Incidental Mutation 'R3898:Cln6'
ID309058
Institutional Source Beutler Lab
Gene Symbol Cln6
Ensembl Gene ENSMUSG00000032245
Gene Nameceroid-lipofuscinosis, neuronal 6
SynonymsD9Bwg1455e, 1810065L06Rik
MMRRC Submission 040906-MU
Accession Numbers
Is this an essential gene? Non essential (E-score: 0.000) question?
Stock #R3898 (G1)
Quality Score225
Status Not validated
Chromosome9
Chromosomal Location62838785-62852006 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to G at 62850652 bp
ZygosityHeterozygous
Amino Acid Change Phenylalanine to Cysteine at position 231 (F231C)
Ref Sequence ENSEMBL: ENSMUSP00000034776 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034776] [ENSMUST00000141821]
Predicted Effect probably damaging
Transcript: ENSMUST00000034776
AA Change: F231C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000034776
Gene: ENSMUSG00000032245
AA Change: F231C

DomainStartEndE-ValueType
Pfam:CLN6 27 306 1.3e-167 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000124984
AA Change: F113C
SMART Domains Protein: ENSMUSP00000115675
Gene: ENSMUSG00000032245
AA Change: F113C

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 probably benign
Transcript: ENSMUST00000141821
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156423
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.8%
Validation Efficiency
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
1700028P14Rik A G 19: 23,593,102 V101A probably benign Het
Alg1 A C 16: 5,236,389 I154L possibly damaging Het
Ankra2 C T 13: 98,273,809 L136F probably benign Het
Anpep A G 7: 79,839,225 S372P probably benign Het
Cabyr T C 18: 12,751,523 S356P probably benign Het
Cad G T 5: 31,074,022 C1633F probably benign Het
Cadps2 G A 6: 23,528,126 R425W probably damaging Het
Ccdc180 A G 4: 45,912,799 K593E possibly damaging Het
Cdh8 T A 8: 99,171,373 E436V probably damaging Het
Cul2 A G 18: 3,434,033 K677E probably benign Het
Cyp2c69 T C 19: 39,876,390 I215V probably benign Het
Dhx36 T C 3: 62,492,369 D393G probably damaging Het
Dnah7b T C 1: 46,243,257 V2850A probably damaging Het
Dnah8 G A 17: 30,854,898 R4514H probably damaging Het
Drg2 T A 11: 60,456,634 S50T probably benign Het
Ecscr A G 18: 35,713,652 S230P possibly damaging Het
Eif2ak4 T C 2: 118,430,923 V527A probably damaging Het
Elfn1 G A 5: 139,971,964 R241H probably damaging Het
Fchsd2 A G 7: 101,191,799 K172E possibly damaging Het
Fli1 C T 9: 32,476,722 G24R possibly damaging Het
Frmd3 A G 4: 74,074,109 D71G probably damaging Het
Ggnbp1 A G 17: 27,025,338 probably benign Het
Gpat2 T C 2: 127,435,098 F713S probably damaging Het
H2-Q2 C T 17: 35,342,767 P78S probably damaging Het
Kcnq2 C T 2: 181,109,686 A306T probably damaging Het
Lmntd1 G A 6: 145,413,426 P333S probably benign Het
Lrp1 G A 10: 127,592,100 R535* probably null Het
Mmrn2 G T 14: 34,399,560 probably null Het
Nlrp1a G A 11: 71,122,874 P517S probably benign Het
Olfr1383 A T 11: 49,524,559 I279F probably damaging Het
Pou4f1 T C 14: 104,465,729 *422W probably null Het
Ptpn14 C T 1: 189,850,531 P525L probably benign Het
Pyroxd2 C A 19: 42,740,392 G190C probably damaging Het
Rd3 T C 1: 191,985,256 V114A probably damaging Het
Sptbn5 T C 2: 120,057,210 noncoding transcript Het
Tbc1d5 A T 17: 50,963,744 F153Y probably damaging Het
Thop1 G A 10: 81,080,444 G429S probably damaging Het
Trim30d T A 7: 104,483,529 I184L probably benign Het
Ubr5 T C 15: 37,997,739 S1727G probably benign Het
Vezf1 T C 11: 88,076,173 F77L probably benign Het
Vmn2r12 C T 5: 109,090,504 A457T probably benign Het
Xirp1 A T 9: 120,019,340 M159K probably benign Het
Zkscan17 C T 11: 59,503,437 A113T probably damaging Het
Zyg11a T A 4: 108,210,194 N40Y probably damaging Het
Other mutations in Cln6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01586:Cln6 APN 9 62844618 missense probably damaging 0.98
IGL01601:Cln6 APN 9 62846970 missense probably damaging 0.99
IGL02351:Cln6 APN 9 62847125 missense probably benign 0.01
IGL02358:Cln6 APN 9 62847125 missense probably benign 0.01
boost UTSW 9 62847093 missense probably damaging 1.00
R1113:Cln6 UTSW 9 62850861 missense probably damaging 1.00
R1308:Cln6 UTSW 9 62850861 missense probably damaging 1.00
R3690:Cln6 UTSW 9 62846970 missense possibly damaging 0.87
R3746:Cln6 UTSW 9 62847002 missense probably benign
R4576:Cln6 UTSW 9 62838949 missense probably benign 0.35
R4996:Cln6 UTSW 9 62850655 missense probably damaging 0.98
R5027:Cln6 UTSW 9 62847093 missense probably damaging 1.00
R6048:Cln6 UTSW 9 62844626 missense probably damaging 1.00
R7348:Cln6 UTSW 9 62849176 missense probably benign 0.14
R7450:Cln6 UTSW 9 62850630 missense probably damaging 1.00
R7565:Cln6 UTSW 9 62850757 missense possibly damaging 0.86
R7837:Cln6 UTSW 9 62849048 missense
R7920:Cln6 UTSW 9 62849048 missense
Predicted Primers PCR Primer
(F):5'- ACACTCGGTCCACTCACTAG -3'
(R):5'- CACTGTTGACTGCTAACGTGG -3'

Sequencing Primer
(F):5'- CACTAGGTGAGATGTTCCGATTGAC -3'
(R):5'- AGATGACACCAGGGTACTTCTTTCTG -3'
Posted On2015-04-17