Difference between revisions of "Canavan Disease: Task 07 - Supplement"

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(Created page with "Researching SNPs == HGMD == be found in '''<xr id="misnon"> Table </xr>'''. <figtable id="misnon"> {| border="1" cellpadding="5"…")
 
(→‎DBSNP)
 
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−
[[Canavan_Disease:_Task_07_-_Researching_SNPs|Researching SNPs]]
 +
Link back to Task 07: [[Canavan_Disease:_Task_07_-_Researching_SNPs|Researching SNPs]]
   
 
== HGMD ==
  
== HGMD ==
   
−
be found in '''<xr id="misnon"> Table </xr>'''.
 +
All mutations found in HGMD are listed in the following '''<xr id="misnon"></xr>'''.
 
<figtable id="misnon">
  
<figtable id="misnon">
 
{| border="1" cellpadding="5" cellspacing="0" align="center"
  
{| border="1" cellpadding="5" cellspacing="0" align="center"
 
|-
  
|-
−
! colspan="5" style="background:#87CEFA;" | Missense and Nonsense Mutations
 +
! colspan="5" style="background:#87CEFA;" | HGMD: Missense and Nonsense Mutations
 
|-
  
|-
 
! style="background:#BFBFBF;" align="center" | Type
  
! style="background:#BFBFBF;" align="center" | Type
Line 164: Line 164:
 
|-
  
|-
 
|}
  
|}
−
<center><small>'''<caption>''' Overview of the dataset composition for Task 04, containing a brief description of the the chosen structures. Sequence identity and CATH classification similarities with respect to reference sequence 2I3C.</caption></small></center>
 +
<center><small>'''<caption>''' List of all mutations found using HGMD.</caption></small></center>
  +
</figtable>
  +
  +
== dbSNP ==
  +
All mutations found in dbSNP are listed in the following '''<xr id="dbsnp"></xr>''' and '''<xr id="dbsnp2"></xr>'''.
  +
  +
<figtable id="dbsnp">
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
  +
|-
  +
! colspan="5" style="background:#87CEFA;" | dbSNP: Silent Mutations
  +
|-
  +
! style="background:#BFBFBF;" align="center" | ID
  +
! colspan="2" style="background:#BFBFBF;" align="center" | Mutation
  +
! style="background:#BFBFBF;" align="center" | Position
  +
|-
  +
| rs145616193
  +
|| ACC-ACT || Tyr-Tyr || 26
  +
|-
  +
| rs144639820
  +
|| GCT-GCC || Ala-Ala || 93
  +
|-
  +
| rs141755746
  +
|| TAC-TAT || Tyr-Tyr || 153
  +
|-
  +
|rs369805590
  +
|| CAT-CAC || His-His || 207
  +
|-
  +
|rs149189911
  +
|| AAT-AAC || Asn-Asn || 236
  +
|-
  +
|rs373410075
  +
|| GAC-GAT || Asp-Asp || 251
  +
|-
  +
|rs78677072
  +
|| ACC-ACT || Thr-Thr || 277
  +
|-
  +
|rs148081446
  +
|| CCC-CCT || Pro-Pro || 280
  +
|-
  +
|rs370915844
  +
|| AAT-AAC || Asn-Asn || 284
  +
|-
  +
|rs138062143
  +
|| GCC-GCT || Ala-Ala || 286
  +
|-
  +
|rs375736464
  +
|| TAC-TAT || Tyr-Tyr || 289
  +
|-
  +
|rs371394875
  +
|| ACG-ACA || Thr-Thr || 302
  +
|-
  +
|}
  +
<center><small>'''<caption>''' List of all silent mutations found using dbSNP.</caption></small></center>
  +
</figtable>
  +
<br>
  +
<figtable id="dbsnp2">
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
  +
|-
  +
! colspan="5" style="background:#87CEFA;" | dbSNP: Mutations associated with Canavan Disease
  +
|-
  +
! style="background:#BFBFBF;" align="center" | ID
  +
! colspan="2" style="background:#BFBFBF;" align="center" | Mutation
  +
! style="background:#BFBFBF;" align="center" | Position
  +
|-
  +
|rs104894551
  +
|| GAG-GGG || Glu-Gly || 24
  +
|-
  +
|rs104894553
  +
|| CGC-CAG || Arg-His || 71
  +
|-
  +
|rs104894548
  +
|| TGC-CGC || Cys-Arg || 152
  +
|-
  +
|rs104894549
  +
|| TGC-TGA || Cys-Term || 218
  +
|-
  +
|rs12948217
  +
|| TAC-TAA || Tyr-Term || 231
  +
|-
  +
|rs104894550
  +
|| TAC-TGC || Tyr-Cys || 231
  +
|-
  +
|rs104894552
  +
|| GAT-GTT || Asp-Val || 249
  +
|-
  +
|rs111033260
  +
|| CGA-TGA || Arg-Term || 250
  +
|-
  +
|rs28940279
  +
|| GAG-GCG || Glu-Ala || 285
  +
|-
  +
|rs28940574
  +
|| GCA-GAA || Ala-Glu || 305
  +
|-
  +
|}
  +
<center><small>'''<caption>''' List of all mutations associated with Canavan Disease found using dbSNP.</caption></small></center>
  +
</figtable>
  +
  +
== OMIM ==
  +
All mutations found in OMIM are listed in the following '''<xr id="omim"></xr>'''.
  +
  +
<figtable id="omim">
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
  +
|-
  +
! colspan="5" style="background:#87CEFA;" | OMIM: Mutations associated with Canavan Disease
  +
|-
  +
! style="background:#BFBFBF;" align="center" | Type
  +
! style="background:#BFBFBF;" align="center" | ID
  +
! style="background:#BFBFBF;" align="center" | Mutation
  +
! style="background:#BFBFBF;" align="center" | Position
  +
|-
  +
! rowspan="9" | '''Mutation'''
  +
|rs104894551
  +
|| GLU-GLY || 24
  +
|-
  +
|rs104894553
  +
|| ARG-HIS || 71
  +
|-
  +
|rs104894548
  +
|| CYS-ARG || 152
  +
|-
  +
|rs104894549
  +
|| CYS-TER || 218
  +
|-
  +
|rs12948217
  +
|| TYR-TER || 231
  +
|-
  +
|rs104894550
  +
|| TYR-CYS || 231
  +
|-
  +
|rs104894552
  +
|| ASP-VAL || 249
  +
|-
  +
|rs28940279
  +
|| GLU-ALA || 285
  +
|-
  +
|rs28940574
  +
|| ALA-GLU || 305
  +
|-
  +
! rowspan="3" | other
  +
| 4-BP DEL
  +
|| AGAA || 876
  +
|-
  +
|1-BP DEL
  +
|| T || 32
  +
|-
  +
|EX4 DEL
  +
|| ||
  +
|-
  +
|}
  +
<center><small>'''<caption>''' List of all mutations found using OMIM.</caption></small></center>
  +
</figtable>
  +
  +
  +
== SNPdbe ==
  +
All mutations found in SNPdbe are listed in the following '''<xr id="snpdbe"></xr>'''.
  +
  +
<figtable id="snpdbe">
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
  +
|-
  +
! colspan="5" style="background:#87CEFA;" | SNPdbe: Mutations for ASPA
  +
|-
  +
! style="background:#BFBFBF;" align="center" | ID
  +
! style="background:#BFBFBF;" align="center" | Mutation
  +
! style="background:#BFBFBF;" align="center" | Position
  +
! style="background:#BFBFBF;" align="center" | Canavan
  +
|-
  +
|rs142041344
  +
|| Cys-Arg || 4 ||
  +
|-
  +
|N/A
  +
|| Ile-Thr || 16 || *
  +
|-
  +
|N/A
  +
|| His-Pro || 21 || *
  +
|-
  +
|rs104894551
  +
|| Glu-Gly || 24 || *
  +
|-
  +
|N/A
  +
|| Gly-Arg || 27 || *
  +
|-
  +
|rs138158568
  +
|| His-Arg || 33 ||
  +
|-
  +
|rs17850703
  +
|| Thr-Ala || 53 ||
  +
|-
  +
|N/A
  +
|| Ala-Thr || 57 || *
  +
|-
  +
|N/A
  +
|| Asp-Ala || 68 || *
  +
|-
  +
|N/A
  +
|| Arg-Lys || 71 ||
  +
|-
  +
|rs104894553
  +
|| Arg-His || 71 ||
  +
|-
  +
|rs80099330
  +
|| Met-Thr || 82 ||
  +
|-
  +
|rs181347986
  +
|| Ile-Val || 111 ||
  +
|-
  +
|N/A
  +
|| Asp-Glu || 114 || *
  +
|-
  +
|N/A
  +
|| Asp-Tyr || 114 || *
  +
|-
  +
|rs148451498
  +
|| Asn-Asp || 121 ||
  +
|-
  +
|N/A
  +
|| Gly-Glu || 123 || *
  +
|-
  +
|N/A
  +
|| Ile-Thr || 143 || *
  +
|-
  +
|N/A
  +
|| Ile-Val || 143 ||
  +
|-
  +
|N/A
  +
|| Cys-Trp || 152 || *
  +
|-
  +
|N/A
  +
|| Cys-Tyr || 152 || *
  +
|-
  +
|rs104894548
  +
|| Cys-Arg || 152 || *
  +
|-
  +
|rs2228435
  +
|| Val-Ile || 154 ||
  +
|-
  +
|rs140357187
  +
|| Ile-Thr || 157 ||
  +
|-
  +
|N/A
  +
|| Tyr-Phe || 164 ||
  +
|-
  +
|N/A
  +
|| Arg-Lys || 168 ||
  +
|-
  +
|N/A
  +
|| Arg-Cys || 168 || *
  +
|-
  +
|N/A
  +
|| Arg-His || 168 || *
  +
|-
  +
|rs144321760
  +
|| Ile-Thr || 170 ||
  +
|-
  +
|N/A
  +
|| Glu-Ala || 178 ||
  +
|-
  +
|N/A
  +
|| Pro-Thr || 181 || *
  +
|-
  +
|N/A
  +
|| Pro-His || 183 || *
  +
|-
  +
|N/A
  +
|| Val-Phe || 186 || *
  +
|-
  +
|N/A
  +
|| Met-Arg || 195 || *
  +
|-
  +
|rs147763700
  +
|| Ala-Ser || 202 ||
  +
|-
  +
|rs139053885
  +
|| Ile-Thr || 220 ||
  +
|-
  +
|rs104894550
  +
|| Tyr-Cys || 231 || *
  +
|-
  +
|rs149842031
  +
|| Glu-Lys || 235 ||
  +
|-
  +
|rs145085349
  +
|| Ile-Thr || 239 ||
  +
|-
  +
|N/A
  +
|| His-Arg || 244 || *
  +
|-
  +
|rs104894552
  +
|| Asp-Val || 249 || *
  +
|-
  +
|N/A
  +
|| Ile-Thr || 270 ||
  +
|-
  +
|N/A
  +
|| Gly-Arg || 274 || *
  +
|-
  +
|rs140581464
  +
|| Val-Met || 278 ||
  +
|-
  +
|rs145717248
  +
|| Tyr-His || 279 ||
  +
|-
  +
|N/A
  +
|| Pro-Leu || 280 || *
  +
|-
  +
|N/A
  +
|| Pro-Ser || 280 || *
  +
|-
  +
|rs141858640
  +
|| Val-Met || 281 ||
  +
|-
  +
|N/A
  +
|| Glu-Asp || 285 ||
  +
|-
  +
|rs28940279
  +
|| Glu-Ala || 285 || *
  +
|-
  +
|N/A
  +
|| Ala-Thr || 287 || *
  +
|-
  +
|N/A
  +
|| Tyr-Phe || 288 ||
  +
|-
  +
|N/A
  +
|| Phe-Ser || 295 || *
  +
|-
  +
|rs28940574
  +
|| Ala-Glu || 305 || *
  +
|-
  +
|N/A
  +
|| Cys-Gly || 310 ||
  +
|-
  +
|}
  +
<center><small>'''<caption>''' List of all mutations found using SNPdbe. Those associated with Canavan Disease are marked with an asterisk.</caption></small></center>
  +
</figtable>
  +
  +
== SNPedia ==
  +
All mutations found in SNPedia are listed in the following '''<xr id="snpedia"></xr>'''.
  +
  +
<figtable id="snpedia">
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
  +
|-
  +
! colspan="5" style="background:#87CEFA;" | SNPedia: Mutations
  +
|-
  +
! style="background:#BFBFBF;" align="center" | ID
  +
! style="background:#BFBFBF;" align="center" | Mutation
  +
! style="background:#BFBFBF;" align="center" | Position
  +
! style="background:#BFBFBF;" align="center" | Canavan
  +
|-
  +
|rs104894551
  +
|| Glu-Gly || 24 ||
  +
|-
  +
|rs104894553
  +
|| Arg-His || 71 || *
  +
|-
  +
|rs104894548
  +
|| Cys-Arg || 152 ||
  +
|-
  +
|rs104894549
  +
|| Cys-Term || 218 ||
  +
|-
  +
|rs104894550
  +
|| Tyr-Cys || 231 ||
  +
|-
  +
|rs12948217
  +
|| Tyr-X || 231 || *
  +
|-
  +
|rs104894552
  +
|| Asp-Val || 249 ||
  +
|-
  +
|rs28940279
  +
|| Glu-Ala || 285 || *
  +
|-
  +
|rs28940574
  +
|| Ala-Glu || 305 || *
  +
|-
  +
|rs923375
  +
|| || ||
  +
|-
  +
|}
  +
<center><small>'''<caption>''' List of all mutations found using SNPedia. Those associated with Canavan Disease are marked with an asterisk.</caption></small></center>
 
</figtable>
  
</figtable>

Latest revision as of 15:27, 4 September 2013

Link back to Task 07: Researching SNPs

HGMD

All mutations found in HGMD are listed in the following <xr id="misnon"></xr>. <figtable id="misnon">

HGMD: Missense and Nonsense Mutations
Type ID Mutation Position
Missense CM100918 ATG-ACG Met-Thr 1
CM063852 GTT-GGT Val-Gly 14
CM960084 ATC-ACC Ile-Thr 16
CM067343 tGGA-AGA Gly-Arg 18
CM001608 CAT-CCT His-Pro 21
CM023602 GAG-GGG Glu-Gly 24
CM960085 cGGA-AGA Gly-Arg 27
CM001609 aGCA-ACA Ala-Thr 57
CM023603 GAC-GCC Asp-Ala 68
CM100919 AAT-AGT Asn-Ser 70
CM060201 CGC-CAC Arg-His 71
CM960086 GACc-GAA Asp-Glu 114
CM023014 tGAC-TAC Asp-Tyr 114
CM063846 AAC-ATC Asn-Ile 121
CM960087 GGG-GAG Gly-Glu 123
CM980125 ATT-ACT Ile-Thr 143
CM063849 cATT-TTT Ile-Phe 143
CM950102 cTGC-CGC Cys-Arg 152
CM960088 TGC-TAC Cys-Tyr 152
CM023604 TGCt-TGG Cys-Trp 152
CM063847 ACC-ATC Thr-Ile 166
CM001610 CGT-CAT Arg-His 168
CM960089 tCGT-TGT Arg-Cys 168
CM063850 CCT-CTT Pro-Leu 181
CM001611 tCCT-ACT Pro-Thr 181
CM990193 CCT-CAT Pro-His 183
CM990194 gGTT-TTT Val-Phe 186
CM990195 ATG-AGG Met-Arg 195
CM055097 aAAA-GAA Lys-Glu 213
CM086530 ATA-ACA Ile-Thr 226
CM994594 TAC-TGC Tyr-Cys 231
CM023607 CAT-CGT His-Arg 244
CM063848 CAT-CTT His-Leu 244
CM023015 GAT-GTT Asp-Val 249
CM063851 CTG-CCG Leu-Pro 272
CM950104 cGGA-AGA Gly-Arg 274
CM990196 CCC-CTC Pro-Leu 280
CM990197 cCCC-TCC Pro-Ser 280
CM930046 GAG-GCG Glu-Ala 285
CM990198 cGCA-ACA Ala-Thr 287
CM034717 TAT-TGT Tyr-Cys 288
CM950105 TTT-TCT Phe-Ser 295
CM940124 GCA-GAA Ala-Glu 305
CM023608 TAG-TGG Term-Trp 314
Nonsense CM990192 TATg-TAG Tyr-Term 109
CM023605 tCAA-TAA Gln-Term 184
CM023606 aGAA-TAA Glu-Term 214
CM950103 TGCg-TGA Cys-Term 218
CM940123 TACc-TAA Tyr-Term 231
List of all mutations found using HGMD.

</figtable>

dbSNP

All mutations found in dbSNP are listed in the following <xr id="dbsnp"></xr> and <xr id="dbsnp2"></xr>.

<figtable id="dbsnp">

dbSNP: Silent Mutations
ID Mutation Position
rs145616193 ACC-ACT Tyr-Tyr 26
rs144639820 GCT-GCC Ala-Ala 93
rs141755746 TAC-TAT Tyr-Tyr 153
rs369805590 CAT-CAC His-His 207
rs149189911 AAT-AAC Asn-Asn 236
rs373410075 GAC-GAT Asp-Asp 251
rs78677072 ACC-ACT Thr-Thr 277
rs148081446 CCC-CCT Pro-Pro 280
rs370915844 AAT-AAC Asn-Asn 284
rs138062143 GCC-GCT Ala-Ala 286
rs375736464 TAC-TAT Tyr-Tyr 289
rs371394875 ACG-ACA Thr-Thr 302
List of all silent mutations found using dbSNP.

</figtable>
<figtable id="dbsnp2">

dbSNP: Mutations associated with Canavan Disease
ID Mutation Position
rs104894551 GAG-GGG Glu-Gly 24
rs104894553 CGC-CAG Arg-His 71
rs104894548 TGC-CGC Cys-Arg 152
rs104894549 TGC-TGA Cys-Term 218
rs12948217 TAC-TAA Tyr-Term 231
rs104894550 TAC-TGC Tyr-Cys 231
rs104894552 GAT-GTT Asp-Val 249
rs111033260 CGA-TGA Arg-Term 250
rs28940279 GAG-GCG Glu-Ala 285
rs28940574 GCA-GAA Ala-Glu 305
List of all mutations associated with Canavan Disease found using dbSNP.

</figtable>

OMIM

All mutations found in OMIM are listed in the following <xr id="omim"></xr>.

<figtable id="omim">

OMIM: Mutations associated with Canavan Disease
Type ID Mutation Position
Mutation rs104894551 GLU-GLY 24
rs104894553 ARG-HIS 71
rs104894548 CYS-ARG 152
rs104894549 CYS-TER 218
rs12948217 TYR-TER 231
rs104894550 TYR-CYS 231
rs104894552 ASP-VAL 249
rs28940279 GLU-ALA 285
rs28940574 ALA-GLU 305
other 4-BP DEL AGAA 876
1-BP DEL T 32
EX4 DEL
List of all mutations found using OMIM.

</figtable>


SNPdbe

All mutations found in SNPdbe are listed in the following <xr id="snpdbe"></xr>.

<figtable id="snpdbe">

SNPdbe: Mutations for ASPA
ID Mutation Position Canavan
rs142041344 Cys-Arg 4
N/A Ile-Thr 16 *
N/A His-Pro 21 *
rs104894551 Glu-Gly 24 *
N/A Gly-Arg 27 *
rs138158568 His-Arg 33
rs17850703 Thr-Ala 53
N/A Ala-Thr 57 *
N/A Asp-Ala 68 *
N/A Arg-Lys 71
rs104894553 Arg-His 71
rs80099330 Met-Thr 82
rs181347986 Ile-Val 111
N/A Asp-Glu 114 *
N/A Asp-Tyr 114 *
rs148451498 Asn-Asp 121
N/A Gly-Glu 123 *
N/A Ile-Thr 143 *
N/A Ile-Val 143
N/A Cys-Trp 152 *
N/A Cys-Tyr 152 *
rs104894548 Cys-Arg 152 *
rs2228435 Val-Ile 154
rs140357187 Ile-Thr 157
N/A Tyr-Phe 164
N/A Arg-Lys 168
N/A Arg-Cys 168 *
N/A Arg-His 168 *
rs144321760 Ile-Thr 170
N/A Glu-Ala 178
N/A Pro-Thr 181 *
N/A Pro-His 183 *
N/A Val-Phe 186 *
N/A Met-Arg 195 *
rs147763700 Ala-Ser 202
rs139053885 Ile-Thr 220
rs104894550 Tyr-Cys 231 *
rs149842031 Glu-Lys 235
rs145085349 Ile-Thr 239
N/A His-Arg 244 *
rs104894552 Asp-Val 249 *
N/A Ile-Thr 270
N/A Gly-Arg 274 *
rs140581464 Val-Met 278
rs145717248 Tyr-His 279
N/A Pro-Leu 280 *
N/A Pro-Ser 280 *
rs141858640 Val-Met 281
N/A Glu-Asp 285
rs28940279 Glu-Ala 285 *
N/A Ala-Thr 287 *
N/A Tyr-Phe 288
N/A Phe-Ser 295 *
rs28940574 Ala-Glu 305 *
N/A Cys-Gly 310
List of all mutations found using SNPdbe. Those associated with Canavan Disease are marked with an asterisk.

</figtable>

SNPedia

All mutations found in SNPedia are listed in the following <xr id="snpedia"></xr>.

<figtable id="snpedia">

SNPedia: Mutations
ID Mutation Position Canavan
rs104894551 Glu-Gly 24
rs104894553 Arg-His 71 *
rs104894548 Cys-Arg 152
rs104894549 Cys-Term 218
rs104894550 Tyr-Cys 231
rs12948217 Tyr-X 231 *
rs104894552 Asp-Val 249
rs28940279 Glu-Ala 285 *
rs28940574 Ala-Glu 305 *
rs923375
List of all mutations found using SNPedia. Those associated with Canavan Disease are marked with an asterisk.

</figtable>

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