(used for mutation description)
(last modified February 4, 2011)
This file was created to facilitate the description of sequence variants in the CAPN3 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008660.1, covering CAPN3 transcript NM_000070.2. Several differentially spliced CAPN3-transcripts have been described; variant-2 (NM_024344.1) lacking exon 15 and variant-3 (NM_173087.1) lacking exons 6, 15 and 16. Transcript variant-7 (NM_212465.2) uses an upstream promoter/first exon 01b and 5 exons replacing the normal exon 1 and lacks exon 15. Other transcripts use an alterantive promoter/first-exon in intron 12 (variant-4, NM_173088.1) or intron 14 (variant-6 lacking exon 16, NM_173090.1) and variant-5 (lacking exons 15 and 16, NM_173089.1).
Please note that introns are available by clicking on the exon numbers above the sequence.
(upstream sequence)
^ alternative promoter/first exon 01b
g.16403
cactct c.-301
. . . . . . g.16463
ctttctctctccctctggcatgcatgctgctggtaggagacccccaagtcaacattgctt c.-241
. . . . . . g.16523
cagaaatcctttagcactcatttctcaggagaacttatggcttcagaatcacagctcggt c.-181
. . . . . . g.16583
ttttaagatggacataacctgtacgaccttctgatgggctttcaactttgaactggatgt c.-121
. . . . . . g.16643
ggacacttttctctcagatgacagaattactccaacttcccctttgcagttgcttccttt c.-61
. . . . . . g.16703
ccttgaaggtagctgtatcttattttctttaaaaagctttttcttccaaagccacttgcc c.-1
. . . . . . g.16763
ATGCCGACCGTCATTAGCGCATCTGTGGCTCCAAGGACAGCGGCTGAGCCCCGGTCCCCA c.60
M P T V I S A S V A P R T A A E P R S P p.20
. . . . . . g.16823
GGGCCAGTTCCTCACCCGGCCCAGAGCAAGGCCACTGAGGCTGGGGGTGGAAACCCAAGT c.120
G P V P H P A Q S K A T E A G G G N P S p.40
. . . . . . g.16883
GGCATCTATTCAGCCATCATCAGCCGCAATTTTCCTATTATCGGAGTGAAAGAGAAGACA c.180
G I Y S A I I S R N F P I I G V K E K T p.60
. . . . . . g.16943
TTCGAGCAACTTCACAAGAAATGTCTAGAAAAGAAAGTTCTTTATGTGGACCCTGAGTTC c.240
F E Q L H K K C L E K K V L Y V D P E F p.80
. . . . . . g.17003
CCACCGGATGAGACCTCTCTCTTTTATAGCCAGAAGTTCCCCATCCAGTTCGTCTGGAAG c.300
P P D E T S L F Y S Q K F P I Q F V W K p.100
| 02 . . . . . g.41431
AGACCTCCG | GAAATTTGCGAGAATCCCCGATTTATCATTGATGGAGCCAACAGAACTGAC c.360
R P P | E I C E N P R F I I D G A N R T D p.120
. | 03 . . . . g.43105
ATCTGTCAAGGAGAGCTAG | GGGACTGCTGGTTTCTCGCAGCCATTGCCTGCCTGACCCTG c.420
I C Q G E L G | D C W F L A A I A C L T L p.140
. . . . . . g.43165
AACCAGCACCTTCTTTTCCGAGTCATACCCCATGATCAAAGTTTCATCGAAAACTACGCA c.480
N Q H L L F R V I P H D Q S F I E N Y A p.160
. | 04 . . . . g.44692
GGGATCTTCCACTTCCAG | TTCTGGCGCTATGGAGAGTGGGTGGACGTGGTTATAGATGAC c.540
G I F H F Q | F W R Y G E W V D V V I D D p.180
. . . . . . g.44752
TGCCTGCCAACGTACAACAATCAACTGGTTTTCACCAAGTCCAACCACCGCAATGAGTTC c.600
C L P T Y N N Q L V F T K S N H R N E F p.200
. . . | 05 . . . g.45853
TGGAGTGCTCTGCTGGAGAAGGCTTATGCTAA | GCTCCATGGTTCCTACGAAGCTCTGAAA c.660
W S A L L E K A Y A K | L H G S Y E A L K p.220
. . . . . . g.45913
GGTGGGAACACCACAGAGGCCATGGAGGACTTCACAGGAGGGGTGGCAGAGTTTTTTGAG c.720
G G N T T E A M E D F T G G V A E F F E p.240
. . . . . . g.45973
ATCAGGGATGCTCCTAGTGACATGTACAAGATCATGAAGAAAGCCATCGAGAGAGGCTCC c.780
I R D A P S D M Y K I M K K A I E R G S p.260
. . | 06 . . . . g.46889
CTCATGGGCTGCTCCATTGAT | GATGGCACGAACATGACCTATGGAACCTCTCCTTCTGGT c.840
L M G C S I D | D G T N M T Y G T S P S G p.280
. . . . . . g.46949
CTGAACATGGGGGAGTTGATTGCACGGATGGTAAGGAATATGGATAACTCACTGCTCCAG c.900
L N M G E L I A R M V R N M D N S L L Q p.300
. . . . | 07 . . g.49551
GACTCAGACCTCGACCCCAGAGGCTCAGATGAAAGACCGACCCGG | ACAATCATTCCGGTT c.960
D S D L D P R G S D E R P T R | T I I P V p.320
. . . . . . g.49611
CAGTATGAGACAAGAATGGCCTGCGGGCTGGTCAGAGGTCACGCCTACTCTGTCACGGGG c.1020
Q Y E T R M A C G L V R G H A Y S V T G p.340
| 08 . . . . . g.51204
CTGGATGAG | GTCCCGTTCAAAGGTGAGAAAGTGAAGCTGGTGCGGCTGCGGAATCCGTGG c.1080
L D E | V P F K G E K V K L V R L R N P W p.360
. . . | 09 . . . g.53722
GGCCAGGTGGAGTGGAACGGTTCTTGGAGTGATAG | ATGGAAGGACTGGAGCTTTGTGGAC c.1140
G Q V E W N G S W S D R | W K D W S F V D p.380
. . . . . | 10 . g.56396
AAAGATGAGAAGGCCCGTCTGCAGCACCAGGTCACTGAGGATGGAGAGTTCTG | GATGTCC c.1200
K D E K A R L Q H Q V T E D G E F W | M S p.400
. . . . . . g.56456
TATGAGGATTTCATCTACCATTTCACAAAGTTGGAGATCTGCAACCTCACGGCCGATGCT c.1260
Y E D F I Y H F T K L E I C N L T A D A p.420
. . . . . . g.56516
CTGCAGTCTGACAAGCTTCAGACCTGGACAGTGTCTGTGAACGAGGGCCGCTGGGTACGG c.1320
L Q S D K L Q T W T V S V N E G R W V R p.440
. . . | 11 . . . g.58564
GGTTGCTCTGCCGGAGGCTGCCGCAACTTCCCAG | ATACTTTCTGGACCAACCCTCAGTAC c.1380
G C S A G G C R N F P D | T F W T N P Q Y p.460
. . . . . . g.58624
CGTCTGAAGCTCCTGGAGGAGGACGATGACCCTGATGACTCGGAGGTGATTTGCAGCTTC c.1440
R L K L L E E D D D P D D S E V I C S F p.480
. . . . . . g.58684
CTGGTGGCCCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGGCCAGTCTCTTC c.1500
L V A L M Q K N R R K D R K L G A S L F p.500
. . | 12 . | 13 . . . g.59715
ACCATTGGCTTCGCCATCTACGAG | GTTCCCAAAGAG | ATGCACGGGAACAAGCAGCACCTG c.1560
T I G F A I Y E | V P K E | M H G N K Q H L p.520
^ alternative promoter/first exon 13b
. . . . . . g.59775
CAGAAGGACTTCTTCCTGTACAACGCCTCCAAGGCCAGGAGCAAAACCTACATCAACATG c.1620
Q K D F F L Y N A S K A R S K T Y I N M p.540
. . . . . . g.59835
CGGGAGGTGTCCCAGCGCTTCCGCCTGCCTCCCAGCGAGTACGTCATCGTGCCCTCCACC c.1680
R E V S Q R F R L P P S E Y V I V P S T p.560
. . . . . . g.59895
TACGAGCCCCACCAGGAGGGGGAATTCATCCTCCGGGTCTTCTCTGAAAAGAGGAACCTC c.1740
Y E P H Q E G E F I L R V F S E K R N L p.580
| 14 . . . . | 15 . . g.62841
TCTGA | GGAAGTTGAAAATACCATCTCCGTGGATCGGCCAGTG | AAAAAGAAAAAAACCAAG c.1800
S E | E V E N T I S V D R P V | K K K K T K p.600
^ alternative promoter/first exon 15b
| 16 . . . . . . g.65168
| CCCATCATCTTCGTTTCGGACAGAGCAAACAGCAACAAGGAGCTGGGTGTGGACCAGGAG c.1860
| P I I F V S D R A N S N K E L G V D Q E p.620
. . . . . | 17 . g.66206
TCAGAGGAGGGCAAAGGCAAAACAAGCCCTGATAAGCAAAAGCAGTCCCCACAG | CCACAG c.1920
S E E G K G K T S P D K Q K Q S P Q | P Q p.640
. . . . . . g.66266
CCTGGCAGCTCTGATCAGGAAAGTGAGGAACAGCAACAATTCCGGAACATTTTCAAGCAG c.1980
P G S S D Q E S E E Q Q Q F R N I F K Q p.660
. | 18 . . . . . g.66732
ATAGCAGGAGAT | GACATGGAGATCTGTGCAGATGAGCTCAAGAAGGTCCTTAACACAGTC c.2040
I A G D | D M E I C A D E L K K V L N T V p.680
. | 19 . . . . . g.66878
GTGAACAAAC | ACAAGGACCTGAAGACACACGGGTTCACACTGGAGTCCTGCCGTAGCATG c.2100
V N K H | K D L K T H G F T L E S C R S M p.700
. | 20 . . . . . g.67370
ATTGCGCTCATGGAT | ACAGATGGCTCTGGAAAGCTCAACCTGCAGGAGTTCCACCACCTC c.2160
I A L M D | T D G S G K L N L Q E F H H L p.720
. . | 21 . . . . g.67521
TGGAACAAGATTAAGGCCTGGCAG | AAAATTTTCAAACACTATGACACAGACCAGTCCGGC c.2220
W N K I K A W Q | K I F K H Y D T D Q S G p.740
. . . . | 22 . . g.67798
ACCATCAACAGCTACGAGATGCGAAATGCAGTCAACGACGCAG | GATTCCACCTCAACAAC c.2280
T I N S Y E M R N A V N D A G | F H L N N p.760
. . . . . . g.67858
CAGCTCTATGACATCATTACCATGCGGTACGCAGACAAACACATGAACATCGACTTTGAC c.2340
Q L Y D I I T M R Y A D K H M N I D F D p.780
. . . . | 23 . . g.68204
AGTTTCATCTGCTGCTTCGTTAGGCTGGAGGGCATGTTCA | GAGCTTTTCATGCATTTGAC c.2400
S F I C C F V R L E G M F R | A F H A F D p.800
. . . | 24 . . g.68665
AAGGATGGAGATGGTATCATCAAGCTCAACGTTCTGGAG | TGGCTGCAGCTCACCATGTAT c.2460
K D G D G I I K L N V L E | W L Q L T M Y p.820
g.68671
GCCTGA c.2466
A X p.821
. . . . . . g.68731
accaggctggcctcatccaaagccatgcaggatcactcaggatttcagtttcaccctcta c.*60
. . . . . . g.68791
tttccaaagccatttacctcaaaggacccagcagctacacccctacaggcttccaggcac c.*120
. . . . . . g.68851
ctcatcagtcatgctcctcctccattttaccccctacccatccttgatcggtcatgccta c.*180
. . . . . . g.68911
gcctgaccctttagtaaagcaatgaggtaggaagaacaaacccttgtccctttgccatgt c.*240
. . . . . . g.68971
ggaggaaagtgcctgcctctggtccgagccgcctcggttctgaagcgagtgctcctgctt c.*300
. . . . . . g.69031
accttgctctaggctgtctgcagaagcacctgccggtggcactcagcacctccttgtgct c.*360
. . . . . . g.69091
agagccctccatcaccttcacgctgtcccaccatgggccaggaaccaaaccagcactggg c.*420
. . . . . . g.69151
ttctactgctgtggggtaaactaactcagtggaatagggctggttactttgggctgtcca c.*480
. . . . . . g.69211
actcataagtttggctgcattttgaaaaaagctgatctaaataaaggcatgtgtatggct c.*540
g.69215
ggtc c.*544
(downstream sequence)
Legend:
Powered by LOVDv.2.0-20 Build 20
©2004-2009 Leiden University Medical Center