Task 5 - Mapping SNPs Canavan

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

link to search

SNPdbe

• 55 total, includes predicted functional effect. 29 of these 55 labelled as involved in Canavan Disease.

link to search

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	year	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

MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKKCTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLF
   R         G T R  P  G TR     R                   A   T          A  K          T          A       
GPKDSEDSYDIIFDLHNTTSNMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVGPQPQGVLRADILDQMRKMIK
        r V  Y      D E                   V        RYI  T      F I H T       A  T Hr F        R     
HALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIAAIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
 S          Er   r T     K    r   KN  T    R    V                    T P R  TMHLM   AATF      S     
LTLNAKSIRCCLH-
    E    G   W