
146 Pro->Ser cCCT-TCT
147 Gly->Arg tGGG-AGG
148 Ser->Asn AGT-AAT
148 Ser->Arg AGTt-AGG
151 Tyr->Ter TACt-TAG
152 Tyr->Ter TACg-TAA
155 Asp->His tGAT-CAT
156 Ala->Val GCC-GTC
156 Ala->Thr tGCC-ACC
157 Gln->Ter cCAG-TAG
162 Trp->Arg cTGG-CGG
162 Trp->Ter TGG-TAG
162 Trp->Cys TGGg-TGC
163 Gly->Val GGA-GTA
165 Asp->His aGAT-CAT
165 Asp->Val GAT-GTT
166 Leu->Val tCTG-GTG
167 Leu->Pro CTA-CCA
168 Lys->Arg AAA-AGA
169 Phe->Ser TTT-TCT
170 Asp->Val GAT-GTT
170 Asp->His tGAT-CAT
171 Gly->Asp GGT-GAT
171 Gly->Arg tGGT-CGT
172 Cys->Tyr TGT-TAT
172 Cys->Phe TGT-TTT
172 Cys->Trp TGTt-TGG
172 Cys->Arg tTGT-CGT
172 Cys->Gly tTGT-GGT
173 Tyr->Ter TACt-TAA
177 Leu->Ter TTG-TAG
183 Gly->Asp GGT-GAT
183 Gly->Ser tGGT-AGT
187 Met->Thr ATG-ACG
187 Met->Val cATG-GTG
191 Leu->Gln CTG-CAG
191 Leu->Pro CTG-CCG
194 Thr->Ile ACT-ATT
199 Val->Met tGTG-ATG
201 Ser->Tyr TCC-TAC
201 Ser->Phe TCC-TTC
202 Cys->Tyr TGT-TAT
202 Cys->Trp TGTg-TGG
204 Trp->Ter TGG-TAG
205 Pro->Arg CCT-CGT
205 Pro->Leu CCT-CTT
205 Pro->Thr gCCT-ACT
207 Tyr->Ser TAT-TCT
215 Asn->Ser AAT-AGT
216 Tyr->Asp tTAT-GAT
220 Arg->Ter cCGA-TGA
221 Gln->Ter aCAG-TAG
222 Tyr->Ter TACt-TAA
223 Cys->Arg cTGC-CGC
223 Cys->Gly cTGC-GGC
223 Cys->Tyr TGC-TAC
224 Asn->Ser AAT-AGT
224 Asn->Asp cAAT-GAT
225 His->Arg CAC-CGC
226 Trp->Arg cTGG-CGG
226 Trp->Ter TGG-TAG
226 Trp->Cys TGGc-TGT
227 Arg->Gln CGA-CAA
227 Arg->Ter gCGA-TGA
230 Ala->Thr tGCT-ACT
231 Asp->Val GAC-GTC
231 Asp->Asn tGAC-AAC
234 Asp->Glu GATt-GAG
234 Asp->Tyr tGAT-TAT
235 Ser->Cys TCC-TGC
235 Ser->Phe TCC-TTC
236 Trp->Arg cTGG-CGG
236 Trp->Ter TGG-TAG
236 Trp->Leu TGG-TTG
236 Trp->Cys TGGa-TGC
239 Ile->Thr ATA-ACA
242 Ile->Asn ATC-AAC
243 Leu->Phe TTGg-TTC
244 Asp->Asn gGAC-AAC
244 Asp->His gGAC-CAC
245 Trp->Ter TGG-TAG
247 Ser->Pro aTCT-CCT
247 Ser->Cys TCT-TGT
250 Gln->Ter cCAG-TAG
251 Glu->Ter gGAG-TAG
257 Ala->Pro tGCT-CCT
258 Gly->Val GGA-GTA
258 Gly->Arg tGGA-CGA
259 Pro->Arg CCA-CGA
259 Pro->Leu CCA-CTA
260 Gly->Ala GGG-GCG
261 Gly->Asp GGT-GAT
262 Trp->Ter TGG-TAG
262 Trp->Cys TGGa-TGC
263 Asn->Ser AAT-AGT
264 Asp->Val GAC-GTC
264 Asp->Tyr tGAC-TAC
265 Pro->Arg CCA-CGA
265 Pro->Leu CCA-CTA
266 Asp->Asn aGAT-AAT
266 Asp->His aGAT-CAT
266 Asp->Val GAT-GTT
266 Asp->Glu GATa-GAA
267 Met->Arg ATG-AGG
267 Met->Ile ATGg-ATA
268 Leu->Ser TTA-TCA
269 Val->Met aGTG-ATG
269 Val->Ala GTG-GCG
270 Ile->Thr ATT-ACT
271 Gly->Val GGC-GTC
271 Gly->Ser tGGC-AGC
271 Gly->Cys tGGC-TGC
272 Asn->Lys AACt-AAA
276 Ser->Asn AGC-AAC
276 Ser->Gly cAGC-GGC
277 Trp->Ter TGG-TAG
279 Gln->Arg CAG-CGG
279 Gln->His CAGc-CAC
279 Gln->Glu tCAG-GAG
280 Gln->His CAAg-CAT
280 Gln->Lys gCAA-AAA
282 Thr->Ala aACT-GCT
282 Thr->Asn ACT-AAT
283 Gln->Pro CAG-CCG
284 Met->Thr ATG-ACG
285 Ala->Asp GCC-GAC
285 Ala->Pro gGCC-CCC
287 Trp->Gly cTGG-GGG
287 Trp->Ter TGGg-TGA
287 Trp->Cys TGGg-TGT
288 Ala->Asp GCT-GAT
288 Ala->Pro gGCT-CCT
289 Ile->Ser ATC-AGC
289 Ile->Phe tATC-TTC
290 Met->Ile ATGg-ATA
292 Ala->Thr tGCT-ACT
293 Pro->Thr tCCT-ACT
293 Pro->Ala tCCT-GCT
293 Pro->Ser tCCT-TCT
294 Leu->Ter TTA-TGA
296 Met->Ile ATGt-ATA
296 Met->Val cATG-GTG
297 Ser->Cys TCT-TGT
297 Ser->Phe TCT-TTT
298 Asn->Ser AAT-AGT
298 Asn->Lys AATg-AAG
298 Asn->His tAAT-CAT
300 Leu->Phe cCTC-TTC
300 Leu->His CTC-CAC
301 Arg->Gly cCGA-GGA
301 Arg->Ter cCGA-TGA
301 Arg->Gln CGA-CAA
301 Arg->Pro CGA-CCA
303 Ile->Asn ATC-AAC
306 Gln->Ter tCAA-TAA
308 Lys->Asn AAAg-AAT
310 Leu->Phe tCTC-TTC
312 Gln->Arg CAG-CGG
312 Gln->His CAGg-CAT
313 Asp->Tyr gGAT-TAT
316 Val->Glu GTA-GAA
317 Ile->Asn ATT-AAT
317 Ile->Thr ATT-ACT
320 Asn->Ile AAT-ATT
320 Asn->Lys AATc-AAG
320 Asn->Tyr cAAT-TAT
321 Gln->Arg CAG-CGG
321 Gln->Leu CAG-CTG
321 Gln->Glu tCAG-GAG
321 Gln->Ter tCAG-TAG
325 Gly->Asp GGC-GAC
327 Gln->Lys gCAA-AAA
327 Gln->Glu gCAA-GAA
328 Gly->Arg aGGG-AGG
328 Gly->Ala GGG-GCG
328 Gly->Val GGG-GTG
330 Gln->Ter cCAG-TAG
333 Gln->Ter aCAG-TAG
338 Glu->Lys tGAA-AAA
338 Glu->Ter tGAA-TAA
340 Trp->Arg gTGG-CGG
340 Trp->Ter TGGg-TGA
341 Glu->Asp GAAc-GAC
341 Glu->Lys gGAA-AAA
342 Arg->Ter aCGA-TGA
342 Arg->Gln CGA-CAA
344 Leu->Pro CTC-CCC
345 Ser->Pro cTCA-CCA
348 Ala->Pro aGCC-CCC
349 Trp->Ter TGG-TAG
350 Ala->Pro gGCT-CCT
352 Ala->Asp GCT-GAT
355 Asn->Lys AACc-AAA
356 Arg->Trp cCGG-TGG
357 Gln->Ter gCAG-TAG
358 Glu->Ala GAG-GCG
358 Glu->Gly GAG-GGG
358 Glu->Lys gGAG-AAG
360 Gly->Ser tGGT-AGT
360 Gly->Cys tGGT-TGT
361 Gly->Arg tGGA-AGA
362 Pro->Leu CCT-CTT
363 Arg->His CGC-CAC
363 Arg->Cys tCGC-TGC
365 Tyr->Ter TATa-TAA
373 Gly->Ser gGGT-AGT
373 Gly->Asp GGT-GAT
377 Ala->Asp GCC-GAC
378 Cys->Arg cTGT-CGT
378 Cys->Tyr TGT-TAT
382 Cys->Tyr TGC-TAC
382 Cys->Trp TGCt-TGG
384 Ile->Asn ATC-AAC
385 Thr->Pro cACA-CCA
386 Gln->Ter aCAG-TAG
386 Gln->Pro CAG-CCG
398 Glu->Lys tGAA-AAA
398 Glu->Ter tGAA-TAA
399 Trp->Ter TGG-TAG
401 Ser->Ter TCA-TGA
403 Leu->Ser TTA-TCA
407 Ile->Lys ATA-AAA
409 Pro->Thr tCCC-ACC
409 Pro->Ala tCCC-GCC
409 Pro->Ser tCCC-TCC
410 Thr->Lys ACA-AAA
410 Thr->Pro cACA-CCA
410 Thr->Ala cACA-GCA
411 Gly->Asp GGC-GAC
414 Leu->Ser TTG-TCG
415 Leu->Pro CTT-CCT

dbSNP

Identifier AA-Position Triplet Allele Residue
rs77934640 143 GCA -> GCG A -> G A -> A
rs74795363 112 CGC -> CGT C -> T R -> R
rs117579981 92 GAT -> GAC A -> C T -> T
rs78630710 119 CAG -> CAA G -> A V -> V
rs77056043 157 CAG -> CAC G -> C L -> L
rs72635973 130 AAG -> AAA C -> A P -> P
rs1062874 227 CGA -> CGA G -> A L -> L
rs1062869 217 ACA -> ACT C -> T Y -> Y

Mutation Map

References

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