Incidental Mutation 'R1793:Clcn1'
ID 201925
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 039823-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1793 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 42263619-42292690 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to A at 42275860 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000031894 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031894] [ENSMUST00000164091] [ENSMUST00000168660]
AlphaFold Q64347
Predicted Effect probably null
Transcript: ENSMUST00000031894
SMART Domains Protein: ENSMUSP00000031894
Gene: ENSMUSG00000029862

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 noncoding transcript
Transcript: ENSMUST00000114684
SMART Domains Protein: ENSMUSP00000110332
Gene: ENSMUSG00000029862

DomainStartEndE-ValueType
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

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
Meta Mutation Damage Score 0.9495 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.4%
  • 20x: 92.9%
Validation Efficiency 100% (122/122)
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: 118 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522L14Rik A T 5: 109,884,144 (GRCm39) H571Q probably damaging Het
Abcf2 T A 5: 24,773,774 (GRCm39) M372L probably benign Het
Acaca A C 11: 84,206,795 (GRCm39) T1552P probably damaging Het
Acaca A G 11: 84,229,219 (GRCm39) D1682G probably damaging Het
Acvr1b T C 15: 101,091,906 (GRCm39) V62A probably benign Het
Aimp1 C T 3: 132,379,825 (GRCm39) V97M probably benign Het
Aldh1l1 C T 6: 90,554,813 (GRCm39) T557I possibly damaging Het
Alpk1 T C 3: 127,471,447 (GRCm39) T1012A probably damaging Het
Amot G A X: 144,233,585 (GRCm39) probably benign Het
Arap1 T A 7: 101,037,829 (GRCm39) H477Q probably benign Het
Arhgap18 T A 10: 26,736,732 (GRCm39) probably benign Het
Arhgef10l C T 4: 140,242,684 (GRCm39) V862M probably damaging Het
Arl4d A G 11: 101,557,554 (GRCm39) I27V probably benign Het
Asb18 G A 1: 89,942,277 (GRCm39) P8L probably damaging Het
Ash1l A G 3: 88,977,616 (GRCm39) H2682R probably damaging Het
Aspm T A 1: 139,385,079 (GRCm39) V241E probably benign Het
Atf7ip G T 6: 136,586,217 (GRCm39) probably benign Het
AY358078 T G 14: 52,042,051 (GRCm39) M142R unknown Het
C3 T A 17: 57,526,592 (GRCm39) K796N possibly damaging Het
Ceacam16 T C 7: 19,590,041 (GRCm39) T301A probably damaging Het
Ceacam5 T G 7: 17,481,320 (GRCm39) Y356D probably benign Het
Cep192 C T 18: 67,984,838 (GRCm39) A1616V possibly damaging Het
Cfap91 T A 16: 38,141,781 (GRCm39) N384Y possibly damaging Het
Cherp A T 8: 73,216,994 (GRCm39) H645Q probably benign Het
CK137956 T C 4: 127,845,242 (GRCm39) D167G probably benign Het
Cntn1 C T 15: 92,189,552 (GRCm39) T625I possibly damaging Het
Cpn2 T A 16: 30,078,142 (GRCm39) N520Y probably damaging Het
Crocc G A 4: 140,746,620 (GRCm39) R1762W probably damaging Het
Cts3 C A 13: 61,715,967 (GRCm39) V100F probably benign Het
Ddx56 A T 11: 6,216,934 (GRCm39) V87D probably damaging Het
Dnah9 C T 11: 66,010,420 (GRCm39) probably null Het
Dock1 T A 7: 134,700,456 (GRCm39) probably null Het
Dst T A 1: 34,191,552 (GRCm39) Y291* probably null Het
Eif4g3 T C 4: 137,898,442 (GRCm39) I1071T probably damaging Het
Fblim1 T C 4: 141,322,549 (GRCm39) Q78R probably damaging Het
Fcamr C T 1: 130,739,284 (GRCm39) P195S probably benign Het
Fcho1 G A 8: 72,161,666 (GRCm39) Q835* probably null Het
Frem3 A G 8: 81,339,741 (GRCm39) N678S probably benign Het
Frk G A 10: 34,483,878 (GRCm39) R413H probably benign Het
Gm10619 C A 7: 73,459,758 (GRCm39) noncoding transcript Het
Gm12185 G A 11: 48,806,583 (GRCm39) R203* probably null Het
Gm12886 A G 4: 121,280,174 (GRCm39) V34A probably benign Het
Gna12 A T 5: 140,746,707 (GRCm39) I246N probably damaging Het
Gpm6a T C 8: 55,507,867 (GRCm39) M201T probably benign Het
Gpsm2 T G 3: 108,608,225 (GRCm39) D220A probably benign Het
Grip2 C G 6: 91,760,623 (GRCm39) V325L probably benign Het
Grk5 C A 19: 61,065,200 (GRCm39) A288D probably damaging Het
Herpud2 G A 9: 25,021,953 (GRCm39) A231V possibly damaging Het
Hmcn1 T C 1: 150,624,834 (GRCm39) S1024G probably benign Het
Hp1bp3 A G 4: 137,957,820 (GRCm39) D295G probably damaging Het
Igsf21 T C 4: 139,761,703 (GRCm39) H325R probably damaging Het
Ing2 T A 8: 48,122,364 (GRCm39) L61F probably damaging Het
Jak3 T C 8: 72,138,590 (GRCm39) probably benign Het
Kcnn3 T A 3: 89,516,712 (GRCm39) C374S probably benign Het
Klk1b22 A G 7: 43,765,775 (GRCm39) probably benign Het
Larp1 T C 11: 57,940,764 (GRCm39) M630T possibly damaging Het
Lhx5 T A 5: 120,572,725 (GRCm39) C115S probably damaging Het
Lmcd1 C A 6: 112,305,712 (GRCm39) T271K probably benign Het
Lpar1 G A 4: 58,486,798 (GRCm39) R158* probably null Het
Lyst T A 13: 13,821,668 (GRCm39) C1347* probably null Het
Map3k8 G A 18: 4,332,389 (GRCm39) Q441* probably null Het
Mboat1 T C 13: 30,403,633 (GRCm39) V144A probably damaging Het
Mcur1 C T 13: 43,713,491 (GRCm39) G38S unknown Het
Med13 T A 11: 86,220,177 (GRCm39) M276L probably benign Het
Mefv A G 16: 3,526,528 (GRCm39) S699P possibly damaging Het
Mfsd4a C A 1: 131,987,077 (GRCm39) A62S probably damaging Het
Mmp27 A G 9: 7,571,459 (GRCm39) M1V probably null Het
Myo1c C T 11: 75,548,415 (GRCm39) T58I probably damaging Het
Myom3 A T 4: 135,538,066 (GRCm39) D1316V probably benign Het
Naa25 T A 5: 121,555,478 (GRCm39) C235S possibly damaging Het
Naa25 C A 5: 121,558,656 (GRCm39) R333S probably damaging Het
Nav3 G A 10: 109,539,233 (GRCm39) T2056I probably benign Het
Nol4 A G 18: 22,902,878 (GRCm39) Y378H probably damaging Het
Npat G A 9: 53,463,589 (GRCm39) R124Q probably damaging Het
Npr3 T A 15: 11,848,665 (GRCm39) E434V probably benign Het
Nptx2 A G 5: 144,485,130 (GRCm39) T208A probably benign Het
Obscn C T 11: 58,968,606 (GRCm39) V2798M probably damaging Het
Odad4 C A 11: 100,460,679 (GRCm39) probably null Het
Or10j7 A T 1: 173,011,976 (GRCm39) H8Q probably benign Het
Or52r1 A G 7: 102,537,250 (GRCm39) Y37H probably benign Het
Or5b122 C T 19: 13,562,779 (GRCm39) T37I probably benign Het
Padi1 G A 4: 140,541,967 (GRCm39) P652S probably damaging Het
Pcdh1 G T 18: 38,331,938 (GRCm39) P355Q probably damaging Het
Pck2 G A 14: 55,781,422 (GRCm39) R189H possibly damaging Het
Pcsk5 T A 19: 17,432,114 (GRCm39) K1500N possibly damaging Het
Phc3 A T 3: 31,002,865 (GRCm39) S218T probably damaging Het
Piezo2 T A 18: 63,239,355 (GRCm39) M510L possibly damaging Het
Polr1g T C 7: 19,091,904 (GRCm39) T68A possibly damaging Het
Ppp1r3a A T 6: 14,754,717 (GRCm39) Y177N probably damaging Het
Psme2b A T 11: 48,836,361 (GRCm39) D195E probably damaging Het
Ptprr T C 10: 116,088,827 (GRCm39) V463A probably damaging Het
Pwwp2b G A 7: 138,836,281 (GRCm39) R574Q probably damaging Het
Rap1gds1 T A 3: 138,756,314 (GRCm39) T14S possibly damaging Het
Rbm11 A T 16: 75,397,685 (GRCm39) K205M probably damaging Het
Rfx1 T A 8: 84,793,050 (GRCm39) probably benign Het
Rnasel C A 1: 153,630,169 (GRCm39) H228Q probably damaging Het
Sap130 T A 18: 31,831,640 (GRCm39) I710K probably benign Het
Slc27a4 C A 2: 29,695,733 (GRCm39) D89E probably benign Het
Spata31d1b T C 13: 59,863,779 (GRCm39) V309A probably benign Het
Syt7 T G 19: 10,421,354 (GRCm39) Y420D probably damaging Het
Tanc2 A G 11: 105,515,859 (GRCm39) probably null Het
Tbc1d10b A G 7: 126,802,930 (GRCm39) S333P possibly damaging Het
Tenm2 G A 11: 35,914,209 (GRCm39) P2442S probably damaging Het
Tenm3 C T 8: 49,127,579 (GRCm39) C33Y probably damaging Het
Timmdc1 A G 16: 38,319,419 (GRCm39) L245P possibly damaging Het
Tlr5 T C 1: 182,800,012 (GRCm39) F5L probably benign Het
Ttll4 T A 1: 74,726,999 (GRCm39) F784L possibly damaging Het
Tulp4 A G 17: 6,189,387 (GRCm39) T70A possibly damaging Het
Txndc17 T A 11: 72,099,571 (GRCm39) N81K probably benign Het
Ubr3 C T 2: 69,830,895 (GRCm39) probably benign Het
Uri1 A C 7: 37,681,116 (GRCm39) V96G probably damaging Het
Uspl1 T A 5: 149,150,246 (GRCm39) I482N probably damaging Het
Vmn1r229 A G 17: 21,034,974 (GRCm39) N73S possibly damaging Het
Vwa7 G T 17: 35,243,388 (GRCm39) G689* probably null Het
Zfp114 T A 7: 23,877,164 (GRCm39) probably null Het
Zfp618 A G 4: 63,051,474 (GRCm39) S659G probably damaging Het
Zfp872 A G 9: 22,111,349 (GRCm39) K275R probably damaging Het
Zzef1 C T 11: 72,777,535 (GRCm39) P1789S probably damaging 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
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
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'- GCAGACTCACAACTCAGGTG -3'
(R):5'- CCTACTAGCATCTCGCCATG -3'

Sequencing Primer
(F):5'- AGGTGAAGCTCCTGAGGTC -3'
(R):5'- GCCATGCTTATACTCTCAAACCATG -3'
Posted On 2014-06-23