Mapping SNPs GLA

^{by Benjamin Drexler and Fabian Grandke}

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

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

MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKF
DGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFE
VWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL

References

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