Difference between revisions of "Task 5 - Mapping SNPs Canavan"
From Bioinformatikpedia
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===SNPedia === |
===SNPedia === |
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links to other pages |
links to other pages |
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| + | == Coding SNPs == |
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| + | <table><tr><td>pos</td><td>id</td><td>ref</td><td>snp type</td><td>mutation</td></tr><tr><td>114</td><td>, CM960086, CM023014</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>D114Y</td></tr> |
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| + | <tr><td>111</td><td>rs181347986, rs181347986 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>I111V</td></tr> |
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| + | <tr><td>195</td><td>, CM990195</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>M195R</td></tr> |
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| + | <tr><td>281</td><td>rs141858640, rs141858640 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>V281M</td></tr> |
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| + | <tr><td>280</td><td>, rs148081446, rs148081446 , CM990196, CM990197</td><td>SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>P280L</td></tr> |
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| + | <tr><td>33</td><td>rs138158568, rs138158568 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>H33R</td></tr> |
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| + | <tr><td>157</td><td>rs140357187, rs140357187 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>I157T</td></tr> |
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| + | <tr><td>285</td><td>rs28940279, rs28940279 , CM930046</td><td>OMIM, SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>E285A</td></tr> |
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| + | <tr><td>154</td><td>rs2228435, rs147193431 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>V154I</td></tr> |
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| + | <tr><td>152</td><td>rs104894548, rs104894548 , CM950102, CM960088, CM023604</td><td>OMIM, SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>C152R</td></tr> |
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| + | <tr><td>288</td><td>, CM034717</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>Y288F</td></tr> |
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| + | <tr><td>153</td><td>rs141755746, rs141755746 </td><td>dbSNP</td><td>-</td><td>synonymous</td><td>Y153Y</td></tr> |
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| + | <tr><td>286</td><td>rs138062143, rs138062143 </td><td>dbSNP</td><td>-</td><td>synonymous</td><td>A286A</td></tr> |
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| + | <tr><td>287</td><td>, CM990198</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>A287T</td></tr> |
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| + | <tr><td>82</td><td>rs80099330, rs80099330 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>M82T</td></tr> |
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| + | <tr><td>244</td><td>, CM023607, CM063848</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>H244R</td></tr> |
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| + | <tr><td>249</td><td>rs104894552, rs104894552 , CM023015</td><td>SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>D249V</td></tr> |
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| + | <tr><td>202</td><td>rs147763700, rs147763700 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>A202S</td></tr> |
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| + | <tr><td>68</td><td>, CM023603</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>D68A</td></tr> |
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| + | <tr><td>121</td><td>rs148451498, rs148451498 , CM063846</td><td>SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>N121D</td></tr> |
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| + | <tr><td>123</td><td>, CM960087</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>G123E</td></tr> |
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| + | <tr><td>305</td><td>rs28940574, rs28940574 , CM940124</td><td>OMIM, SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>A305E</td></tr> |
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| + | <tr><td>24</td><td>rs104894551, rs104894551 , CM023602</td><td>OMIM, SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>E24G</td></tr> |
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| + | <tr><td>270</td><td>, rs200126822</td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>I270T</td></tr> |
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| + | <tr><td>272</td><td>CM063851</td><td>HGMD</td><td>2006</td><td>missense</td><td>L272P</td></tr> |
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| + | <tr><td>166</td><td>CM063847</td><td>HGMD</td><td>2006</td><td>missense</td><td>T166I</td></tr> |
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| + | <tr><td>26</td><td>rs145616193, rs145616193 </td><td>dbSNP</td><td>-</td><td>synonymous</td><td>T26T</td></tr> |
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| + | <tr><td>27</td><td>, CM960085</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>G27R</td></tr> |
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| + | <tr><td>168</td><td>, CM001610, CM960089</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>R168H</td></tr> |
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| + | <tr><td>274</td><td>, CM950104</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>G274R</td></tr> |
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| + | <tr><td>239</td><td>rs145085349, rs145085349 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>I239T</td></tr> |
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| + | <tr><td>277</td><td>rs78677072, rs78677072 </td><td>dbSNP</td><td>-</td><td>synonymous</td><td>T277T</td></tr> |
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| + | <tr><td>164</td><td></td><td>SNPDBe</td><td>-</td><td>missense</td><td>Y164F</td></tr> |
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| + | <tr><td>278</td><td>rs140581464, rs140581464 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>V278M</td></tr> |
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| + | <tr><td>279</td><td>rs145717248, rs145717248 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>Y279H</td></tr> |
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| + | <tr><td>4</td><td>rs142041344, rs142041344 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>C4R</td></tr> |
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| + | <tr><td>231</td><td>rs12948217, rs104894550, rs1805136, rs104894550 , rs12948217 , CM994594, CM940123</td><td>OMIM, SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>Y231Ter</td></tr> |
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| + | <tr><td>71</td><td>, rs104894553, rs104894553 , CM060201</td><td>SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>R71K</td></tr> |
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| + | <tr><td>236</td><td>rs149189911, rs149189911 </td><td>dbSNP</td><td>-</td><td>synonymous</td><td>N236N</td></tr> |
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| + | <tr><td>235</td><td>rs149842031, rs149842031 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>E235K</td></tr> |
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| + | <tr><td>57</td><td>, CM001609</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>A57T</td></tr> |
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| + | <tr><td>213</td><td>CM055097</td><td>HGMD</td><td>2005</td><td>missense</td><td>K213E</td></tr> |
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| + | <tr><td>214</td><td>CM023606</td><td>HGMD</td><td>2002</td><td>missense</td><td>E214Ter</td></tr> |
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| + | <tr><td>314</td><td>CM023608</td><td>HGMD</td><td>2002</td><td>missense</td><td>Ter314W</td></tr> |
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| + | <tr><td>18</td><td>CM067343</td><td>HGMD</td><td>2006</td><td>missense</td><td>G18R</td></tr> |
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| + | <tr><td>178</td><td></td><td>SNPDBe</td><td>-</td><td>missense</td><td>E178A</td></tr> |
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| + | <tr><td>218</td><td>rs104894549, rs104894549 , CM950103</td><td>OMIM, dbSNP, HGMD</td><td>-</td><td>missense</td><td>C218Ter</td></tr> |
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| + | <tr><td>16</td><td>, CM960084</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>I16T</td></tr> |
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| + | <tr><td>310</td><td></td><td>SNPDBe</td><td>-</td><td>missense</td><td>C310G</td></tr> |
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| + | <tr><td>14</td><td>CM063852</td><td>HGMD</td><td>2006</td><td>missense</td><td>V14G</td></tr> |
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| + | <tr><td>21</td><td>, CM001608</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>H21P</td></tr> |
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| + | <tr><td>170</td><td>rs144321760, rs144321760 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>I170T</td></tr> |
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| + | <tr><td>109</td><td>CM990192</td><td>HGMD</td><td>1999</td><td>missense</td><td>Y109Ter</td></tr> |
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| + | <tr><td>143</td><td>, rs199565861, CM980125, CM063849</td><td>SNPDBe, dbSNP, HGMD</td><td>-</td><td>missense</td><td>I143V</td></tr> |
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| + | <tr><td>220</td><td>rs139053885, rs139053885 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>I220T</td></tr> |
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| + | <tr><td>93</td><td>rs144639820, rs144639820 </td><td>dbSNP</td><td>-</td><td>synonymous</td><td>A93A</td></tr> |
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| + | <tr><td>226</td><td>rs201887670, CM086530</td><td>dbSNP, HGMD</td><td>-</td><td>missense</td><td>I226K</td></tr> |
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| + | <tr><td>295</td><td>, CM950105</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>F295S</td></tr> |
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| + | <tr><td>181</td><td>, CM063850, CM001611</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>P181T</td></tr> |
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| + | <tr><td>183</td><td>, CM990193</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>P183H</td></tr> |
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| + | <tr><td>184</td><td>CM023605</td><td>HGMD</td><td>2002</td><td>missense</td><td>Q184Ter</td></tr> |
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| + | <tr><td>186</td><td>, CM990194</td><td>SNPDBe, HGMD</td><td>-</td><td>missense</td><td>V186F</td></tr> |
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| + | <tr><td>53</td><td>rs17850703, rs17850703 </td><td>SNPDBe, dbSNP</td><td>-</td><td>missense</td><td>T53A</td></tr> |
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| + | </table> |
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Revision as of 09:21, 8 June 2012
First impression
Protocol
Further information can be found in the protocol.
HGMD
74 (79 in 2012 professional) total for cDNA sequence NM_000049.2 and amino acid sequence NP_000040.1, out of which
- 47 missense/nonsense
- 5 splicing
- 12 small deletions
- 2 small insertions
- 1 indel
- 7 gross deletions
SNPdbe
- 55 total, includes predicted functional effect. 29 of these 55 labelled as involved in Canavan Disease.
dbSNP
- same identifiers for sequence as HGMD
- "synonymous-codon"[Function_Class] AND ASPA[GENE] AND "human"[ORGN] AND "snp"[SNP_CLASS] yields only 9 results
- 505 results for SNPs in general in human
- 458 for NP_000040.1 (coding: 23)
- 493 for NP_001121557.1 (coding: 23)
SNPedia
links to other pages
Coding SNPs
| pos | id | ref | snp type | mutation | |
| 114 | , CM960086, CM023014 | SNPDBe, HGMD | - | missense | D114Y |
| 111 | rs181347986, rs181347986 | SNPDBe, dbSNP | - | missense | I111V |
| 195 | , CM990195 | SNPDBe, HGMD | - | missense | M195R |
| 281 | rs141858640, rs141858640 | SNPDBe, dbSNP | - | missense | V281M |
| 280 | , rs148081446, rs148081446 , CM990196, CM990197 | SNPDBe, dbSNP, HGMD | - | missense | P280L |
| 33 | rs138158568, rs138158568 | SNPDBe, dbSNP | - | missense | H33R |
| 157 | rs140357187, rs140357187 | SNPDBe, dbSNP | - | missense | I157T |
| 285 | rs28940279, rs28940279 , CM930046 | OMIM, SNPDBe, dbSNP, HGMD | - | missense | E285A |
| 154 | rs2228435, rs147193431 | SNPDBe, dbSNP | - | missense | V154I |
| 152 | rs104894548, rs104894548 , CM950102, CM960088, CM023604 | OMIM, SNPDBe, dbSNP, HGMD | - | missense | C152R |
| 288 | , CM034717 | SNPDBe, HGMD | - | missense | Y288F |
| 153 | rs141755746, rs141755746 | dbSNP | - | synonymous | Y153Y |
| 286 | rs138062143, rs138062143 | dbSNP | - | synonymous | A286A |
| 287 | , CM990198 | SNPDBe, HGMD | - | missense | A287T |
| 82 | rs80099330, rs80099330 | SNPDBe, dbSNP | - | missense | M82T |
| 244 | , CM023607, CM063848 | SNPDBe, HGMD | - | missense | H244R |
| 249 | rs104894552, rs104894552 , CM023015 | SNPDBe, dbSNP, HGMD | - | missense | D249V |
| 202 | rs147763700, rs147763700 | SNPDBe, dbSNP | - | missense | A202S |
| 68 | , CM023603 | SNPDBe, HGMD | - | missense | D68A |
| 121 | rs148451498, rs148451498 , CM063846 | SNPDBe, dbSNP, HGMD | - | missense | N121D |
| 123 | , CM960087 | SNPDBe, HGMD | - | missense | G123E |
| 305 | rs28940574, rs28940574 , CM940124 | OMIM, SNPDBe, dbSNP, HGMD | - | missense | A305E |
| 24 | rs104894551, rs104894551 , CM023602 | OMIM, SNPDBe, dbSNP, HGMD | - | missense | E24G |
| 270 | , rs200126822 | SNPDBe, dbSNP | - | missense | I270T |
| 272 | CM063851 | HGMD | 2006 | missense | L272P |
| 166 | CM063847 | HGMD | 2006 | missense | T166I |
| 26 | rs145616193, rs145616193 | dbSNP | - | synonymous | T26T |
| 27 | , CM960085 | SNPDBe, HGMD | - | missense | G27R |
| 168 | , CM001610, CM960089 | SNPDBe, HGMD | - | missense | R168H |
| 274 | , CM950104 | SNPDBe, HGMD | - | missense | G274R |
| 239 | rs145085349, rs145085349 | SNPDBe, dbSNP | - | missense | I239T |
| 277 | rs78677072, rs78677072 | dbSNP | - | synonymous | T277T |
| 164 | SNPDBe | - | missense | Y164F | |
| 278 | rs140581464, rs140581464 | SNPDBe, dbSNP | - | missense | V278M |
| 279 | rs145717248, rs145717248 | SNPDBe, dbSNP | - | missense | Y279H |
| 4 | rs142041344, rs142041344 | SNPDBe, dbSNP | - | missense | C4R |
| 231 | rs12948217, rs104894550, rs1805136, rs104894550 , rs12948217 , CM994594, CM940123 | OMIM, SNPDBe, dbSNP, HGMD | - | missense | Y231Ter |
| 71 | , rs104894553, rs104894553 , CM060201 | SNPDBe, dbSNP, HGMD | - | missense | R71K |
| 236 | rs149189911, rs149189911 | dbSNP | - | synonymous | N236N |
| 235 | rs149842031, rs149842031 | SNPDBe, dbSNP | - | missense | E235K |
| 57 | , CM001609 | SNPDBe, HGMD | - | missense | A57T |
| 213 | CM055097 | HGMD | 2005 | missense | K213E |
| 214 | CM023606 | HGMD | 2002 | missense | E214Ter |
| 314 | CM023608 | HGMD | 2002 | missense | Ter314W |
| 18 | CM067343 | HGMD | 2006 | missense | G18R |
| 178 | SNPDBe | - | missense | E178A | |
| 218 | rs104894549, rs104894549 , CM950103 | OMIM, dbSNP, HGMD | - | missense | C218Ter |
| 16 | , CM960084 | SNPDBe, HGMD | - | missense | I16T |
| 310 | SNPDBe | - | missense | C310G | |
| 14 | CM063852 | HGMD | 2006 | missense | V14G |
| 21 | , CM001608 | SNPDBe, HGMD | - | missense | H21P |
| 170 | rs144321760, rs144321760 | SNPDBe, dbSNP | - | missense | I170T |
| 109 | CM990192 | HGMD | 1999 | missense | Y109Ter |
| 143 | , rs199565861, CM980125, CM063849 | SNPDBe, dbSNP, HGMD | - | missense | I143V |
| 220 | rs139053885, rs139053885 | SNPDBe, dbSNP | - | missense | I220T |
| 93 | rs144639820, rs144639820 | dbSNP | - | synonymous | A93A |
| 226 | rs201887670, CM086530 | dbSNP, HGMD | - | missense | I226K |
| 295 | , CM950105 | SNPDBe, HGMD | - | missense | F295S |
| 181 | , CM063850, CM001611 | SNPDBe, HGMD | - | missense | P181T |
| 183 | , CM990193 | SNPDBe, HGMD | - | missense | P183H |
| 184 | CM023605 | HGMD | 2002 | missense | Q184Ter |
| 186 | , CM990194 | SNPDBe, HGMD | - | missense | V186F |
| 53 | rs17850703, rs17850703 | SNPDBe, dbSNP | - | missense | T53A |
