Incidental Mutation 'R3746:Cln6'
ID 309815
Institutional Source Beutler Lab
Gene Symbol Cln6
Ensembl Gene ENSMUSG00000032245
Gene Name ceroid-lipofuscinosis, neuronal 6
Synonyms D9Bwg1455e, 1810065L06Rik
MMRRC Submission 040732-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3746 (G1)
Quality Score 183
Status Validated
Chromosome 9
Chromosomal Location 62746067-62759288 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 62754284 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 109 (I109V)
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: I109V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000034776
Gene: ENSMUSG00000032245
AA Change: I109V

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 noncoding transcript
Transcript: ENSMUST00000132250
Predicted Effect probably benign
Transcript: ENSMUST00000138276
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139570
Predicted Effect probably benign
Transcript: ENSMUST00000141821
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156423
Meta Mutation Damage Score 0.0614 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 95.1%
Validation Efficiency 100% (45/45)
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aasdh C A 5: 77,036,501 (GRCm39) E347* probably null Het
Abcb5 T C 12: 118,838,355 (GRCm39) D1069G probably damaging Het
Ago1 A G 4: 126,354,837 (GRCm39) I125T probably benign Het
Ccdc40 T C 11: 119,155,252 (GRCm39) V1164A probably benign Het
Chd7 G A 4: 8,752,537 (GRCm39) V345M probably damaging Het
Csmd3 A T 15: 47,713,162 (GRCm39) F1604Y probably benign Het
Cx3cr1 T C 9: 119,881,132 (GRCm39) H90R probably damaging Het
Dip2c A T 13: 9,651,509 (GRCm39) D674V probably damaging Het
Dnah17 T C 11: 117,973,742 (GRCm39) S1935G probably benign Het
Eif3g G A 9: 20,805,993 (GRCm39) R295C probably benign Het
Epha5 T C 5: 84,206,963 (GRCm39) K998E probably damaging Het
Fam171b A T 2: 83,709,944 (GRCm39) T539S probably damaging Het
Fer1l4 G T 2: 155,876,968 (GRCm39) H1159N probably benign Het
Fsip1 A G 2: 118,063,531 (GRCm39) C313R probably damaging Het
Gm37240 T G 3: 84,426,919 (GRCm39) N168T probably benign Het
Gm7589 T C 9: 59,053,138 (GRCm39) noncoding transcript Het
Igkv20-101-2 A T 6: 68,451,942 (GRCm39) I66L possibly damaging Het
Irf3 T C 7: 44,648,297 (GRCm39) F54S probably damaging Het
Lrba T G 3: 86,283,260 (GRCm39) L1858R probably damaging Het
Lrp10 A T 14: 54,706,723 (GRCm39) N520I possibly damaging Het
Map3k21 A G 8: 126,661,839 (GRCm39) K479E probably damaging Het
Mpdz A C 4: 81,281,384 (GRCm39) V609G probably damaging Het
Opcml G A 9: 28,812,826 (GRCm39) V173M possibly damaging Het
Or51b6 T A 7: 103,556,267 (GRCm39) M207K probably benign Het
Osbpl7 T C 11: 96,946,879 (GRCm39) V223A probably damaging Het
Pcdh17 A T 14: 84,770,477 (GRCm39) Y985F probably benign Het
Piezo1 G T 8: 123,219,377 (GRCm39) F1084L probably damaging Het
Pkhd1 A G 1: 20,128,524 (GRCm39) *4060Q probably null Het
Plekhn1 T C 4: 156,310,051 (GRCm39) T88A probably benign Het
Pramel18 T A 4: 101,767,073 (GRCm39) D107E possibly damaging Het
Rmdn2 T A 17: 79,977,981 (GRCm39) probably null Het
Selenom A G 11: 3,467,132 (GRCm39) E137G probably benign Het
Slc38a7 A G 8: 96,570,380 (GRCm39) probably benign Het
Slc39a12 T C 2: 14,400,878 (GRCm39) probably benign Het
Slk T G 19: 47,608,248 (GRCm39) D400E possibly damaging Het
Supt16 A G 14: 52,417,596 (GRCm39) L306P probably damaging Het
Tas2r136 A T 6: 132,754,200 (GRCm39) F309Y probably damaging Het
Tmem63a G A 1: 180,790,679 (GRCm39) D446N possibly damaging Het
Trim63 G A 4: 134,042,665 (GRCm39) C44Y probably damaging Het
Ush2a G A 1: 188,542,489 (GRCm39) G3352S probably benign Het
Vmn1r4 A G 6: 56,934,116 (GRCm39) R207G probably damaging Het
Vmn2r76 A G 7: 85,874,763 (GRCm39) V738A probably benign Het
Vwa5b2 A G 16: 20,417,076 (GRCm39) probably benign Het
Zfhx4 G A 3: 5,308,225 (GRCm39) E484K possibly damaging 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
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
R7348:Cln6 UTSW 9 62,756,458 (GRCm39) missense probably benign 0.14
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'- TGATCAGTAGCTAGGCTGCC -3'
(R):5'- AGACAACAGTGCCTTCCCTC -3'

Sequencing Primer
(F):5'- TAGCTAGGCTGCCCTGCTAAG -3'
(R):5'- ATACAATCTATGGTCAGCCTGGGC -3'
Posted On 2015-04-17