Incidental Mutation 'R3690:Cln6'
ID 269735
Institutional Source Beutler Lab
Gene Symbol Cln6
Ensembl Gene ENSMUSG00000032245
Gene Name ceroid-lipofuscinosis, neuronal 6
Synonyms D9Bwg1455e, 1810065L06Rik
MMRRC Submission 040685-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3690 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 62746067-62759288 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 62754252 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Threonine at position 98 (I98T)
Ref Sequence ENSEMBL: ENSMUSP00000034776 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034776] [ENSMUST00000141821]
AlphaFold Q3U466
Predicted Effect possibly damaging
Transcript: ENSMUST00000034776
AA Change: I98T

PolyPhen 2 Score 0.872 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000034776
Gene: ENSMUSG00000032245
AA Change: I98T

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 0.2568 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 95.0%
Validation Efficiency 98% (54/55)
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: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aass T A 6: 23,091,328 (GRCm39) Y629F probably benign Het
Abcb5 T A 12: 118,836,668 (GRCm39) D1081V probably damaging Het
Afdn A G 17: 14,108,671 (GRCm39) E1398G probably damaging Het
Atp8b5 T C 4: 43,368,055 (GRCm39) C893R probably damaging Het
Avl9 C T 6: 56,713,812 (GRCm39) H357Y probably benign Het
Bclaf1 C T 10: 20,201,143 (GRCm39) T423I possibly damaging Het
Btbd19 A T 4: 116,977,789 (GRCm39) probably benign Het
Cap1 A G 4: 122,758,419 (GRCm39) S254P probably damaging Het
Cdc42ep1 T C 15: 78,731,629 (GRCm39) S25P probably benign Het
Cul9 T C 17: 46,814,957 (GRCm39) probably null Het
Dcx T C X: 142,660,240 (GRCm39) E268G possibly damaging Het
Ddias G A 7: 92,509,366 (GRCm39) P183L probably benign Het
Dnase2b A T 3: 146,299,326 (GRCm39) Y42* probably null Het
Dusp16 C T 6: 134,738,082 (GRCm39) probably benign Het
Egfr T C 11: 16,821,881 (GRCm39) probably benign Het
Fam171a1 T C 2: 3,227,393 (GRCm39) V842A probably benign Het
Folr1 T C 7: 101,507,745 (GRCm39) S232G probably benign Het
Foxj3 T C 4: 119,473,839 (GRCm39) probably benign Het
Fpr-rs6 T C 17: 20,403,137 (GRCm39) M75V probably benign Het
Fxyd5 G T 7: 30,735,864 (GRCm39) L128M possibly damaging Het
Gigyf2 T C 1: 87,349,238 (GRCm39) S500P possibly damaging Het
Inppl1 A G 7: 101,481,275 (GRCm39) L268P probably damaging Het
Klk1b24 A T 7: 43,841,243 (GRCm39) H192L probably benign Het
Llgl1 T G 11: 60,597,828 (GRCm39) Y316D probably damaging Het
Lmbrd1 T A 1: 24,801,374 (GRCm39) *143R probably null Het
Map3k15 T A X: 158,905,568 (GRCm39) N1295K possibly damaging Het
Mcm3ap A G 10: 76,318,513 (GRCm39) E678G probably damaging Het
Mrpl44 T A 1: 79,757,366 (GRCm39) Y270* probably null Het
Nav1 T A 1: 135,395,382 (GRCm39) I996L probably benign Het
Neb T C 2: 52,027,397 (GRCm39) E6868G probably damaging Het
Nexmif A T X: 103,131,213 (GRCm39) Y235N probably damaging Het
Nup50 C T 15: 84,823,994 (GRCm39) T449M probably damaging Het
Or14a256 G A 7: 86,265,686 (GRCm39) P56S probably damaging Het
Or2b6 A G 13: 21,823,508 (GRCm39) F62L probably damaging Het
Or51aa2 T C 7: 103,188,274 (GRCm39) T56A probably benign Het
Or52e8b A G 7: 104,673,902 (GRCm39) L95P probably damaging Het
Or52n2 T C 7: 104,542,724 (GRCm39) Y37C possibly damaging Het
Pald1 A T 10: 61,191,587 (GRCm39) probably null Het
Pde11a T A 2: 76,121,510 (GRCm39) K357I probably damaging Het
Ric3 A G 7: 108,637,817 (GRCm39) V312A possibly damaging Het
Scaper C T 9: 55,791,205 (GRCm39) G231D probably benign Het
Smc1b T A 15: 85,001,464 (GRCm39) probably benign Het
Smcr8 A G 11: 60,668,854 (GRCm39) M1V probably null Het
Smtn T C 11: 3,477,687 (GRCm39) probably benign Het
Spatc1 A T 15: 76,152,495 (GRCm39) K42* probably null Het
Taf7l A T X: 133,365,074 (GRCm39) I449K probably damaging Het
Tex47 A G 5: 7,354,777 (GRCm39) probably benign Het
Tram2 T A 1: 21,075,824 (GRCm39) Y198F probably damaging Het
Ttn C G 2: 76,629,588 (GRCm39) W14284C probably damaging Het
Ube3a A G 7: 58,926,547 (GRCm39) K442E probably damaging Het
Vmn2r116 T A 17: 23,603,798 (GRCm39) F8I unknown Het
Vmn2r59 A G 7: 41,661,370 (GRCm39) F815S possibly damaging Het
Zap70 T C 1: 36,820,493 (GRCm39) C563R probably damaging Het
Zfp579 T C 7: 4,997,719 (GRCm39) H64R probably 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
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
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'- CTGCTGGGTTTACACTCCAC -3'
(R):5'- TAGACAACAGTGCCTTCCCTC -3'

Sequencing Primer
(F):5'- CACCATGATCAGTAGCTAGGCTG -3'
(R):5'- ATACAATCTATGGTCAGCCTGGGC -3'
Posted On 2015-02-19