Incidental Mutation 'R2356:Clcn1'
ID 246925
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 040338-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2356 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 42263619-42292690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 42268559 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Aspartic acid at position 155 (G155D)
Ref Sequence ENSEMBL: ENSMUSP00000126045 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031894] [ENSMUST00000164091] [ENSMUST00000168660]
AlphaFold Q64347
Predicted Effect probably damaging
Transcript: ENSMUST00000031894
AA Change: G188D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000031894
Gene: ENSMUSG00000029862
AA Change: G188D

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 unknown
Transcript: ENSMUST00000163936
AA Change: G158D
SMART Domains Protein: ENSMUSP00000130148
Gene: ENSMUSG00000029862
AA Change: G158D

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 damaging
Transcript: ENSMUST00000164091
AA Change: G188D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000131354
Gene: ENSMUSG00000029862
AA Change: G188D

DomainStartEndE-ValueType
low complexity region 121 130 N/A INTRINSIC
Pfam:Voltage_CLC 170 256 2.9e-20 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000165780
AA Change: G158D
SMART Domains Protein: ENSMUSP00000130550
Gene: ENSMUSG00000029862
AA Change: G158D

DomainStartEndE-ValueType
low complexity region 92 101 N/A INTRINSIC
Pfam:Voltage_CLC 141 227 9.7e-22 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000168660
AA Change: G155D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000126045
Gene: ENSMUSG00000029862
AA Change: G155D

DomainStartEndE-ValueType
low complexity region 88 97 N/A INTRINSIC
Pfam:Voltage_CLC 136 257 1.1e-22 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000169024
AA Change: G158D
SMART Domains Protein: ENSMUSP00000130968
Gene: ENSMUSG00000029862
AA Change: G158D

DomainStartEndE-ValueType
low complexity region 92 101 N/A INTRINSIC
Pfam:Voltage_CLC 141 261 2.9e-24 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000170028
AA Change: G158D
SMART Domains Protein: ENSMUSP00000132154
Gene: ENSMUSG00000029862
AA Change: G158D

DomainStartEndE-ValueType
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: 97.5%
  • 20x: 95.7%
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcf3 G T 16: 20,379,249 (GRCm39) R705L probably benign Het
Adcy6 A T 15: 98,494,897 (GRCm39) probably null Het
Ank1 A T 8: 23,575,688 (GRCm39) T145S probably damaging Het
Aph1a T C 3: 95,801,544 (GRCm39) F21S probably benign Het
Apoa5 T A 9: 46,181,341 (GRCm39) V139E probably damaging Het
Arhgap44 T C 11: 64,900,851 (GRCm39) K595R probably damaging Het
Arhgap5 C T 12: 52,565,930 (GRCm39) P967L probably benign Het
Atp13a5 A T 16: 29,099,887 (GRCm39) I683N probably damaging Het
Cdc6 A G 11: 98,810,118 (GRCm39) T476A probably benign Het
Cdk10 T C 8: 123,955,908 (GRCm39) V199A probably damaging Het
Ces2h G A 8: 105,742,570 (GRCm39) C94Y probably damaging Het
Cxcr4 A G 1: 128,517,251 (GRCm39) Y135H probably damaging Het
Dapp1 A G 3: 137,643,510 (GRCm39) V184A possibly damaging Het
Dhrs7 A C 12: 72,699,155 (GRCm39) S276A probably benign Het
Dlg5 A G 14: 24,220,496 (GRCm39) probably null Het
Dnaaf1 T A 8: 120,315,026 (GRCm39) F278Y probably damaging Het
Dnaaf2 A G 12: 69,244,992 (GRCm39) F23S probably benign Het
En2 G T 5: 28,371,330 (GRCm39) probably benign Het
Erbb4 T A 1: 68,117,755 (GRCm39) M887L probably benign Het
Exoc5 T C 14: 49,253,738 (GRCm39) M482V probably benign Het
Foxk1 A G 5: 142,441,164 (GRCm39) I571V possibly damaging Het
Fry G A 5: 150,394,897 (GRCm39) G650D probably benign Het
Gm8225 T C 17: 26,762,378 (GRCm39) S190P probably damaging Het
Gpx5 G C 13: 21,475,538 (GRCm39) H63D possibly damaging Het
Ipo9 A T 1: 135,334,555 (GRCm39) S285T probably benign Het
Itga8 T C 2: 12,204,952 (GRCm39) H495R probably benign Het
Klf11 T C 12: 24,703,582 (GRCm39) S6P probably damaging Het
Krtap8-1 A T 16: 89,284,789 (GRCm39) Y3N possibly damaging Het
Krtap8-1 G T 16: 89,284,790 (GRCm39) Y2* probably null Het
Lama1 T A 17: 68,117,109 (GRCm39) L2468Q probably damaging Het
Lmo7 T C 14: 102,124,381 (GRCm39) L280S probably damaging Het
Matk G A 10: 81,097,377 (GRCm39) probably null Het
Mcmdc2 A G 1: 10,001,026 (GRCm39) T434A possibly damaging Het
Mst1r T A 9: 107,795,069 (GRCm39) L1283Q probably damaging Het
Muc21 A G 17: 35,932,563 (GRCm39) probably benign Het
Nbn T A 4: 15,970,863 (GRCm39) I282N probably damaging Het
Ncln A G 10: 81,328,756 (GRCm39) V174A probably benign Het
Nipa2 G A 7: 55,582,714 (GRCm39) H344Y probably benign Het
Nlrp4g A G 9: 124,349,306 (GRCm38) noncoding transcript Het
Or56b1 G T 7: 104,285,834 (GRCm39) E318* probably null Het
Or6c38 T C 10: 128,929,761 (GRCm39) I27M probably benign Het
Pik3r5 T C 11: 68,383,743 (GRCm39) S521P probably damaging Het
Pkhd1l1 C T 15: 44,396,415 (GRCm39) T1979M probably benign Het
Plekhn1 T G 4: 156,307,158 (GRCm39) D464A probably damaging Het
Ppp4r1 T A 17: 66,140,045 (GRCm39) Y648N probably damaging Het
Prkaa2 C T 4: 104,896,918 (GRCm39) probably null Het
Prkdc T A 16: 15,502,068 (GRCm39) H828Q probably benign Het
Prss40 A T 1: 34,598,984 (GRCm39) Y69* probably null Het
Prx C T 7: 27,207,284 (GRCm39) probably benign Het
Psmd11 T A 11: 80,319,530 (GRCm39) S7T possibly damaging Het
Psmd14 A T 2: 61,630,351 (GRCm39) H287L probably benign Het
Rcor1 T C 12: 111,076,226 (GRCm39) Y297H probably damaging Het
Rnf40 T G 7: 127,190,748 (GRCm39) V272G probably damaging Het
Serpina3f G T 12: 104,183,626 (GRCm39) E163* probably null Het
Setd4 G A 16: 93,387,871 (GRCm39) T205I probably damaging Het
Shroom1 A T 11: 53,357,274 (GRCm39) T646S probably benign Het
Smg8 G C 11: 86,976,554 (GRCm39) S342R probably benign Het
Spata31h1 A G 10: 82,119,789 (GRCm39) V4407A possibly damaging Het
Trhde T C 10: 114,237,421 (GRCm39) Y986C probably damaging Het
Tulp2 A T 7: 45,168,052 (GRCm39) T155S possibly damaging Het
Vmn1r212 A T 13: 23,068,120 (GRCm39) L71* probably null Het
Wnk2 A T 13: 49,192,644 (GRCm39) C2032* probably null Het
Zfp429 A G 13: 67,538,746 (GRCm39) Y233H probably benign Het
Zfp809 C A 9: 22,154,336 (GRCm39) T351K probably benign 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
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'- ATGCCCAGATGAAGCCTAGC -3'
(R):5'- TGTCCATAGCCGAGTTCAGG -3'

Sequencing Primer
(F):5'- AGATGAAGCCTAGCCTTCCTCTG -3'
(R):5'- ATAGCCGAGTTCAGGCAGCTC -3'
Posted On 2014-10-30