Mapping SNPs GLA
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 |
The professional version provides many more mutations. The mutations in the free version are at least 2.5 years old (date of publication).
The table below shows all missense and nonsense mutations from HGMD.
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
We used DbSNP to search for silent mutations, as they are not listed in HGMD (because the do not lead to a disease). The query "synonymous-codon"[Function_Class] AND gla[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS]
only output two results, thus we decided to use a different approach: We searched for gla
only and chose the "FlatFile" view. The pages were parsed for the term "synonymous-codon" and the results are shown in the table below.
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
The results from the database searches were mapped to the sequence and highlighted with different colors. As many mutations from HGMD occur at the same amino acid position in the sequence, there are less red or blue letters than mutations in the table in the HGMD section.
- red: missense/nonsense mutation (HGMD)
- green: silent mutation (DbSNP)
- blue: as well missense/nonsense as silent mutation
MQLRNPELHL
GCALALRFLA
LVSWDIPGAR
ALDNGLARTP
TMGWLHWERF
MCNLDCQEEP
DSCISEKLFM
EMAELMVSEG
WKDAGYEYLC
IDDCWMAPQR
DSEGRLQADP
QRFPHGIRQL
ANYVHSKGLK
LGIYADVGNK
TCAGFPGSFG
YYDIDAQTFA
DWGVDLLKFD
GCYCDSLENL
ADGYKHMSLA
LNRTGRSIVY
SCEWPLYMWP
FQKPNYTEIR
QYCNHWRNFA
DIDDSWKSIK
SILDWTSFNQ
ERIVDVAGPG
GWNDPDMLVI
GNFGLSWNQQ
VTQMALWAIM
AAPLFMSNDL
RHISPQAKAL
LQDKDVIAIN
QDPLGKQGYQ
LRQGDNFEVW
ERPLSGLAWA
VAMINRQEIG
GPRSYTIAVA
SLGKGVACNP
ACFITQLLPV
KRKLGFYEWT
SRLRSHINPT
GTVLLQLENT
MQMSLKDLL
References
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