Incidental Mutation 'R5085:Clcn1'
ID 387366
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 042674-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5085 (G1)
Quality Score 192
Status Validated
Chromosome 6
Chromosomal Location 42263619-42292690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 42290814 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 896 (T896I)
Ref Sequence ENSEMBL: ENSMUSP00000031894 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031891] [ENSMUST00000031894] [ENSMUST00000095974] [ENSMUST00000143278] [ENSMUST00000168660] [ENSMUST00000164091]
AlphaFold Q64347
Predicted Effect probably benign
Transcript: ENSMUST00000031891
SMART Domains Protein: ENSMUSP00000031891
Gene: ENSMUSG00000029861

DomainStartEndE-ValueType
Pfam:FAM131 49 341 7.4e-128 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000031894
AA Change: T896I

PolyPhen 2 Score 0.410 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000031894
Gene: ENSMUSG00000029862
AA Change: T896I

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: ENSMUST00000095974
SMART Domains Protein: ENSMUSP00000093670
Gene: ENSMUSG00000029861

DomainStartEndE-ValueType
Pfam:FAM131 33 325 4.5e-128 PFAM
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: ENSMUST00000143278
SMART Domains Protein: ENSMUSP00000116779
Gene: ENSMUSG00000029861

DomainStartEndE-ValueType
Pfam:FAM131 61 353 1.9e-113 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163235
SMART Domains Protein: ENSMUSP00000132387
Gene: ENSMUSG00000029862

DomainStartEndE-ValueType
low complexity region 12 36 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000163936
AA Change: T824I
SMART Domains Protein: ENSMUSP00000130148
Gene: ENSMUSG00000029862
AA Change: T824I

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 noncoding transcript
Transcript: ENSMUST00000169902
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: 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: 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
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: 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
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency 92% (69/75)
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930562C15Rik A T 16: 4,653,837 (GRCm39) K129* probably null Het
Adamts6 A T 13: 104,443,751 (GRCm39) D162V probably damaging Het
Alms1 C A 6: 85,597,714 (GRCm39) P1316T possibly damaging Het
AU040320 A T 4: 126,722,664 (GRCm39) N394I possibly damaging Het
Cacng8 T C 7: 3,464,096 (GRCm39) L416P possibly damaging Het
Ccdc136 T A 6: 29,419,313 (GRCm39) N944K probably damaging Het
Col16a1 A T 4: 129,947,964 (GRCm39) Y228F probably damaging Het
Cyfip1 A G 7: 55,548,083 (GRCm39) D561G probably benign Het
Ddr1 T A 17: 35,993,667 (GRCm39) probably null Het
Dedd2 A T 7: 24,918,411 (GRCm39) L48Q probably damaging Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Het
Dph3b-ps A G 13: 106,683,558 (GRCm39) noncoding transcript Het
Dppa3 T C 6: 122,606,891 (GRCm39) F127S probably damaging Het
Dpy19l4 C T 4: 11,265,943 (GRCm39) probably null Het
Flrt3 T C 2: 140,502,177 (GRCm39) T484A probably damaging Het
Gldc T C 19: 30,128,936 (GRCm39) E179G probably damaging Het
Gm14403 A G 2: 177,200,282 (GRCm39) E76G probably benign Het
Gm6421 G A 13: 117,494,969 (GRCm39) noncoding transcript Het
Grk5 T C 19: 61,065,122 (GRCm39) V262A probably damaging Het
Grp A G 18: 66,013,230 (GRCm39) Q132R probably benign Het
Hap1 A G 11: 100,246,537 (GRCm39) F123L probably damaging Het
Hrc A G 7: 44,986,445 (GRCm39) D532G probably damaging Het
Igsf9b C A 9: 27,228,733 (GRCm39) F164L probably benign Het
Irag1 G T 7: 110,470,700 (GRCm39) L672I probably damaging Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Kansl1 C T 11: 104,315,168 (GRCm39) R290Q probably damaging Het
Kifc2 T A 15: 76,545,496 (GRCm39) L81Q probably damaging Het
Klrc3 T C 6: 129,616,538 (GRCm39) R160G probably damaging Het
Mal A G 2: 127,482,193 (GRCm39) M70T probably benign Het
Mep1a T G 17: 43,789,035 (GRCm39) R580S probably damaging Het
Methig1 A T 15: 100,251,130 (GRCm39) I14F probably damaging Het
Mtf1 T C 4: 124,715,101 (GRCm39) L242P probably damaging Het
Nfkb1 C A 3: 135,309,568 (GRCm39) A509S probably benign Het
Or2h2b-ps1 C G 17: 37,480,858 (GRCm39) S227T probably benign Het
Or2n1b G A 17: 38,460,003 (GRCm39) D175N probably damaging Het
Or5ac24 A T 16: 59,165,449 (GRCm39) I205K probably damaging Het
Or7a36 G T 10: 78,819,928 (GRCm39) M101I probably benign Het
Or8k23 A T 2: 86,186,318 (GRCm39) M136K probably damaging Het
Pabpc2 A T 18: 39,907,635 (GRCm39) N300I probably damaging Het
Peg10 C T 6: 4,755,864 (GRCm39) probably benign Het
Ppp1r3a T A 6: 14,719,603 (GRCm39) D437V probably damaging Het
Prickle1 A G 15: 93,398,783 (GRCm39) S682P probably damaging Het
Prkab2 T C 3: 97,580,308 (GRCm39) probably benign Het
Pus3 T A 9: 35,476,932 (GRCm39) L243Q possibly damaging Het
Relch A G 1: 105,605,905 (GRCm39) S182G probably damaging Het
Rgs19 G A 2: 181,331,336 (GRCm39) T99M possibly damaging Het
Ripk2 A G 4: 16,127,663 (GRCm39) S360P possibly damaging Het
Rock1 A G 18: 10,140,210 (GRCm39) I127T probably damaging Het
Serpinb10 T G 1: 107,469,947 (GRCm39) M143R probably damaging Het
Sipa1l3 G A 7: 29,048,000 (GRCm39) S247F probably damaging Het
Skint6 T A 4: 113,093,465 (GRCm39) Q226L probably damaging Het
Slc6a19 T C 13: 73,839,872 (GRCm39) M137V probably benign Het
Supv3l1 A T 10: 62,271,291 (GRCm39) N415K probably benign Het
Tekt4 A G 17: 25,692,749 (GRCm39) R192G probably damaging Het
Trgv7 A T 13: 19,362,598 (GRCm39) K96* probably null Het
Tshz1 T C 18: 84,032,053 (GRCm39) N785S probably benign Het
Usb1 A G 8: 96,070,679 (GRCm39) T202A probably damaging Het
Utp18 A T 11: 93,761,363 (GRCm39) D348E possibly damaging Het
Vmn1r42 T G 6: 89,821,598 (GRCm39) I324L probably benign Het
Wnt8a A T 18: 34,678,656 (GRCm39) R157* probably null Het
Ypel1 A G 16: 16,902,472 (GRCm39) probably null Het
Zfp235 A G 7: 23,836,546 (GRCm39) K31E probably damaging Het
Zhx2 G C 15: 57,686,089 (GRCm39) W486S 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
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
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'- ACTGCTTTGTCAGGGATAGCC -3'
(R):5'- TGCAAGATGTCAGCCAGCTC -3'

Sequencing Primer
(F):5'- TCAGGGATAGCCTTGTCTTTC -3'
(R):5'- AGCTCCTCCTCAGGCTCTAGG -3'
Posted On 2016-06-06