Incidental Mutation 'R7048:Clcn1'
ID 547430
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 045146-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7048 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 42263619-42292690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 42284477 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 605 (V605A)
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: V605A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000031894
Gene: ENSMUSG00000029862
AA Change: V605A

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000163235
SMART Domains Protein: ENSMUSP00000132387
Gene: ENSMUSG00000029862

DomainStartEndE-ValueType
low complexity region 12 36 N/A INTRINSIC
Predicted Effect
SMART Domains Protein: ENSMUSP00000130148
Gene: ENSMUSG00000029862
AA Change: V533A

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
low complexity region 92 101 N/A INTRINSIC
Pfam:Voltage_CLC 141 261 2.9e-24 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000170028
SMART Domains Protein: ENSMUSP00000132154
Gene: ENSMUSG00000029862

DomainStartEndE-ValueType
low complexity region 92 101 N/A INTRINSIC
Pfam:Voltage_CLC 141 235 8e-22 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 97% (66/68)
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrl2 T C 3: 148,552,565 (GRCm39) D629G probably damaging Het
Akap11 T A 14: 78,749,954 (GRCm39) Q811L Het
Ank2 T A 3: 126,819,267 (GRCm39) Q468L probably benign Het
Ano3 A T 2: 110,513,116 (GRCm39) Y626* probably null Het
Ap1m1 A G 8: 73,003,642 (GRCm39) N114S probably damaging Het
Asb3 T A 11: 31,051,121 (GRCm39) I525N probably damaging Het
Atg4a-ps A G 3: 103,552,672 (GRCm39) I223T probably damaging Het
B3gnt7 T C 1: 86,233,308 (GRCm39) Y68H probably benign Het
Bbs5 T C 2: 69,484,705 (GRCm39) I125T probably benign Het
Cd180 A G 13: 102,841,431 (GRCm39) N159S probably damaging Het
Cd37 T C 7: 44,887,888 (GRCm39) probably benign Het
Cdk14 T A 5: 5,143,005 (GRCm39) Q242L probably damaging Het
Cped1 G A 6: 22,119,469 (GRCm39) M309I probably benign Het
Cyp2r1 A T 7: 114,151,971 (GRCm39) Y120N probably damaging Het
Ddx3y A T Y: 1,279,491 (GRCm39) S124R probably benign Het
Dlec1 A T 9: 118,972,472 (GRCm39) probably null Het
Dnah17 T C 11: 117,936,944 (GRCm39) E3420G possibly damaging Het
Dnajc13 C T 9: 104,080,613 (GRCm39) probably null Het
Dusp23 A T 1: 172,459,253 (GRCm39) Y136* probably null Het
Eif4b A G 15: 102,001,571 (GRCm39) probably benign Het
F13a1 A G 13: 37,082,117 (GRCm39) V529A probably benign Het
Fhl2 A G 1: 43,162,808 (GRCm39) Y236H probably damaging Het
Gm826 C T 2: 160,169,026 (GRCm39) W94* probably null Het
Gpsm2 C T 3: 108,610,361 (GRCm39) R33H probably damaging Het
Hmcn1 T C 1: 150,475,404 (GRCm39) probably null Het
Ifit1bl2 T C 19: 34,596,551 (GRCm39) D355G probably benign Het
Itga8 A G 2: 12,115,895 (GRCm39) V77A probably damaging Het
Kcmf1 C T 6: 72,826,450 (GRCm39) R40K probably damaging Het
Kdm7a T C 6: 39,145,982 (GRCm39) E315G probably damaging Het
Kmt2b C T 7: 30,268,731 (GRCm39) G2666D probably damaging Het
Lrrtm1 A G 6: 77,221,152 (GRCm39) N203S probably damaging Het
Mdn1 A G 4: 32,767,969 (GRCm39) N5301D probably benign Het
Mest T G 6: 30,742,723 (GRCm39) H108Q probably damaging Het
Mettl25b A G 3: 87,837,167 (GRCm39) I36T probably damaging Het
Moxd1 C A 10: 24,157,374 (GRCm39) D335E probably damaging Het
Ncf2 A C 1: 152,683,921 (GRCm39) N47H probably benign Het
Npc1 A G 18: 12,337,822 (GRCm39) probably null Het
Or14j2 A T 17: 37,886,114 (GRCm39) S67T probably damaging Het
Pcid2 A G 8: 13,128,243 (GRCm39) V386A probably benign Het
Phactr2 T A 10: 13,121,168 (GRCm39) T444S probably benign Het
Plekha7 T C 7: 115,747,559 (GRCm39) N710D probably benign Het
Ppp1r16b C T 2: 158,599,174 (GRCm39) T382I probably benign Het
Pramel15 T C 4: 144,103,754 (GRCm39) D124G probably benign Het
Ptprz1 A T 6: 22,961,622 (GRCm39) Y111F probably benign Het
Rbbp8 A G 18: 11,865,277 (GRCm39) E722G possibly damaging Het
Rimbp3 A G 16: 17,028,190 (GRCm39) D538G probably benign Het
Rims1 A G 1: 22,511,901 (GRCm39) S551P probably damaging Het
Rsrc1 A G 3: 67,088,164 (GRCm39) D166G probably damaging Het
Selenon T C 4: 134,270,154 (GRCm39) N350S probably benign Het
Sh3gl2 T A 4: 85,295,802 (GRCm39) L168H probably damaging Het
Smc3 T C 19: 53,617,682 (GRCm39) Y560H probably benign Het
Syce1 C T 7: 140,359,281 (GRCm39) D147N possibly damaging Het
Syt10 A C 15: 89,675,008 (GRCm39) V446G probably damaging Het
Taar1 T C 10: 23,796,722 (GRCm39) L140P probably benign Het
Tfpi2 C A 6: 3,968,032 (GRCm39) C36F probably damaging Het
Thoc5 G A 11: 4,876,237 (GRCm39) probably null Het
Tnrc6c T A 11: 117,612,800 (GRCm39) N319K probably benign Het
Trhr2 C T 8: 123,085,418 (GRCm39) D189N probably damaging Het
Trim42 A T 9: 97,245,474 (GRCm39) F442Y probably damaging Het
Ubap2 G A 4: 41,196,033 (GRCm39) T949I possibly damaging Het
Ugt1a8 T C 1: 88,016,024 (GRCm39) F146L probably benign Het
Vmn2r80 C A 10: 79,030,153 (GRCm39) Q660K probably damaging Het
Vstm2b C T 7: 40,578,800 (GRCm39) T258I possibly damaging Het
Washc2 T C 6: 116,197,544 (GRCm39) L259P possibly damaging Het
Zscan18 A T 7: 12,508,671 (GRCm39) probably benign Het
Zzef1 T G 11: 72,757,525 (GRCm39) Y1193* probably null Het
Other mutations in Clcn1
AlleleSourceChrCoordTypePredicted EffectPPH 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
R5628:Clcn1 UTSW 6 42,275,823 (GRCm39) missense probably damaging 0.96
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
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'- AAGCTTCCCTATCTGCCAGAC -3'
(R):5'- AACCTGCTAGTCACCAGCTG -3'

Sequencing Primer
(F):5'- TTGGAACCAGCTCAGGTCAG -3'
(R):5'- GGGTAGTCTTAGTTGGCATCCTTAC -3'
Posted On 2019-05-13