(used for variant description)
(last modified January 20, 2019)
This file was created to facilitate the description of sequence variants in the CHRNA1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008172.1, covering CHRNA1 transcript-1 (NM_001039523.2). Transcript variant-2 lacks the alternatively spliced exon 4 (NM_000079.3). The protein is N-terminally cleaved to obtain the mature CHRNA1 protein, removing the signal peptide (amino acids 1-20). Publications describing variants in CHRNA1 originally used the mature protein as a reference (also excl. the 25 amino acids encoded by exon 4).
Please note that introns are available by clicking on the exon numbers above the sequence. (upstream sequence)
. g.5018
agacaagcacccagccag c.-61
. . . . . . g.5078
agtgccagtgagaagcacaggccaccactctgccctggtccacacaagctccggtagccc c.-1
. . . . | 02 . . g.9856
ATGGAGCCCTGGCCTCTCCTCCTGCTCTTTAGCCTTTGCTCAG | CTGGCCTCGTCCTGGGC c.60
M E P W P L L L L F S L C S A | G L V L G p.20
. . . . . . g.9916
TCCGAACATGAGACCCGTCTGGTGGCAAAGCTATTTAAAGACTACAGCAGCGTGGTGCGG c.120
S E H E T R L V A K L F K D Y S S V V R p.40
. . . . . . g.9976
CCAGTGGAAGACCACCGCCAGGTCGTGGAGGTCACCGTGGGCCTGCAGCTGATACAGCTC c.180
P V E D H R Q V V E V T V G L Q L I Q L p.60
| 03 . . . . | 04 . g.11458
ATCAATGTG | GATGAAGTAAATCAGATCGTGACAACCAATGTGCGTCTGAAACAG | GGTGAC c.240
I N V | D E V N Q I V T T N V R L K Q | G D p.80
^ alternatively spliced exon
. . . . . . g.11518
ATGGTAGATCTGCCACGCCCCAGCTGCGTGACTTTGGGAGTTCCTTTGTTTTCTCATCTG c.300
M V D L P R P S C V T L G V P L F S H L p.100
| 05 . . . . . g.11848
CAGAATGAG | CAATGGGTGGATTACAACCTAAAATGGAATCCAGATGACTATGGCGGTGTG c.360
Q N E | Q W V D Y N L K W N P D D Y G G V p.120
. . . . . | 06 g.15059
AAAAAAATTCACATTCCTTCAGAAAAGATCTGGCGCCCAGACCTTGTTCTCTATAACAA | T c.420
K K I H I P S E K I W R P D L V L Y N N | p.140
. . . . . . g.15119
GCAGATGGTGACTTTGCTATTGTCAAGTTCACCAAAGTGCTCCTGCAGTACACTGGCCAC c.480
A D G D F A I V K F T K V L L Q Y T G H p.160
. . . . . . g.15179
ATCACGTGGACACCTCCAGCCATCTTTAAAAGCTACTGTGAGATCATCGTCACCCACTTT c.540
I T W T P P A I F K S Y C E I I V T H F p.180
. . . . . . g.15239
CCCTTTGATGAACAGAACTGCAGCATGAAGCTGGGCACCTGGACCTACGACGGCTCTGTC c.600
P F D E Q N C S M K L G T W T Y D G S V p.200
. | 07 . . . . . g.15777
GTGGCCATCAACCCG | GAAAGCGACCAGCCAGACCTGAGCAACTTCATGGAGAGCGGGGAG c.660
V A I N P | E S D Q P D L S N F M E S G E p.220
. . . . . . g.15837
TGGGTGATCAAGGAGTCCCGGGGCTGGAAGCACTCCGTGACCTATTCCTGCTGCCCCGAC c.720
W V I K E S R G W K H S V T Y S C C P D p.240
. . . . . . g.15897
ACCCCCTACCTGGACATCACCTACCACTTCGTCATGCAGCGCCTGCCCCTCTACTTCATC c.780
T P Y L D I T Y H F V M Q R L P L Y F I p.260
. . . . . . g.15957
GTCAACGTCATCATCCCCTGCCTGCTCTTCTCCTTCTTAACTGGCCTGGTATTCTACCTG c.840
V N V I I P C L L F S F L T G L V F Y L p.280
. | 08 . . . . . g.19350
CCCACAGACTCAG | GGGAGAAGATGACTCTGAGCATCTCTGTCTTACTGTCTTTGACTGTG c.900
P T D S G | E K M T L S I S V L L S L T V p.300
. . . . . . g.19410
TTCCTTCTGGTCATCGTGGAGCTGATCCCCTCCACGTCCAGTGCTGTGCCCTTGATTGGA c.960
F L L V I V E L I P S T S S A V P L I G p.320
. . . . . . g.19470
AAATACATGCTGTTCACCATGGTGTTCGTCATTGCCTCCATCATCATCACTGTCATCGTC c.1020
K Y M L F T M V F V I A S I I I T V I V p.340
. . . . . | 09. g.20656
ATCAACACACACCACCGCTCACCCAGCACCCATGTCATGCCCAACTGGGTGCGGAAG | GTT c.1080
I N T H H R S P S T H V M P N W V R K | V p.360
. . . . . . g.20716
TTTATCGACACTATCCCAAATATCATGTTTTTCTCCACAATGAAAAGACCATCCAGAGAA c.1140
F I D T I P N I M F F S T M K R P S R E p.380
. . . . . . g.20776
AAGCAAGACAAAAAGATTTTTACAGAAGACATTGATATCTCTGACATTTCTGGAAAGCCA c.1200
K Q D K K I F T E D I D I S D I S G K P p.400
. . . . . . g.20836
GGGCCTCCACCCATGGGCTTCCACTCTCCCCTGATCAAACACCCCGAGGTGAAAAGTGCC c.1260
G P P P M G F H S P L I K H P E V K S A p.420
. . . . . | 10. g.21220
ATCGAGGGCATCAAGTACATCGCAGAGACCATGAAGTCAGACCAGGAGTCTAACAAT | GCG c.1320
I E G I K Y I A E T M K S D Q E S N N | A p.440
. . . . . . g.21280
GCGGCAGAGTGGAAGTACGTTGCAATGGTGATGGACCACATACTCCTCGGAGTCTTCATG c.1380
A A E W K Y V A M V M D H I L L G V F M p.460
. . . . . . g.21340
CTTGTTTGCATCATCGGAACCCTAGCCGTGTTTGCAGGTCGACTCATTGAATTAAATCAG c.1440
L V C I I G T L A V F A G R L I E L N Q p.480
g.21349
CAAGGATGA c.1449
Q G X p.482
. . . . . . g.21409
gcagaaaatgagctgagcttagctctgccctggaacctaccagagcagagaagggcagga c.*60
. . . . . . g.21469
gaggaagatttgtctacttgctccactcgcacttatcaaacgtgttatattccatactta c.*120
. . . . . . g.21529
ttattgatgataagatttacctttatgtaagtttatggccttgaagtgttttcatattgc c.*180
. . . . . . g.21589
ttctccctttagttctgctgtctccctgaagagtgaaccctctttagtaaatgaaactaa c.*240
. . . . . . g.21649
tcactaaaaaaagtgttcatttccagtgtctggaagagtttttgccaggataaccgaggt c.*300
. . . . . . g.21709
tttctgttgcattgtcattgctgttatatttatatatttacttattttgtctaaccacga c.*360
. . . . . . g.21769
gaccactagggagttgctgatgttctaaatgaagtgtattctttgcttaagagtcagttt c.*420
. . . . . . g.21829
tgtacctactaagaaaaccccatctaccagtcctaaagagataaggcatttgatttggag c.*480
. . . . . g.21881
agagaggaagcagtagaaatgaaataaactaaaatgcaaactgcatcaaaaa c.*532
(downstream sequence)
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