(used for mutation description)
(last modified March 20, 2012)
This file was created to facilitate the description of sequence variants in the BSCL2 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008461.1, covering BSCL2 transcript variant-1 (NM_001122955.3). Several papers have reported variants in relation to transcript variant-2 (NM_032667.6), using an alternative promoter/exon 1b in intron 1 and a transcription initiation site in exon 2 (Met-65). Transcript variant-3 (NM_001130702.2) uses the same promoter but skips exon 7, generating an alternatively translated C-terminal protein.
Please note that introns are available by clicking on the exon numbers above the sequence.
(upstream sequence)
. . . g.6899
gctggtacctgaaggatgaaggatgctagaag c.-481
. . . . . . g.6959
gagctgctcagatcctggagcataccaactgcctggccagtgggggagcctagctgcctg c.-421
. . . . . . g.7019
catccctgcgcacacccccactgtcgctagttcactgcctgcccctcccccattgcaggc c.-361
. . . . . . g.7079
atcctgactctgggctagagacctccccaacagagctgaggccaaggccgactccccctc c.-301
. . . . . . g.7139
tcaaatggcgtggtctgggcctatgacggcccctgcagtggagtctgtactggctgcggg c.-241
. . . . . . g.7199
ggaccctgctcatttgaaaatctgacatcagctgggcagtcgcccccctcctcctttcct c.-181
. . . . . . g.7259
ccctctactctgacacagcacttagcacctgaatcttcgtttctctcccagggaccctcc c.-121
. . . . . . g.7319
attttccatatccaggaaaatgtgatgcgccacaggtatcagcgtctggatcgccacttc c.-61
. . . . . . g.7379
acgttttagccacaagtgactcagtggaagatccagagtcaacagaggctcgtcaggaag c.-1
. . . . . . g.7439
ATGTCTACAGAAAAGGTAGACCAAAAGGAGGAAGCTGGGGAAAAAGAGGTGTGCGGAGAC c.60
M S T E K V D Q K E E A G E K E V C G D p.20
. . | 02. . . . g.8990
CAGATCAAAGGACCGGACAAAGAGGAG | GAACCACCAGCTGCTGCATCCCATGGCCAGGGG c.120
Q I K G P D K E E | E P P A A A S H G Q G p.40
. . . . . . g.9050
TGGCGTCCAGGTGGCAGAGCAGCTAGGAACGCAAGGCCTGAACCTGGGGCCAGACACCCT c.180
W R P G G R A A R N A R P E P G A R H P p.60
. . . . . . g.9110
GCTCTCCCGGCCATGGTCAACGACCCTCCAGTACCTGCCTTACTGTGGGCCCAGGAGGTG c.240
A L P A M V N D P P V P A L L W A Q E V p.80 /16
^ translation start isoform-2
. . . . . . g.9170
GGCCAAGTCTTGGCAGGCCGTGCCCGCAGGCTGCTGCTGCAGTTTGGGGTGCTCTTCTGC c.300
G Q V L A G R A R R L L L Q F G V L F C p.100 /36
. . . . . . g.9230
ACCATCCTCCTTTTGCTCTGGGTGTCTGTCTTCCTCTATGGCTCCTTCTACTATTCCTAT c.360
T I L L L L W V S V F L Y G S F Y Y S Y p.120 /56
. . . . | 03 . . g.12041
ATGCCGACAGTCAGCCACCTCAGCCCTGTGCATTTCTACTACAG | GACCGACTGTGATTCC c.420
M P T V S H L S P V H F Y Y R | T D C D S p.140 /76
. . . . . . g.12101
TCCACCACCTCACTCTGCTCCTTCCCTGTTGCCAATGTCTCGCTGACTAAGGGTGGACGT c.480
S T T S L C S F P V A N V S L T K G G R p.160 /96
| 04 . . . . . . g.19917
GATCGG | GTGCTGATGTATGGACAGCCGTATCGTGTTACCTTAGAGCTTGAGCTGCCAGAG c.540
D R | V L M Y G Q P Y R V T L E L E L P E p.180 /116
. . . . . . g.19977
TCCCCTGTGAATCAAGATTTGGGCATGTTCTTGGTCACCATTTCCTGCTACACCAGAGGT c.600
S P V N Q D L G M F L V T I S C Y T R G p.200 /136
. . . | 05 . . . g.21807
GGCCGAATCATCTCCACTTCTTCGCGTTCG | GTGATGCTGCATTACCGCTCAGACCTGCTC c.660
G R I I S T S S R S | V M L H Y R S D L L p.220 /156
. . . . . . g.21867
CAGATGCTGGACACACTGGTCTTCTCTAGCCTCCTGCTATTTGGCTTTGCAGAGCAGAAG c.720
Q M L D T L V F S S L L L F G F A E Q K p.240 /176
. . . . | 06 . . g.22116
CAGCTGCTGGAGGTGGAACTCTACGCAGACTATAGAGAGAACTCG | TACGTGCCGACCACT c.780
Q L L E V E L Y A D Y R E N S | Y V P T T p.260 /196
. . . . . . g.22176
GGAGCGATCATTGAGATCCACAGCAAGCGCATCCAGCTGTATGGAGCCTACCTCCGCATC c.840
G A I I E I H S K R I Q L Y G A Y L R I p.280 /216
. . | 07 . . . . g.23190
CACGCGCACTTCACTGGGCTCAG | ATACCTGCTATACAACTTCCCGATGACCTGCGCCTTC c.900
H A H F T G L R | Y L L Y N F P M T C A F p.300 /236
^ alternatively spliced exon (transcript variant-3)
. . . . . . g.23250
ATAGGTGTTGCCAGCAACTTCACCTTCCTCAGCGTCATCGTGCTCTTCAGCTACATGCAG c.960
I G V A S N F T F L S V I V L F S Y M Q p.320 /256
. . . . | 08 . . g.23448
TGGGTGTGGGGGGGCATCTGGCCCCGACACCGCTTCTCTTTGCAG | GTTAACATCCGAAAA c.1020
W V W G G I W P R H R F S L Q | V N I R K p.340 /276
^ transcript variant-3 uses a shifted reading frame
. . . . . | 09 . g.23715
AGAGACAATTCCCGGAAGGAAGTCCAACGAAGGATCTCTGCTCATCAGCCAG | GGCCTGAA c.1080
R D N S R K E V Q R R I S A H Q P G | P E p.360 /296
. . . . . . g.23775
GGCCAGGAGGAGTCAACTCCGCAATCAGATGTTACAGAGGATGGTGAGAGCCCTGAAGAT c.1140
G Q E E S T P Q S D V T E D G E S P E D p.380 /316
. | 10 . . . . . g.23929
CCCTCAGGGACAG | AGGGTCAGCTGTCCGAGGAGGAGAAACCAGATCAGCAGCCCCTGAGC c.1200
P S G T E | G Q L S E E E K P D Q Q P L S p.400 /336
. . . | 11 . . . g.24079
GGAGAAGAGGAGCTAGAGCCTGAGGCCAGTGATG | GTTCAGGCTCCTGGGAAGATGCAGCT c.1260
G E E E L E P E A S D G | S G S W E D A A p.420 /356
. . . . . . g.24139
TTGCTGACGGAGGCCAACCTGCCTGCTCCTGCTCCTGCTTCTGCTTCTGCCCCTGTCCTA c.1320
L L T E A N L P A P A P A S A S A P V L p.440 /376
. . . . . . g.24199
GAGACTCTGGGCAGCTCTGAACCTGCTGGGGGTGCTCTCCGACAGCGCCCCACCTGCTCT c.1380
E T L G S S E P A G G A L R Q R P T C S p.460 /396
g.24208
AGTTCCTGA c.1389
S S X p.462 /398
. . . . . . g.24268
agaaaaggggcagactcctcacattccagcactttcccacctgactcctctcccctcgtt c.*60
. . . . g.24313
tttccttcaataaactattttgtgtcagcttcttccttgactctg c.*105
(downstream sequence)
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