Incidental Mutation 'R5628:Clcn1'
| ID |
441920 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Clcn1
|
| Ensembl Gene |
ENSMUSG00000029862 |
| Gene Name |
chloride channel, voltage-sensitive 1 |
| Synonyms |
Clc1, SMCC1, NMF355, Clc-1, nmf355 |
| MMRRC Submission |
043167-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R5628 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
6 |
| Chromosomal Location |
42263619-42292690 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 42275823 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 315
(V315A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000031894
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031894]
[ENSMUST00000164091]
[ENSMUST00000168660]
|
| AlphaFold |
Q64347 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000031894
AA Change: V315A
PolyPhen 2
Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000031894
Gene: ENSMUSG00000029862
AA Change: V315A
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
121 |
130 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
170 |
572 |
3.2e-87 |
PFAM |
|
Blast:CBS
|
612 |
662 |
1e-24 |
BLAST |
|
low complexity region
|
723 |
747 |
N/A |
INTRINSIC |
|
Blast:CBS
|
830 |
877 |
4e-19 |
BLAST |
|
low complexity region
|
928 |
950 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000114684
|
| SMART Domains |
Protein: ENSMUSP00000110332
Gene: ENSMUSG00000029862
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Voltage_CLC
|
3 |
254 |
2.6e-42 |
PFAM |
|
CBS
|
294 |
344 |
1.3e1 |
SMART |
|
low complexity region
|
405 |
429 |
N/A |
INTRINSIC |
|
Blast:CBS
|
480 |
524 |
2e-13 |
BLAST |
|
low complexity region
|
575 |
597 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000163936
|
| SMART Domains |
Protein: ENSMUSP00000130148
Gene: ENSMUSG00000029862
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
92 |
101 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
141 |
261 |
1.2e-27 |
PFAM |
|
Pfam:Voltage_CLC
|
258 |
501 |
3.9e-44 |
PFAM |
|
PDB:2D4Z|B
|
520 |
807 |
2e-47 |
PDB |
|
Blast:CBS
|
541 |
591 |
2e-24 |
BLAST |
|
Blast:CBS
|
759 |
806 |
3e-19 |
BLAST |
|
low complexity region
|
857 |
879 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000164091
|
| SMART Domains |
Protein: ENSMUSP00000131354
Gene: ENSMUSG00000029862
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
121 |
130 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
170 |
256 |
2.9e-20 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000165780
|
| SMART Domains |
Protein: ENSMUSP00000130550
Gene: ENSMUSG00000029862
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
92 |
101 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
141 |
227 |
9.7e-22 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000168660
|
| SMART Domains |
Protein: ENSMUSP00000126045
Gene: ENSMUSG00000029862
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
88 |
97 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
136 |
257 |
1.1e-22 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169024
|
| SMART Domains |
Protein: ENSMUSP00000130968
Gene: ENSMUSG00000029862
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
92 |
101 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
141 |
261 |
2.9e-24 |
PFAM |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000170028
AA Change: C259R
|
| SMART Domains |
Protein: ENSMUSP00000132154
Gene: ENSMUSG00000029862
AA Change: C259R
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
92 |
101 |
N/A |
INTRINSIC |
|
Pfam:Voltage_CLC
|
141 |
235 |
8e-22 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.7%
- 10x: 97.3%
- 20x: 95.5%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. The protein encoded by this gene regulates the electric excitability of the skeletal muscle membrane. Mutations in this gene cause two forms of inherited human muscle disorders: recessive generalized myotonia congenita (Becker) and dominant myotonia (Thomsen). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]
PHENOTYPE: Mutant mice exhibit mild to severe spasms of the hind limbs and abnormal hind limb reflexes. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam25 |
A |
G |
8: 41,208,747 (GRCm39) |
D671G |
probably benign |
Het |
| Ap3b1 |
A |
G |
13: 94,613,556 (GRCm39) |
D685G |
unknown |
Het |
| Atp6v1h |
G |
A |
1: 5,206,112 (GRCm39) |
W358* |
probably null |
Het |
| Atr |
T |
A |
9: 95,756,279 (GRCm39) |
Y830* |
probably null |
Het |
| B3galnt2 |
A |
T |
13: 14,169,737 (GRCm39) |
|
probably null |
Het |
| Casz1 |
T |
C |
4: 149,030,553 (GRCm39) |
Y1191H |
probably damaging |
Het |
| Cdc40 |
T |
G |
10: 40,727,049 (GRCm39) |
E169D |
probably benign |
Het |
| Cep55 |
C |
T |
19: 38,058,396 (GRCm39) |
Q330* |
probably null |
Het |
| Cmya5 |
A |
G |
13: 93,226,218 (GRCm39) |
F2957L |
probably damaging |
Het |
| Dnah2 |
C |
T |
11: 69,349,746 (GRCm39) |
R2399Q |
probably benign |
Het |
| Dync1li2 |
T |
C |
8: 105,147,224 (GRCm39) |
N490S |
possibly damaging |
Het |
| Ephb3 |
T |
C |
16: 21,036,869 (GRCm39) |
Y111H |
probably damaging |
Het |
| Fam186a |
A |
C |
15: 99,839,628 (GRCm39) |
H2205Q |
possibly damaging |
Het |
| Fat3 |
T |
C |
9: 15,877,392 (GRCm39) |
Y3407C |
probably damaging |
Het |
| Fbxw8 |
A |
G |
5: 118,230,622 (GRCm39) |
V393A |
probably damaging |
Het |
| Fnip1 |
A |
T |
11: 54,394,459 (GRCm39) |
D965V |
probably benign |
Het |
| Gramd2a |
T |
C |
9: 59,615,006 (GRCm39) |
M3T |
probably benign |
Het |
| Kctd15 |
T |
C |
7: 34,339,720 (GRCm39) |
D283G |
probably damaging |
Het |
| Kif9 |
C |
T |
9: 110,343,621 (GRCm39) |
R547* |
probably null |
Het |
| Map4 |
A |
G |
9: 109,910,915 (GRCm39) |
T245A |
probably benign |
Het |
| Mindy4 |
C |
T |
6: 55,237,579 (GRCm39) |
L385F |
probably damaging |
Het |
| Myo7b |
A |
G |
18: 32,107,240 (GRCm39) |
C1252R |
probably benign |
Het |
| Myt1l |
T |
A |
12: 29,861,620 (GRCm39) |
I134N |
unknown |
Het |
| Or5m10b |
T |
A |
2: 85,699,149 (GRCm39) |
I71N |
probably damaging |
Het |
| Osgin2 |
T |
A |
4: 15,998,998 (GRCm39) |
N208I |
probably benign |
Het |
| Polr2b |
G |
A |
5: 77,461,063 (GRCm39) |
V29M |
probably damaging |
Het |
| Prdm15 |
T |
A |
16: 97,600,823 (GRCm39) |
M812L |
probably damaging |
Het |
| Prr36 |
TGCTTTGCTGGTCTGTGGAAGAGCGGCTTTGCTGGTCTGTGGAAGAGCGGCTTTGCTGGTCTGTGGAAGAGCGGCTTTGC |
TGCTTTGCTGGTCTGTGGAAGAGCGGCTTTGCTGGTCTGTGGAAGAGCGGCTTTGC |
8: 4,266,273 (GRCm39) |
|
probably benign |
Het |
| Rev3l |
T |
A |
10: 39,698,963 (GRCm39) |
N1153K |
probably damaging |
Het |
| Rnf17 |
A |
G |
14: 56,724,409 (GRCm39) |
|
probably null |
Het |
| Rusc2 |
C |
T |
4: 43,425,348 (GRCm39) |
T1151M |
probably damaging |
Het |
| Scrib |
T |
C |
15: 75,921,389 (GRCm39) |
T30A |
possibly damaging |
Het |
| Sephs1 |
T |
C |
2: 4,894,018 (GRCm39) |
I73T |
probably benign |
Het |
| Sf3b1 |
C |
T |
1: 55,037,334 (GRCm39) |
A861T |
probably benign |
Het |
| Shq1 |
A |
G |
6: 100,607,964 (GRCm39) |
W316R |
probably damaging |
Het |
| Slc26a5 |
T |
A |
5: 22,021,974 (GRCm39) |
D484V |
probably benign |
Het |
| Smg1 |
C |
T |
7: 117,753,924 (GRCm39) |
|
probably benign |
Het |
| Stard5 |
T |
C |
7: 83,282,355 (GRCm39) |
I56T |
probably benign |
Het |
| Szt2 |
A |
G |
4: 118,230,414 (GRCm39) |
V2653A |
unknown |
Het |
| Tmem217 |
A |
T |
17: 29,745,430 (GRCm39) |
I100N |
probably damaging |
Het |
| Trpm2 |
C |
T |
10: 77,748,470 (GRCm39) |
R1400Q |
probably benign |
Het |
| Vmn1r82 |
T |
G |
7: 12,039,205 (GRCm39) |
N41K |
probably damaging |
Het |
| Zfp236 |
T |
C |
18: 82,675,247 (GRCm39) |
D367G |
probably damaging |
Het |
| Zfyve1 |
A |
T |
12: 83,621,663 (GRCm39) |
V244E |
probably benign |
Het |
|
| Other mutations in Clcn1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01473:Clcn1
|
APN |
6 |
42,268,637 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01732:Clcn1
|
APN |
6 |
42,287,606 (GRCm39) |
splice site |
probably benign |
|
|
IGL02055:Clcn1
|
APN |
6 |
42,284,489 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02507:Clcn1
|
APN |
6 |
42,284,007 (GRCm39) |
splice site |
probably benign |
|
|
IGL02649:Clcn1
|
APN |
6 |
42,275,763 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02739:Clcn1
|
APN |
6 |
42,263,714 (GRCm39) |
splice site |
probably null |
|
|
IGL03148:Clcn1
|
APN |
6 |
42,276,925 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL03190:Clcn1
|
APN |
6 |
42,267,037 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL03327:Clcn1
|
APN |
6 |
42,288,153 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03346:Clcn1
|
APN |
6 |
42,288,153 (GRCm39) |
missense |
probably benign |
0.00 |
|
Faint
|
UTSW |
6 |
42,284,199 (GRCm39) |
missense |
probably damaging |
1.00 |
|
jack_spratt
|
UTSW |
6 |
42,287,515 (GRCm39) |
missense |
probably benign |
|
|
Limitations
|
UTSW |
6 |
42,286,997 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
maimed
|
UTSW |
6 |
42,275,754 (GRCm39) |
missense |
probably damaging |
1.00 |
|
stunted
|
UTSW |
6 |
42,263,701 (GRCm39) |
start codon destroyed |
possibly damaging |
0.79 |
|
R0167:Clcn1
|
UTSW |
6 |
42,263,770 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0323:Clcn1
|
UTSW |
6 |
42,287,074 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R0491:Clcn1
|
UTSW |
6 |
42,287,515 (GRCm39) |
missense |
probably benign |
|
|
R0573:Clcn1
|
UTSW |
6 |
42,289,979 (GRCm39) |
splice site |
probably null |
|
|
R0615:Clcn1
|
UTSW |
6 |
42,282,509 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0944:Clcn1
|
UTSW |
6 |
42,290,075 (GRCm39) |
missense |
probably benign |
0.00 |
|
R1562:Clcn1
|
UTSW |
6 |
42,277,169 (GRCm39) |
missense |
probably benign |
0.29 |
|
R1566:Clcn1
|
UTSW |
6 |
42,268,374 (GRCm39) |
missense |
possibly damaging |
0.58 |
|
R1692:Clcn1
|
UTSW |
6 |
42,290,032 (GRCm39) |
missense |
possibly damaging |
0.67 |
|
R1728:Clcn1
|
UTSW |
6 |
42,276,448 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R1729:Clcn1
|
UTSW |
6 |
42,276,448 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R1772:Clcn1
|
UTSW |
6 |
42,271,079 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1784:Clcn1
|
UTSW |
6 |
42,276,448 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
R1793:Clcn1
|
UTSW |
6 |
42,275,860 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1861:Clcn1
|
UTSW |
6 |
42,290,925 (GRCm39) |
missense |
possibly damaging |
0.63 |
|
R1864:Clcn1
|
UTSW |
6 |
42,282,475 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1865:Clcn1
|
UTSW |
6 |
42,282,475 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2356:Clcn1
|
UTSW |
6 |
42,268,559 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2403:Clcn1
|
UTSW |
6 |
42,290,046 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R2987:Clcn1
|
UTSW |
6 |
42,275,784 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3082:Clcn1
|
UTSW |
6 |
42,267,112 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R3500:Clcn1
|
UTSW |
6 |
42,269,929 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3747:Clcn1
|
UTSW |
6 |
42,276,849 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3748:Clcn1
|
UTSW |
6 |
42,276,849 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4041:Clcn1
|
UTSW |
6 |
42,286,902 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4749:Clcn1
|
UTSW |
6 |
42,267,131 (GRCm39) |
splice site |
probably null |
|
|
R4836:Clcn1
|
UTSW |
6 |
42,286,898 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R5021:Clcn1
|
UTSW |
6 |
42,287,922 (GRCm39) |
nonsense |
probably null |
|
|
R5085:Clcn1
|
UTSW |
6 |
42,290,814 (GRCm39) |
missense |
probably benign |
0.41 |
|
R5528:Clcn1
|
UTSW |
6 |
42,277,275 (GRCm39) |
missense |
probably benign |
0.01 |
|
R5678:Clcn1
|
UTSW |
6 |
42,284,199 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5943:Clcn1
|
UTSW |
6 |
42,269,900 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6053:Clcn1
|
UTSW |
6 |
42,277,208 (GRCm39) |
nonsense |
probably null |
|
|
R6175:Clcn1
|
UTSW |
6 |
42,291,096 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6394:Clcn1
|
UTSW |
6 |
42,290,172 (GRCm39) |
missense |
possibly damaging |
0.82 |
|
R6394:Clcn1
|
UTSW |
6 |
42,284,524 (GRCm39) |
missense |
possibly damaging |
0.84 |
|
R7012:Clcn1
|
UTSW |
6 |
42,267,542 (GRCm39) |
missense |
probably benign |
0.01 |
|
R7020:Clcn1
|
UTSW |
6 |
42,275,754 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7048:Clcn1
|
UTSW |
6 |
42,284,477 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7212:Clcn1
|
UTSW |
6 |
42,268,323 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R7225:Clcn1
|
UTSW |
6 |
42,270,396 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7264:Clcn1
|
UTSW |
6 |
42,275,772 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7636:Clcn1
|
UTSW |
6 |
42,268,268 (GRCm39) |
nonsense |
probably null |
|
|
R7663:Clcn1
|
UTSW |
6 |
42,286,997 (GRCm39) |
missense |
possibly damaging |
0.79 |
|
R7807:Clcn1
|
UTSW |
6 |
42,287,282 (GRCm39) |
splice site |
probably null |
|
|
R7954:Clcn1
|
UTSW |
6 |
42,263,625 (GRCm39) |
unclassified |
probably benign |
|
|
R8026:Clcn1
|
UTSW |
6 |
42,284,595 (GRCm39) |
critical splice donor site |
probably null |
|
|
R8045:Clcn1
|
UTSW |
6 |
42,267,628 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8499:Clcn1
|
UTSW |
6 |
42,284,133 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8523:Clcn1
|
UTSW |
6 |
42,284,523 (GRCm39) |
nonsense |
probably null |
|
|
R8677:Clcn1
|
UTSW |
6 |
42,267,519 (GRCm39) |
critical splice acceptor site |
probably null |
|
|
R8818:Clcn1
|
UTSW |
6 |
42,282,477 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8945:Clcn1
|
UTSW |
6 |
42,263,701 (GRCm39) |
start codon destroyed |
possibly damaging |
0.79 |
|
R9012:Clcn1
|
UTSW |
6 |
42,268,567 (GRCm39) |
missense |
possibly damaging |
0.75 |
|
R9295:Clcn1
|
UTSW |
6 |
42,290,883 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9433:Clcn1
|
UTSW |
6 |
42,282,494 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9513:Clcn1
|
UTSW |
6 |
42,282,462 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9679:Clcn1
|
UTSW |
6 |
42,263,753 (GRCm39) |
missense |
probably damaging |
0.98 |
|
Z1088:Clcn1
|
UTSW |
6 |
42,284,190 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1088:Clcn1
|
UTSW |
6 |
42,277,294 (GRCm39) |
missense |
probably benign |
0.40 |
|
Z1176:Clcn1
|
UTSW |
6 |
42,284,501 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- CATTGGTGCTTCGCAGACTC -3'
(R):5'- CGCCATGCTTATACTCTCAAAC -3'
Sequencing Primer
(F):5'- TTCGCAGACTCACAACTCAGGTG -3'
(R):5'- AAACCATGATCTAGTTTTCTCCCTAG -3'
|
| Posted On |
2016-11-08 |
Incidental Mutation