Incidental Mutation 'R7348:Cln6'
ID 570365
Institutional Source Beutler Lab
Gene Symbol Cln6
Ensembl Gene ENSMUSG00000032245
Gene Name ceroid-lipofuscinosis, neuronal 6
Synonyms D9Bwg1455e, 1810065L06Rik
MMRRC Submission 045380-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7348 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 62746067-62759288 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 62756458 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 201 (S201G)
Ref Sequence ENSEMBL: ENSMUSP00000034776 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034776] [ENSMUST00000141821]
AlphaFold Q3U466
Predicted Effect probably benign
Transcript: ENSMUST00000034776
AA Change: S201G

PolyPhen 2 Score 0.139 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000034776
Gene: ENSMUSG00000032245
AA Change: S201G

DomainStartEndE-ValueType
Pfam:CLN6 27 306 1.3e-167 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124984
SMART Domains Protein: ENSMUSP00000115675
Gene: ENSMUSG00000032245

DomainStartEndE-ValueType
Pfam:CLN6 1 64 1.3e-34 PFAM
Pfam:CLN6 68 189 2.7e-53 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000138276
Predicted Effect probably benign
Transcript: ENSMUST00000141821
Meta Mutation Damage Score 0.0605 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 98.8%
Validation Efficiency 99% (80/81)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function. [provided by RefSeq, Oct 2008]
PHENOTYPE: Homozygous mutants have progressive retinal atrophy, limb paralysis, and seizures that lead to early death. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abra G A 15: 41,729,555 (GRCm39) R282C probably damaging Het
Adcy2 T A 13: 68,882,794 (GRCm39) E314D possibly damaging Het
Adgrl2 A T 3: 148,523,402 (GRCm39) I274N Het
Adpgk A G 9: 59,221,069 (GRCm39) I292V probably benign Het
Agtrap G T 4: 148,165,054 (GRCm39) F124L probably benign Het
Ankrd26 A G 6: 118,485,525 (GRCm39) Y1450H probably damaging Het
Ap4e1 A T 2: 126,903,896 (GRCm39) S933C probably damaging Het
Ap4e1 G T 2: 126,903,897 (GRCm39) S933I possibly damaging Het
Ap5s1 A T 2: 131,054,572 (GRCm39) T128S possibly damaging Het
Arih1 T C 9: 59,393,341 (GRCm39) Y97C probably damaging Het
Atp1a3 A G 7: 24,678,251 (GRCm39) F1034S unknown Het
Bmp6 T C 13: 38,669,879 (GRCm39) S388P probably benign Het
Ccdc39 A G 3: 33,886,825 (GRCm39) V261A possibly damaging Het
Ccdc66 C T 14: 27,222,293 (GRCm39) C150Y probably damaging Het
Cep89 G A 7: 35,129,353 (GRCm39) R630H probably damaging Het
Cntnap4 T C 8: 113,391,909 (GRCm39) Y125H probably damaging Het
Copa A G 1: 171,929,790 (GRCm39) T286A possibly damaging Het
Cul9 A T 17: 46,821,919 (GRCm39) I1852K possibly damaging Het
Cyp2j8 C A 4: 96,332,877 (GRCm39) A490S probably benign Het
Cyp2t4 A G 7: 26,856,676 (GRCm39) I239V probably benign Het
Dpcd A G 19: 45,560,905 (GRCm39) Y111C probably damaging Het
E2f7 C T 10: 110,616,836 (GRCm39) T692I probably damaging Het
Fastkd5 A G 2: 130,457,055 (GRCm39) Y512H probably damaging Het
Fastkd5 A C 2: 130,458,359 (GRCm39) M77R probably benign Het
Fhod3 A G 18: 25,223,524 (GRCm39) R957G possibly damaging Het
H6pd C A 4: 150,068,359 (GRCm39) probably null Het
Haus5 G T 7: 30,356,391 (GRCm39) P544Q possibly damaging Het
Ifi207 CTGTTGATGAAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG CTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG 1: 173,556,762 (GRCm39) probably benign Het
Igf2r A G 17: 12,922,371 (GRCm39) Y1248H probably damaging Het
Izumo3 T C 4: 92,035,455 (GRCm39) N6S possibly damaging Het
Lrp6 G T 6: 134,427,781 (GRCm39) P1604T probably damaging Het
Map3k8 T A 18: 4,340,561 (GRCm39) H251L probably damaging Het
Mapre3 T C 5: 31,019,173 (GRCm39) Y6H probably benign Het
Mlh3 G T 12: 85,314,215 (GRCm39) P657Q probably damaging Het
Mrgpra1 T C 7: 46,985,157 (GRCm39) Y174C probably benign Het
Ms4a6d G A 19: 11,567,437 (GRCm39) Q155* probably null Het
Myh1 C A 11: 67,093,365 (GRCm39) P152Q probably damaging Het
Myh6 A T 14: 55,189,716 (GRCm39) L1110Q probably damaging Het
Nf1 T A 11: 79,427,676 (GRCm39) S1778T probably benign Het
Nkpd1 G A 7: 19,258,341 (GRCm39) E707K probably damaging Het
Nlrp4a A G 7: 26,143,698 (GRCm39) E21G probably damaging Het
Nr4a3 T G 4: 48,051,290 (GRCm39) S15A possibly damaging Het
Or2f1 T C 6: 42,721,790 (GRCm39) L273S possibly damaging Het
Or5p1 T C 7: 107,916,920 (GRCm39) V273A possibly damaging Het
Or5p64 T C 7: 107,855,330 (GRCm39) D5G probably benign Het
Or7a38 A G 10: 78,753,396 (GRCm39) T241A probably damaging Het
Parg G A 14: 31,972,036 (GRCm39) R677Q possibly damaging Het
Pcsk5 A T 19: 17,434,182 (GRCm39) C1395* probably null Het
Psd2 G A 18: 36,113,389 (GRCm39) S287N possibly damaging Het
Psd3 T C 8: 68,243,583 (GRCm39) N685S possibly damaging Het
Pygb C T 2: 150,628,903 (GRCm39) T39M probably benign Het
Rbfox1 C A 16: 7,225,888 (GRCm39) Y351* probably null Het
Rftn1 A G 17: 50,311,351 (GRCm39) L396P probably damaging Het
S1pr1 A G 3: 115,505,710 (GRCm39) Y295H probably damaging Het
Scn5a T C 9: 119,364,899 (GRCm39) M440V probably benign Het
Sel1l2 T C 2: 140,107,644 (GRCm39) N240S probably benign Het
Skic3 T C 13: 76,331,003 (GRCm39) F1478L possibly damaging Het
Skint1 T C 4: 111,878,770 (GRCm39) L234P probably damaging Het
Skint11 T A 4: 114,101,919 (GRCm39) Y311N probably benign Het
Slc6a5 A T 7: 49,559,915 (GRCm39) probably benign Het
Tas2r134 T C 2: 51,518,414 (GRCm39) S298P possibly damaging Het
Tbcd C A 11: 121,485,137 (GRCm39) A773D probably benign Het
Tgoln1 G C 6: 72,593,261 (GRCm39) T73R probably benign Het
Tmem184a T C 5: 139,799,809 (GRCm39) E24G probably null Het
Tmem207 C A 16: 26,335,577 (GRCm39) W53C possibly damaging Het
Tns1 T A 1: 73,956,076 (GRCm39) H549L possibly damaging Het
Ttc41 G T 10: 86,586,212 (GRCm39) E839* probably null Het
Ufd1 T G 16: 18,634,635 (GRCm39) probably benign Het
Usp28 A G 9: 48,942,177 (GRCm39) E713G probably benign Het
Utrn A G 10: 12,623,762 (GRCm39) W159R probably damaging Het
Vcl C T 14: 21,053,218 (GRCm39) A411V probably benign Het
Vcl T A 14: 21,059,020 (GRCm39) C545* probably null Het
Vmn1r120 A T 7: 20,787,377 (GRCm39) S111R probably damaging Het
Wwox T A 8: 115,199,392 (GRCm39) C146S probably benign Het
Zbtb2 T C 10: 4,324,574 (GRCm39) T57A possibly damaging Het
Zfp362 T C 4: 128,671,010 (GRCm39) D336G possibly damaging Het
Zfp628 G A 7: 4,924,817 (GRCm39) G1013E probably damaging Het
Zfp704 A G 3: 9,539,658 (GRCm39) S231P probably damaging Het
Zhx3 G T 2: 160,624,038 (GRCm39) S43* probably null Het
Other mutations in Cln6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01586:Cln6 APN 9 62,751,900 (GRCm39) missense probably damaging 0.98
IGL01601:Cln6 APN 9 62,754,252 (GRCm39) missense probably damaging 0.99
IGL02351:Cln6 APN 9 62,754,407 (GRCm39) missense probably benign 0.01
IGL02358:Cln6 APN 9 62,754,407 (GRCm39) missense probably benign 0.01
boost UTSW 9 62,754,375 (GRCm39) missense probably damaging 1.00
R1113:Cln6 UTSW 9 62,758,143 (GRCm39) missense probably damaging 1.00
R1308:Cln6 UTSW 9 62,758,143 (GRCm39) missense probably damaging 1.00
R3690:Cln6 UTSW 9 62,754,252 (GRCm39) missense possibly damaging 0.87
R3746:Cln6 UTSW 9 62,754,284 (GRCm39) missense probably benign
R3898:Cln6 UTSW 9 62,757,934 (GRCm39) missense probably damaging 1.00
R4576:Cln6 UTSW 9 62,746,231 (GRCm39) missense probably benign 0.35
R4996:Cln6 UTSW 9 62,757,937 (GRCm39) missense probably damaging 0.98
R5027:Cln6 UTSW 9 62,754,375 (GRCm39) missense probably damaging 1.00
R6048:Cln6 UTSW 9 62,751,908 (GRCm39) missense probably damaging 1.00
R7450:Cln6 UTSW 9 62,757,912 (GRCm39) missense probably damaging 1.00
R7565:Cln6 UTSW 9 62,758,039 (GRCm39) missense possibly damaging 0.86
R7837:Cln6 UTSW 9 62,756,330 (GRCm39) missense
R7982:Cln6 UTSW 9 62,756,450 (GRCm39) missense possibly damaging 0.69
R9206:Cln6 UTSW 9 62,756,465 (GRCm39) missense probably benign 0.24
R9208:Cln6 UTSW 9 62,756,465 (GRCm39) missense probably benign 0.24
R9210:Cln6 UTSW 9 62,757,973 (GRCm39) missense probably damaging 1.00
R9212:Cln6 UTSW 9 62,757,973 (GRCm39) missense probably damaging 1.00
R9311:Cln6 UTSW 9 62,757,900 (GRCm39) missense probably damaging 1.00
R9369:Cln6 UTSW 9 62,754,431 (GRCm39) missense probably damaging 0.98
R9618:Cln6 UTSW 9 62,758,111 (GRCm39) missense probably damaging 0.99
R9627:Cln6 UTSW 9 62,754,303 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTCTTAGGGCAGAAAAGGCTGG -3'
(R):5'- TCTCAAGGTGTCTAGCAACAG -3'

Sequencing Primer
(F):5'- CTGGAAGTAGAGCAGTGTGC -3'
(R):5'- TGTCCTGGAACTCTGTAGACCAAG -3'
Posted On 2019-09-13