Incidental Mutation 'R2021:Clcn6'
ID 223968
Institutional Source Beutler Lab
Gene Symbol Clcn6
Ensembl Gene ENSMUSG00000029016
Gene Name chloride channel, voltage-sensitive 6
Synonyms
MMRRC Submission 040030-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.083) question?
Stock # R2021 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 148088716-148123270 bp(-) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) A to G at 148095109 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000121751 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030879] [ENSMUST00000105711] [ENSMUST00000137724]
AlphaFold O35454
Predicted Effect probably null
Transcript: ENSMUST00000030879
SMART Domains Protein: ENSMUSP00000030879
Gene: ENSMUSG00000029016

DomainStartEndE-ValueType
low complexity region 4 24 N/A INTRINSIC
Pfam:Voltage_CLC 138 571 5.5e-98 PFAM
CBS 609 658 1.68e-3 SMART
CBS 811 859 1.34e-11 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000105711
SMART Domains Protein: ENSMUSP00000101336
Gene: ENSMUSG00000029016

DomainStartEndE-ValueType
low complexity region 4 24 N/A INTRINSIC
Pfam:Voltage_CLC 141 574 1.5e-98 PFAM
CBS 612 661 1.68e-3 SMART
Predicted Effect probably null
Transcript: ENSMUST00000137724
SMART Domains Protein: ENSMUSP00000121751
Gene: ENSMUSG00000029016

DomainStartEndE-ValueType
low complexity region 4 24 N/A INTRINSIC
Pfam:Voltage_CLC 141 574 1.9e-101 PFAM
CBS 612 661 1.68e-3 SMART
CBS 814 862 1.34e-11 SMART
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.2%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a member of the ClC chloride channel and transporter family of proteins. The encoded protein may function as a vesicular Cl-/H+ antiporter. Homozygous knockout mice exhibit decreased pain sensitivity, behavioral abnormalities and features of lysosomal storage disease. [provided by RefSeq, Aug 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired nociception, mild behavioral abnormalities, and a progressive neuropathy of the central and peripheral nervous systems with features of neuronal ceroid lipofuscinosis (a lysosomal storage disease). [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ablim1 A T 19: 57,035,450 (GRCm39) S316T probably damaging Het
Alox8 C T 11: 69,077,114 (GRCm39) V460I probably damaging Het
Aoc1l2 T C 6: 48,908,385 (GRCm39) S462P probably damaging Het
Arvcf G A 16: 18,218,482 (GRCm39) A491T probably damaging Het
Asnsd1 A G 1: 53,386,386 (GRCm39) S414P possibly damaging Het
Btbd7 A G 12: 102,756,968 (GRCm39) L706P probably damaging Het
Camk2d T A 3: 126,574,105 (GRCm39) W171R probably damaging Het
Casc3 T A 11: 98,712,332 (GRCm39) S124T probably benign Het
Casp8ap2 T C 4: 32,644,560 (GRCm39) V1211A probably benign Het
Ccdc182 T C 11: 88,184,962 (GRCm39) V14A possibly damaging Het
Ccdc80 A T 16: 44,943,275 (GRCm39) Q795L probably damaging Het
Ccdc88a T G 11: 29,453,480 (GRCm39) S1614R probably damaging Het
Cemip2 G A 19: 21,822,114 (GRCm39) A1170T possibly damaging Het
Cubn A G 2: 13,313,360 (GRCm39) V3070A probably benign Het
Dst G A 1: 34,205,372 (GRCm39) V1025I possibly damaging Het
Dynlt4 A G 4: 116,985,504 (GRCm39) E109G possibly damaging Het
Elk3 T A 10: 93,101,539 (GRCm39) I71F probably damaging Het
Flt3 A T 5: 147,306,300 (GRCm39) I276N probably damaging Het
Frem1 G T 4: 82,831,795 (GRCm39) T1988K probably benign Het
Golph3l T A 3: 95,524,668 (GRCm39) D306E probably benign Het
Grk2 T A 19: 4,340,698 (GRCm39) I254F probably damaging Het
Hgf C T 5: 16,781,919 (GRCm39) T214I probably benign Het
Hoxc5 C A 15: 102,922,814 (GRCm39) probably null Het
Hsd11b1 T C 1: 192,922,686 (GRCm39) T124A probably benign Het
Ipp A G 4: 116,372,565 (GRCm39) Y198C probably benign Het
Ism1 T A 2: 139,582,047 (GRCm39) probably null Het
Klhl42 A G 6: 146,993,394 (GRCm39) Y122C possibly damaging Het
Klk1b21 A T 7: 43,755,418 (GRCm39) K206* probably null Het
Lcn11 A G 2: 25,668,097 (GRCm39) K85R probably benign Het
Macf1 G T 4: 123,366,523 (GRCm39) A2746E probably damaging Het
Matn4 A G 2: 164,242,573 (GRCm39) V175A probably damaging Het
Myh2 A T 11: 67,082,545 (GRCm39) N1372Y probably damaging Het
Ncl A G 1: 86,284,677 (GRCm39) probably null Het
Nudt2 A G 4: 41,480,255 (GRCm39) D46G probably damaging Het
Obscn C T 11: 58,958,000 (GRCm39) D3567N probably benign Het
Or1j17 G C 2: 36,578,487 (GRCm39) V158L probably benign Het
Or2z9 G T 8: 72,853,930 (GRCm39) V109F possibly damaging Het
Or4a72 A T 2: 89,405,305 (GRCm39) M255K possibly damaging Het
Pamr1 T A 2: 102,464,880 (GRCm39) M343K probably benign Het
Pcdh15 T G 10: 74,467,025 (GRCm39) S1684A possibly damaging Het
Ppm1h T A 10: 122,714,433 (GRCm39) L324* probably null Het
Ppp3r2 T C 4: 49,681,723 (GRCm39) I76V probably benign Het
Prkdc G A 16: 15,494,873 (GRCm39) V748I probably benign Het
Prss47 A G 13: 65,199,591 (GRCm39) V96A probably benign Het
Rsbn1 C T 3: 103,821,789 (GRCm39) T8I probably benign Het
Rsf1 GGCG GGCGACGGCGGCG 7: 97,229,113 (GRCm39) probably benign Het
Serpinb3d A G 1: 107,006,182 (GRCm39) V302A probably benign Het
Sfrp4 A T 13: 19,816,496 (GRCm39) I177F probably benign Het
Sh3bp2 A G 5: 34,701,569 (GRCm39) probably benign Het
Slc7a12 A G 3: 14,562,393 (GRCm39) T257A probably damaging Het
Spata31e5 A T 1: 28,817,234 (GRCm39) V266D probably damaging Het
Specc1l T C 10: 75,103,425 (GRCm39) probably null Het
Stard9 A G 2: 120,534,716 (GRCm39) T3658A probably benign Het
Styxl2 A T 1: 165,928,392 (GRCm39) W407R probably benign Het
Tmem30c T C 16: 57,101,725 (GRCm39) T68A probably damaging Het
Tnr A G 1: 159,679,592 (GRCm39) I189V probably benign Het
Trrap A G 5: 144,790,298 (GRCm39) N3586S possibly damaging Het
Usp14 T C 18: 10,024,632 (GRCm39) T22A probably damaging Het
Vmn1r68 A G 7: 10,261,918 (GRCm39) L60P probably damaging Het
Vmn2r108 G A 17: 20,691,252 (GRCm39) H424Y probably benign Het
Wdr81 C A 11: 75,336,788 (GRCm39) E1534* probably null Het
Zc3h13 A G 14: 75,567,635 (GRCm39) E976G probably damaging Het
Zfp128 T C 7: 12,623,956 (GRCm39) L108P possibly damaging Het
Zfp644 T C 5: 106,783,548 (GRCm39) I1000V possibly damaging Het
Other mutations in Clcn6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00334:Clcn6 APN 4 148,102,359 (GRCm39) critical splice donor site probably null
IGL00434:Clcn6 APN 4 148,098,195 (GRCm39) missense probably damaging 1.00
IGL00973:Clcn6 APN 4 148,098,245 (GRCm39) splice site probably benign
IGL01384:Clcn6 APN 4 148,103,423 (GRCm39) missense probably damaging 1.00
IGL01465:Clcn6 APN 4 148,105,908 (GRCm39) splice site probably benign
IGL01522:Clcn6 APN 4 148,101,992 (GRCm39) missense probably benign 0.44
R0194:Clcn6 UTSW 4 148,097,213 (GRCm39) missense probably damaging 1.00
R0280:Clcn6 UTSW 4 148,093,172 (GRCm39) missense probably damaging 1.00
R0349:Clcn6 UTSW 4 148,108,651 (GRCm39) missense possibly damaging 0.89
R0352:Clcn6 UTSW 4 148,099,063 (GRCm39) missense probably damaging 1.00
R0586:Clcn6 UTSW 4 148,123,206 (GRCm39) unclassified probably benign
R0927:Clcn6 UTSW 4 148,113,849 (GRCm39) missense probably benign 0.30
R1141:Clcn6 UTSW 4 148,098,356 (GRCm39) missense probably damaging 0.99
R1465:Clcn6 UTSW 4 148,098,358 (GRCm39) missense probably damaging 1.00
R1465:Clcn6 UTSW 4 148,098,358 (GRCm39) missense probably damaging 1.00
R1473:Clcn6 UTSW 4 148,108,613 (GRCm39) missense possibly damaging 0.93
R1551:Clcn6 UTSW 4 148,097,235 (GRCm39) missense possibly damaging 0.74
R1571:Clcn6 UTSW 4 148,097,226 (GRCm39) missense possibly damaging 0.63
R1593:Clcn6 UTSW 4 148,099,051 (GRCm39) missense probably benign
R1596:Clcn6 UTSW 4 148,107,836 (GRCm39) missense probably damaging 1.00
R1706:Clcn6 UTSW 4 148,102,025 (GRCm39) missense probably benign 0.00
R1769:Clcn6 UTSW 4 148,098,758 (GRCm39) splice site probably null
R2022:Clcn6 UTSW 4 148,095,109 (GRCm39) critical splice donor site probably null
R2049:Clcn6 UTSW 4 148,108,594 (GRCm39) missense possibly damaging 0.88
R2081:Clcn6 UTSW 4 148,095,525 (GRCm39) missense probably damaging 1.00
R2140:Clcn6 UTSW 4 148,108,594 (GRCm39) missense possibly damaging 0.88
R2141:Clcn6 UTSW 4 148,108,594 (GRCm39) missense possibly damaging 0.88
R2142:Clcn6 UTSW 4 148,108,594 (GRCm39) missense possibly damaging 0.88
R2177:Clcn6 UTSW 4 148,099,057 (GRCm39) missense possibly damaging 0.73
R2511:Clcn6 UTSW 4 148,101,951 (GRCm39) critical splice donor site probably null
R2891:Clcn6 UTSW 4 148,097,073 (GRCm39) critical splice donor site probably null
R3750:Clcn6 UTSW 4 148,108,644 (GRCm39) nonsense probably null
R4014:Clcn6 UTSW 4 148,102,067 (GRCm39) missense probably damaging 0.98
R4023:Clcn6 UTSW 4 148,098,740 (GRCm39) missense possibly damaging 0.91
R4024:Clcn6 UTSW 4 148,098,740 (GRCm39) missense possibly damaging 0.91
R4025:Clcn6 UTSW 4 148,098,740 (GRCm39) missense possibly damaging 0.91
R4667:Clcn6 UTSW 4 148,108,624 (GRCm39) missense possibly damaging 0.61
R4865:Clcn6 UTSW 4 148,104,223 (GRCm39) missense probably damaging 1.00
R4978:Clcn6 UTSW 4 148,093,227 (GRCm39) missense probably benign 0.05
R5140:Clcn6 UTSW 4 148,122,774 (GRCm39) unclassified probably benign
R5345:Clcn6 UTSW 4 148,123,206 (GRCm39) unclassified probably benign
R5467:Clcn6 UTSW 4 148,102,093 (GRCm39) missense possibly damaging 0.81
R5665:Clcn6 UTSW 4 148,099,018 (GRCm39) missense possibly damaging 0.71
R5739:Clcn6 UTSW 4 148,098,646 (GRCm39) missense probably damaging 1.00
R5899:Clcn6 UTSW 4 148,102,049 (GRCm39) missense probably benign 0.01
R6043:Clcn6 UTSW 4 148,093,245 (GRCm39) missense probably damaging 1.00
R6351:Clcn6 UTSW 4 148,101,957 (GRCm39) missense probably benign 0.01
R6593:Clcn6 UTSW 4 148,095,226 (GRCm39) missense probably benign 0.21
R7440:Clcn6 UTSW 4 148,098,652 (GRCm39) missense probably damaging 1.00
R7674:Clcn6 UTSW 4 148,097,151 (GRCm39) missense probably damaging 1.00
R7756:Clcn6 UTSW 4 148,113,896 (GRCm39) missense probably damaging 1.00
R7901:Clcn6 UTSW 4 148,095,202 (GRCm39) missense probably damaging 1.00
R8559:Clcn6 UTSW 4 148,111,032 (GRCm39) missense possibly damaging 0.88
R8747:Clcn6 UTSW 4 148,093,354 (GRCm39) critical splice donor site probably null
R9246:Clcn6 UTSW 4 148,113,866 (GRCm39) missense probably benign 0.25
R9343:Clcn6 UTSW 4 148,098,458 (GRCm39) missense probably benign 0.03
V7732:Clcn6 UTSW 4 148,098,412 (GRCm39) missense probably damaging 0.96
Z1177:Clcn6 UTSW 4 148,107,827 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- ACAGCTGGAGTCAACTTGC -3'
(R):5'- CCTTGTTGCTGGAGAGTACG -3'

Sequencing Primer
(F):5'- GGAGTCAACTTGCCCTCAC -3'
(R):5'- ATACGAGGCAGCGTCTGG -3'
Posted On 2014-08-25