Incidental Mutation 'R0379:Clcn4'
ID 30860
Institutional Source Beutler Lab
Gene Symbol Clcn4
Ensembl Gene ENSMUSG00000000605
Gene Name chloride channel, voltage-sensitive 4
Synonyms Clc4-2, Clcn4-2
MMRRC Submission 038585-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0379 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 7285308-7303837 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 7299791 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 13 (T13A)
Ref Sequence ENSEMBL: ENSMUSP00000147449 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000619] [ENSMUST00000209916] [ENSMUST00000210061] [ENSMUST00000210362] [ENSMUST00000211574] [ENSMUST00000210594]
AlphaFold Q61418
Predicted Effect probably benign
Transcript: ENSMUST00000000619
AA Change: T13A

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000000619
Gene: ENSMUSG00000000605
AA Change: T13A

DomainStartEndE-ValueType
transmembrane domain 57 79 N/A INTRINSIC
Pfam:Voltage_CLC 149 552 2.7e-111 PFAM
CBS 596 646 1.07e-1 SMART
CBS 687 734 4.92e-10 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176903
Predicted Effect probably damaging
Transcript: ENSMUST00000209916
AA Change: T13A

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
Predicted Effect probably benign
Transcript: ENSMUST00000210061
AA Change: T13A

PolyPhen 2 Score 0.086 (Sensitivity: 0.93; Specificity: 0.85)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210318
Predicted Effect probably benign
Transcript: ENSMUST00000210362
AA Change: T13A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Predicted Effect possibly damaging
Transcript: ENSMUST00000211574
AA Change: T13A

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210809
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210444
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210989
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211551
Predicted Effect probably benign
Transcript: ENSMUST00000210594
Meta Mutation Damage Score 0.2150 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.1%
  • 10x: 95.7%
  • 20x: 90.9%
Validation Efficiency 98% (79/81)
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. Chloride channel 4 has an evolutionary conserved CpG island and is conserved in both mouse and hamster. This gene is mapped in close proximity to APXL (Apical protein Xenopus laevis-like) and OA1 (Ocular albinism type I), which are both located on the human X chromosome at band p22.3. The physiological role of chloride channel 4 remains unknown but may contribute to the pathogenesis of neuronal disorders. Alternate splicing results in two transcript variants that encode different proteins. [provided by RefSeq, Mar 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit no obvious phenotype. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930512M02Rik A G 11: 11,539,365 (GRCm39) probably benign Het
Apba1 A C 19: 23,912,194 (GRCm39) N558T probably damaging Het
Arfgef2 T A 2: 166,702,320 (GRCm39) probably null Het
Arsb T C 13: 94,077,135 (GRCm39) S501P probably benign Het
Atp10b A G 11: 43,145,141 (GRCm39) T1295A probably benign Het
Atp8b5 G T 4: 43,361,898 (GRCm39) R648L probably damaging Het
Bcl2a1b T C 9: 89,081,789 (GRCm39) I126T possibly damaging Het
Brd9 T C 13: 74,090,802 (GRCm39) probably benign Het
Cd93 T C 2: 148,283,430 (GRCm39) probably benign Het
Chd5 A G 4: 152,467,778 (GRCm39) K1692R probably benign Het
Clec14a A G 12: 58,315,580 (GRCm39) F14S possibly damaging Het
Clec4g A G 8: 3,768,440 (GRCm39) V97A probably benign Het
Col24a1 G A 3: 145,229,897 (GRCm39) R1483K possibly damaging Het
Crem A T 18: 3,299,226 (GRCm39) V82D probably damaging Het
Ctnna2 T A 6: 77,618,423 (GRCm39) T180S probably benign Het
Cybrd1 T C 2: 70,960,099 (GRCm39) I99T probably benign Het
Cyp4a32 G A 4: 115,478,671 (GRCm39) V468M probably damaging Het
Dlk1 A G 12: 109,420,985 (GRCm39) probably benign Het
Dnaaf9 C T 2: 130,627,466 (GRCm39) probably benign Het
Dnah7b A T 1: 46,179,336 (GRCm39) Y1003F probably benign Het
Egfem1 A C 3: 29,722,399 (GRCm39) E376A possibly damaging Het
Etl4 T A 2: 20,812,165 (GRCm39) I1416K probably damaging Het
Fbxl4 A G 4: 22,386,106 (GRCm39) T238A probably benign Het
Fer1l6 A G 15: 58,420,187 (GRCm39) I33M probably benign Het
Fndc3a A G 14: 72,794,049 (GRCm39) S830P probably damaging Het
Fras1 C T 5: 96,903,368 (GRCm39) R3082* probably null Het
Galnt13 T C 2: 54,950,504 (GRCm39) V395A possibly damaging Het
Gpd2 C T 2: 57,235,275 (GRCm39) T335I probably damaging Het
Gucy2d C A 7: 98,108,209 (GRCm39) probably null Het
Hydin A G 8: 111,235,759 (GRCm39) probably benign Het
Ints5 G T 19: 8,874,497 (GRCm39) V819L possibly damaging Het
Klhdc10 C G 6: 30,450,669 (GRCm39) Q292E possibly damaging Het
Lmbrd2 G A 15: 9,149,566 (GRCm39) A67T probably benign Het
Lrp1 T G 10: 127,430,838 (GRCm39) T404P probably damaging Het
Marchf7 T C 2: 60,064,470 (GRCm39) S249P probably benign Het
Mcm10 T A 2: 5,013,434 (GRCm39) K66M probably benign Het
Mtmr7 C A 8: 41,004,642 (GRCm39) D645Y probably damaging Het
Muc6 T A 7: 141,216,868 (GRCm39) I2602F possibly damaging Het
Myh13 G A 11: 67,260,121 (GRCm39) probably benign Het
Myo18a G A 11: 77,741,632 (GRCm39) V1776I possibly damaging Het
Ncapg2 T C 12: 116,406,695 (GRCm39) L957S probably damaging Het
Ncoa3 T C 2: 165,896,422 (GRCm39) S442P probably damaging Het
Or5t5 G A 2: 86,616,079 (GRCm39) E2K probably benign Het
Or6x1 G A 9: 40,098,729 (GRCm39) G106D probably damaging Het
Or7g32 T A 9: 19,388,776 (GRCm39) T257S possibly damaging Het
Pdcd6 G T 13: 74,457,831 (GRCm39) N113K possibly damaging Het
Pfkfb4 C T 9: 108,856,810 (GRCm39) probably benign Het
Pfkm A G 15: 98,024,195 (GRCm39) H401R probably benign Het
Phldb2 C A 16: 45,601,814 (GRCm39) D754Y probably damaging Het
Plekhb2 T A 1: 34,902,195 (GRCm39) M49K probably damaging Het
Polrmt A G 10: 79,573,445 (GRCm39) S1057P possibly damaging Het
Prps1l1 A G 12: 35,035,077 (GRCm39) N64S probably benign Het
Prss3l T G 6: 41,422,190 (GRCm39) probably benign Het
Psg16 T C 7: 16,864,583 (GRCm39) S393P probably benign Het
Rundc1 C T 11: 101,315,973 (GRCm39) T15I probably benign Het
Scaf11 A G 15: 96,329,697 (GRCm39) L143S probably damaging Het
Sephs1 A G 2: 4,904,371 (GRCm39) T250A probably benign Het
Serpinf1 T G 11: 75,304,771 (GRCm39) I197L probably benign Het
Siglec1 C T 2: 130,916,445 (GRCm39) probably benign Het
Slc28a1 G A 7: 80,787,925 (GRCm39) V271I probably benign Het
Sntg1 T C 1: 8,853,048 (GRCm39) D34G probably damaging Het
Sptbn4 A T 7: 27,059,161 (GRCm39) probably benign Het
Suclg1 T C 6: 73,233,211 (GRCm39) I51T possibly damaging Het
Syne1 C T 10: 5,491,989 (GRCm39) R9Q probably damaging Het
Trim47 T A 11: 115,997,344 (GRCm39) H470L probably damaging Het
Ttc41 T A 10: 86,548,841 (GRCm39) Y12N possibly damaging Het
Tubgcp2 T C 7: 139,612,105 (GRCm39) E69G probably damaging Het
Tubgcp3 G A 8: 12,691,116 (GRCm39) T474M probably damaging Het
Ubr5 A T 15: 38,019,201 (GRCm39) N777K probably benign Het
Ush2a T C 1: 188,184,016 (GRCm39) L1440P probably damaging Het
Usp28 A C 9: 48,935,367 (GRCm39) D458A possibly damaging Het
Vcan A T 13: 89,851,665 (GRCm39) D1098E probably damaging Het
Vmn1r73 C T 7: 11,490,773 (GRCm39) T197I probably benign Het
Vmn2r15 T C 5: 109,434,344 (GRCm39) S787G probably damaging Het
Vmn2r90 T A 17: 17,948,401 (GRCm39) I549N probably damaging Het
Vps33b T A 7: 79,933,162 (GRCm39) probably null Het
Zfp516 A T 18: 83,005,795 (GRCm39) K900* probably null Het
Zfp974 T A 7: 27,610,357 (GRCm39) N456I probably damaging Het
Other mutations in Clcn4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00978:Clcn4 APN 7 7,290,672 (GRCm39) missense probably damaging 0.99
IGL01090:Clcn4 APN 7 7,297,035 (GRCm39) missense probably benign 0.01
IGL01650:Clcn4 APN 7 7,287,280 (GRCm39) splice site probably benign
IGL02404:Clcn4 APN 7 7,290,857 (GRCm39) missense probably benign 0.04
IGL02493:Clcn4 APN 7 7,287,243 (GRCm39) missense probably damaging 1.00
IGL02556:Clcn4 APN 7 7,299,065 (GRCm39) missense probably benign
IGL02661:Clcn4 APN 7 7,294,730 (GRCm39) splice site probably null
IGL02816:Clcn4 APN 7 7,298,087 (GRCm39) missense probably damaging 1.00
IGL02882:Clcn4 APN 7 7,293,464 (GRCm39) missense probably damaging 1.00
IGL03205:Clcn4 APN 7 7,293,419 (GRCm39) missense probably damaging 1.00
IGL03289:Clcn4 APN 7 7,287,257 (GRCm39) missense probably damaging 1.00
Delipidated UTSW 7 7,296,060 (GRCm39) missense probably damaging 1.00
R0183:Clcn4 UTSW 7 7,298,090 (GRCm39) nonsense probably null
R0555:Clcn4 UTSW 7 7,293,503 (GRCm39) missense possibly damaging 0.65
R0890:Clcn4 UTSW 7 7,291,964 (GRCm39) missense possibly damaging 0.89
R1463:Clcn4 UTSW 7 7,299,763 (GRCm39) nonsense probably null
R1549:Clcn4 UTSW 7 7,294,681 (GRCm39) missense probably damaging 1.00
R1563:Clcn4 UTSW 7 7,296,981 (GRCm39) missense probably damaging 1.00
R1966:Clcn4 UTSW 7 7,287,184 (GRCm39) makesense probably null
R2764:Clcn4 UTSW 7 7,299,798 (GRCm39) missense possibly damaging 0.81
R2874:Clcn4 UTSW 7 7,293,520 (GRCm39) missense probably benign 0.33
R4023:Clcn4 UTSW 7 7,293,427 (GRCm39) missense probably damaging 1.00
R4024:Clcn4 UTSW 7 7,293,427 (GRCm39) missense probably damaging 1.00
R4152:Clcn4 UTSW 7 7,297,833 (GRCm39) missense probably benign 0.02
R4154:Clcn4 UTSW 7 7,297,833 (GRCm39) missense probably benign 0.02
R4298:Clcn4 UTSW 7 7,299,737 (GRCm39) missense possibly damaging 0.93
R4535:Clcn4 UTSW 7 7,290,813 (GRCm39) missense probably benign 0.01
R4574:Clcn4 UTSW 7 7,290,804 (GRCm39) missense probably benign 0.23
R4977:Clcn4 UTSW 7 7,294,436 (GRCm39) missense probably benign 0.00
R5158:Clcn4 UTSW 7 7,294,618 (GRCm39) missense possibly damaging 0.94
R5302:Clcn4 UTSW 7 7,297,050 (GRCm39) missense possibly damaging 0.95
R5369:Clcn4 UTSW 7 7,299,032 (GRCm39) missense probably benign 0.26
R5624:Clcn4 UTSW 7 7,291,943 (GRCm39) missense probably benign 0.35
R5626:Clcn4 UTSW 7 7,292,017 (GRCm39) missense probably damaging 1.00
R5723:Clcn4 UTSW 7 7,294,681 (GRCm39) missense probably damaging 1.00
R6154:Clcn4 UTSW 7 7,294,481 (GRCm39) missense probably benign 0.00
R6259:Clcn4 UTSW 7 7,294,529 (GRCm39) missense possibly damaging 0.92
R6396:Clcn4 UTSW 7 7,297,024 (GRCm39) missense probably damaging 1.00
R6783:Clcn4 UTSW 7 7,302,181 (GRCm39) unclassified probably benign
R7320:Clcn4 UTSW 7 7,294,827 (GRCm39) missense probably benign 0.19
R7562:Clcn4 UTSW 7 7,298,081 (GRCm39) missense possibly damaging 0.92
R7586:Clcn4 UTSW 7 7,296,958 (GRCm39) missense probably benign 0.00
R7752:Clcn4 UTSW 7 7,296,936 (GRCm39) missense probably benign
R7860:Clcn4 UTSW 7 7,296,060 (GRCm39) missense probably damaging 1.00
R7872:Clcn4 UTSW 7 7,290,780 (GRCm39) missense probably benign
R7895:Clcn4 UTSW 7 7,298,167 (GRCm39) missense probably benign 0.26
R8069:Clcn4 UTSW 7 7,299,758 (GRCm39) missense probably damaging 0.99
R8083:Clcn4 UTSW 7 7,294,427 (GRCm39) missense possibly damaging 0.69
R9185:Clcn4 UTSW 7 7,287,197 (GRCm39) missense possibly damaging 0.74
R9281:Clcn4 UTSW 7 7,294,813 (GRCm39) missense probably benign 0.16
R9333:Clcn4 UTSW 7 7,292,192 (GRCm39) missense probably damaging 1.00
R9682:Clcn4 UTSW 7 7,299,797 (GRCm39) missense probably benign 0.02
X0019:Clcn4 UTSW 7 7,294,609 (GRCm39) missense probably damaging 1.00
Z1177:Clcn4 UTSW 7 7,297,755 (GRCm39) missense probably damaging 0.96
Z1177:Clcn4 UTSW 7 7,296,039 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- TTTCTCTCTGTGGAACCGACATGC -3'
(R):5'- AGAGTTCCTGAATCATGCCGCC -3'

Sequencing Primer
(F):5'- TGGAACCGACATGCGACAC -3'
(R):5'- GAATCATGCCGCCATATCTATGTTG -3'
Posted On 2013-04-24