Incidental Mutation 'R1562:Clcn1'
ID 170671
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 039601-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1562 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 42263619-42292690 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 42277169 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Leucine at position 420 (P420L)
Ref Sequence ENSEMBL: ENSMUSP00000031894 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031894] [ENSMUST00000164091] [ENSMUST00000168660]
AlphaFold Q64347
Predicted Effect probably benign
Transcript: ENSMUST00000031894
AA Change: P420L

PolyPhen 2 Score 0.290 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000031894
Gene: ENSMUSG00000029862
AA Change: P420L

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 unknown
Transcript: ENSMUST00000163936
AA Change: P348L
SMART Domains Protein: ENSMUSP00000130148
Gene: ENSMUSG00000029862
AA Change: P348L

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: 99.1%
  • 3x: 98.2%
  • 10x: 95.8%
  • 20x: 91.0%
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
Abca2 A G 2: 25,336,331 (GRCm39) I2201V probably benign Het
Adam22 T C 5: 8,145,007 (GRCm39) N817S probably damaging Het
Alox12 C A 11: 70,140,991 (GRCm39) R348L probably damaging Het
Asb17 A T 3: 153,559,143 (GRCm39) T285S probably benign Het
Casp4 T C 9: 5,324,733 (GRCm39) S182P possibly damaging Het
Cenpe T C 3: 134,944,155 (GRCm39) M985T possibly damaging Het
Coro2a T C 4: 46,548,917 (GRCm39) I126V probably benign Het
Cubn T C 2: 13,432,778 (GRCm39) Y1181C probably damaging Het
Cyp2d22 A T 15: 82,258,179 (GRCm39) L147Q probably damaging Het
Dna2 C T 10: 62,784,966 (GRCm39) R28W probably benign Het
Ecm1 G A 3: 95,643,275 (GRCm39) R342C probably damaging Het
Fat2 T C 11: 55,200,800 (GRCm39) N758S probably damaging Het
Fbxo43 T C 15: 36,163,162 (GRCm39) D15G probably damaging Het
Flt3 T C 5: 147,281,323 (GRCm39) E803G probably damaging Het
Folr1 T G 7: 101,507,801 (GRCm39) D213A probably damaging Het
Fus T C 7: 127,579,094 (GRCm39) V359A probably damaging Het
Gabrb3 C T 7: 57,415,262 (GRCm39) R111* probably null Het
Gm17324 T C 9: 78,355,964 (GRCm39) probably benign Het
Hormad2 A T 11: 4,358,848 (GRCm39) probably null Het
Ifi27l2b T A 12: 103,422,780 (GRCm39) probably null Het
Isg20 G T 7: 78,569,891 (GRCm39) C176F probably benign Het
Katnip C A 7: 125,442,020 (GRCm39) S643Y probably damaging Het
Krt15 C A 11: 100,024,007 (GRCm39) V346L probably benign Het
Liat1 A T 11: 75,894,024 (GRCm39) I134F probably damaging Het
Med13l A G 5: 118,876,584 (GRCm39) K920R probably damaging Het
Mlh3 A T 12: 85,313,694 (GRCm39) F831I probably benign Het
Mtmr9 A G 14: 63,771,786 (GRCm39) S267P probably benign Het
Mybpc1 C T 10: 88,389,193 (GRCm39) A406T probably damaging Het
Myh1 T C 11: 67,102,196 (GRCm39) M829T probably benign Het
Myo10 A G 15: 25,780,497 (GRCm39) Q209R possibly damaging Het
Nceh1 T A 3: 27,293,701 (GRCm39) V153D probably damaging Het
Oog3 A T 4: 143,889,169 (GRCm39) I3N probably damaging Het
Or1j19 A G 2: 36,676,696 (GRCm39) D53G probably damaging Het
Or2ag1b C T 7: 106,288,187 (GRCm39) M250I probably benign Het
Or4c103 T A 2: 88,513,423 (GRCm39) I218F probably benign Het
Or8c20 C A 9: 38,260,658 (GRCm39) S87* probably null Het
Pcnt G A 10: 76,203,164 (GRCm39) T2646M probably benign Het
Phf10 A T 17: 15,166,512 (GRCm39) C453S probably damaging Het
Plcb4 T A 2: 135,812,367 (GRCm39) probably null Het
Plekhh1 A G 12: 79,123,482 (GRCm39) H1185R probably benign Het
Prmt3 G T 7: 49,476,602 (GRCm39) V404L probably benign Het
Ptprb T A 10: 116,175,372 (GRCm39) D1122E probably benign Het
Rars1 A G 11: 35,711,921 (GRCm39) probably null Het
Rasa2 G T 9: 96,427,803 (GRCm39) N687K possibly damaging Het
Rbm11 A G 16: 75,393,423 (GRCm39) T40A probably damaging Het
Rem2 T C 14: 54,713,775 (GRCm39) V16A probably benign Het
Rlf A T 4: 121,007,588 (GRCm39) M574K possibly damaging Het
Rpap3 A T 15: 97,592,098 (GRCm39) V186D possibly damaging Het
Sertad3 G A 7: 27,176,048 (GRCm39) E161K probably damaging Het
Sh3gl2 T C 4: 85,304,130 (GRCm39) S278P probably benign Het
Strn3 T C 12: 51,680,401 (GRCm39) T400A probably benign Het
Sycp2 A T 2: 178,024,178 (GRCm39) I402N probably damaging Het
Synj1 C T 16: 90,784,290 (GRCm39) V283I probably benign Het
Tas2r108 A G 6: 40,471,000 (GRCm39) probably null Het
Ttpal A G 2: 163,457,323 (GRCm39) N265S probably benign Het
Unc80 G A 1: 66,677,116 (GRCm39) G2015D probably damaging Het
Upf1 C T 8: 70,796,017 (GRCm39) W138* probably null Het
Vmn1r25 T G 6: 57,955,786 (GRCm39) M168L probably benign Het
Vmn2r18 A T 5: 151,510,301 (GRCm39) F24Y probably benign Het
Vmn2r4 G T 3: 64,296,865 (GRCm39) T640N probably damaging Het
Wdr75 T A 1: 45,843,030 (GRCm39) probably null Het
Zdbf2 T G 1: 63,342,747 (GRCm39) S375R possibly damaging Het
Zfp648 A G 1: 154,080,138 (GRCm39) Q99R probably benign Het
Zfp964 C T 8: 70,115,654 (GRCm39) P85S 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
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
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'- GGTCAATTCATGGCTGGAGAGGTC -3'
(R):5'- AGAAGCTGAAGCTCTATCCCTCCTG -3'

Sequencing Primer
(F):5'- AACTCATACCTGTGGCTCTGG -3'
(R):5'- TTCTGTACACAGACAGAAGCTG -3'
Posted On 2014-04-13