Incidental Mutation 'R0326:Cln3'
ID 25849
Institutional Source Beutler Lab
Gene Symbol Cln3
Ensembl Gene ENSMUSG00000030720
Gene Name CLN3 lysosomal/endosomal transmembrane protein, battenin
Synonyms battenin
MMRRC Submission 038536-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0326 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 126170571-126184991 bp(-) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) T to G at 126182217 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Leucine at position 1 (M1L)
Ref Sequence ENSEMBL: ENSMUSP00000118054 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032962] [ENSMUST00000039522] [ENSMUST00000084589] [ENSMUST00000098036] [ENSMUST00000116269] [ENSMUST00000125508] [ENSMUST00000150311] [ENSMUST00000147086] [ENSMUST00000128970] [ENSMUST00000131860] [ENSMUST00000144173] [ENSMUST00000137646] [ENSMUST00000138558] [ENSMUST00000150917] [ENSMUST00000150587]
AlphaFold Q61124
Predicted Effect possibly damaging
Transcript: ENSMUST00000032962
AA Change: M1L

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 438 3.5e-215 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000039522
SMART Domains Protein: ENSMUSP00000042028
Gene: ENSMUSG00000042759

DomainStartEndE-ValueType
low complexity region 45 59 N/A INTRINSIC
low complexity region 171 181 N/A INTRINSIC
low complexity region 351 363 N/A INTRINSIC
low complexity region 381 396 N/A INTRINSIC
low complexity region 465 476 N/A INTRINSIC
low complexity region 588 608 N/A INTRINSIC
low complexity region 837 862 N/A INTRINSIC
low complexity region 869 881 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000084589
AA Change: M1L

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 438 3.5e-215 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000098036
AA Change: M1L

PolyPhen 2 Score 0.802 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 414 4.3e-191 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000116269
AA Change: M1L

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 39 437 1.6e-140 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000125508
AA Change: M1L

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 76 1.2e-17 PFAM
Pfam:CLN3 73 151 2.8e-38 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000150311
AA Change: M1L

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000116160
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 69 1.5e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000147086
AA Change: M1L

PolyPhen 2 Score 0.135 (Sensitivity: 0.92; Specificity: 0.86)
Predicted Effect possibly damaging
Transcript: ENSMUST00000128970
AA Change: M1L

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 196 1.2e-87 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000131860
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128225
Predicted Effect probably benign
Transcript: ENSMUST00000144173
Predicted Effect probably benign
Transcript: ENSMUST00000137646
Predicted Effect probably benign
Transcript: ENSMUST00000138558
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134246
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128049
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134406
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134498
Predicted Effect possibly damaging
Transcript: ENSMUST00000150917
AA Change: M1L

PolyPhen 2 Score 0.924 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 77 1.6e-18 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000150587
AA Change: M1L

PolyPhen 2 Score 0.965 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720
AA Change: M1L

DomainStartEndE-ValueType
Pfam:CLN3 37 70 4.1e-15 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153790
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184825
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.0%
  • 10x: 95.8%
  • 20x: 91.8%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a transmembrane protein called battenin that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis genes, cause a number of neurodegenerative diseases collectively known as neuronal ceroid lipofuscinoses, the most common of which is juvenile neuronal ceroid-lipofuscinosis (Batten disease). Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2016]
PHENOTYPE: Nullizygous mutations can result in neuronal ceroid lipofuscinosis, degeneration of the retina, cerebral cortex and cerebellum, hypertrophy of hippocampal interneuron populations, gliosis, neurological deficits, and premature death. Homozygotes for a null allele show impaired water and K+ balance. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 99 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
AA986860 C T 1: 130,670,635 (GRCm39) P286S possibly damaging Het
Aagab T A 9: 63,526,444 (GRCm39) S156T probably damaging Het
Abca14 T G 7: 119,823,642 (GRCm39) Y390D probably damaging Het
Abcc2 T A 19: 43,814,386 (GRCm39) I1122N possibly damaging Het
Adamts16 T C 13: 70,927,730 (GRCm39) E503G possibly damaging Het
Adamts9 A T 6: 92,835,038 (GRCm39) C697* probably null Het
Adgrv1 T C 13: 81,623,112 (GRCm39) D3837G possibly damaging Het
Ahcyl T A 16: 45,974,246 (GRCm39) D377V probably benign Het
Aire T A 10: 77,878,433 (GRCm39) R128S probably damaging Het
Alkbh2 A C 5: 114,262,011 (GRCm39) *240E probably null Het
Als2 T C 1: 59,219,742 (GRCm39) Y1191C probably damaging Het
Anapc5 A T 5: 122,952,667 (GRCm39) V186E probably benign Het
Apob C T 12: 8,040,307 (GRCm39) A548V probably damaging Het
B3galt4 A T 17: 34,169,722 (GRCm39) V172E probably damaging Het
Bbs7 A C 3: 36,646,525 (GRCm39) C432G possibly damaging Het
Cacna2d3 T A 14: 28,767,601 (GRCm39) E758V probably damaging Het
Cactin T G 10: 81,158,496 (GRCm39) L154R probably benign Het
Ccdc88a A C 11: 29,411,021 (GRCm39) R502S probably benign Het
Ccnf A T 17: 24,450,784 (GRCm39) I398N possibly damaging Het
Chd1 A T 17: 15,988,828 (GRCm39) D1527V probably damaging Het
Chd1 A T 17: 15,988,830 (GRCm39) M1528L probably benign Het
Chrac1 G A 15: 72,964,675 (GRCm39) probably null Het
Cnot6 T C 11: 49,568,263 (GRCm39) Y442C probably damaging Het
Col19a1 A T 1: 24,324,132 (GRCm39) probably null Het
Col1a2 T C 6: 4,537,838 (GRCm39) F1116L unknown Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Cops4 T G 5: 100,676,408 (GRCm39) V53G probably damaging Het
Crnkl1 A G 2: 145,761,875 (GRCm39) S561P probably benign Het
Ctnnb1 C A 9: 120,780,778 (GRCm39) Q99K probably benign Het
Cxcr5 T C 9: 44,424,578 (GRCm39) S360G probably benign Het
Dab2 G A 15: 6,447,797 (GRCm39) V60M probably damaging Het
Ddx3y A T Y: 1,263,321 (GRCm39) Y648* probably null Het
Dennd2a T A 6: 39,474,044 (GRCm39) D430V probably damaging Het
Dsp G T 13: 38,376,846 (GRCm39) E1544* probably null Het
Efcab7 A T 4: 99,719,631 (GRCm39) M38L possibly damaging Het
Fto A G 8: 92,136,155 (GRCm39) N141S probably damaging Het
Gabrp A G 11: 33,504,362 (GRCm39) F318L probably damaging Het
Gmeb1 A C 4: 131,969,663 (GRCm39) C103W probably damaging Het
Heatr9 T C 11: 83,405,365 (GRCm39) D365G probably damaging Het
Hif3a G A 7: 16,778,325 (GRCm39) R436W probably benign Het
Hint2 A G 4: 43,654,378 (GRCm39) V145A probably damaging Het
Hmcn2 T A 2: 31,313,237 (GRCm39) L3482* probably null Het
Hsd3b1 A T 3: 98,760,590 (GRCm39) Y134N probably damaging Het
Impg2 T A 16: 56,080,848 (GRCm39) V775E probably damaging Het
Ipo5 A G 14: 121,159,635 (GRCm39) I154M probably benign Het
Itgad T A 7: 127,797,550 (GRCm39) F893Y probably benign Het
Itprid1 A T 6: 55,875,228 (GRCm39) M393L possibly damaging Het
Kdm4a T C 4: 118,018,903 (GRCm39) R438G probably benign Het
Klk1b11 T A 7: 43,425,943 (GRCm39) M1K probably null Het
Lama5 A T 2: 179,824,219 (GRCm39) V2602D possibly damaging Het
Lrch3 T C 16: 32,799,870 (GRCm39) S35P probably damaging Het
Mfn2 A G 4: 147,967,745 (GRCm39) L441P probably damaging Het
Mgat4c A T 10: 102,224,565 (GRCm39) I260F probably damaging Het
Mon1b T A 8: 114,364,375 (GRCm39) S51T probably benign Het
Myh11 T C 16: 14,036,744 (GRCm39) D993G probably benign Het
Myo1a A G 10: 127,552,166 (GRCm39) N762D probably benign Het
Nacc2 A T 2: 25,950,345 (GRCm39) Y464N probably damaging Het
Nckap1 A G 2: 80,383,714 (GRCm39) I150T probably benign Het
Ndufv2 G T 17: 66,387,816 (GRCm39) P119T probably damaging Het
Noc4l G A 5: 110,800,241 (GRCm39) R95* probably null Het
Ntng1 A T 3: 110,042,819 (GRCm39) Y2* probably null Het
Oog4 T C 4: 143,165,773 (GRCm39) N53D probably benign Het
Or10ak11 A T 4: 118,687,022 (GRCm39) V205D possibly damaging Het
Or4d11 C T 19: 12,013,525 (GRCm39) V194I probably benign Het
Or6c6c A G 10: 129,541,638 (GRCm39) E297G possibly damaging Het
Or9i1b C T 19: 13,896,873 (GRCm39) T163I probably benign Het
Phkg2 T G 7: 127,173,075 (GRCm39) L11R probably damaging Het
Pogz A G 3: 94,777,424 (GRCm39) D368G probably damaging Het
Prex2 T A 1: 11,355,289 (GRCm39) L1530Q probably damaging Het
Prmt1 C T 7: 44,628,878 (GRCm39) E144K probably damaging Het
Prss8 T A 7: 127,526,348 (GRCm39) I121F probably benign Het
Psmd13 T C 7: 140,477,624 (GRCm39) L314P probably damaging Het
Ptch2 G A 4: 116,966,081 (GRCm39) G467D probably damaging Het
Rbm20 C A 19: 53,852,596 (GRCm39) P1192Q probably damaging Het
Rpl19 T A 11: 97,919,200 (GRCm39) D45E probably benign Het
Rsph10b C T 5: 143,903,946 (GRCm39) A219V probably damaging Het
Rtraf C T 14: 19,864,600 (GRCm39) probably null Het
Scaf1 T A 7: 44,658,175 (GRCm39) T235S probably damaging Het
Shank1 T A 7: 43,968,594 (GRCm39) C296S unknown Het
Slc39a7 A T 17: 34,247,924 (GRCm39) V426D probably damaging Het
Slc41a2 A T 10: 83,119,610 (GRCm39) V384D probably damaging Het
Slco1c1 T C 6: 141,505,499 (GRCm39) L475P probably benign Het
Slco6d1 A C 1: 98,418,359 (GRCm39) K515T probably benign Het
Sos2 T C 12: 69,682,459 (GRCm39) E253G probably damaging Het
Sp6 G T 11: 96,912,361 (GRCm39) D25Y possibly damaging Het
Syt11 A C 3: 88,669,855 (GRCm39) D12E possibly damaging Het
Taf2 A G 15: 54,910,856 (GRCm39) L606P probably damaging Het
Tbc1d5 A G 17: 51,273,764 (GRCm39) Y116H probably damaging Het
Tnfrsf8 A G 4: 145,015,029 (GRCm39) I243T possibly damaging Het
Tnxb A G 17: 34,917,153 (GRCm39) S2183G probably benign Het
Trim66 T C 7: 109,059,379 (GRCm39) Y853C probably benign Het
Ttn T A 2: 76,567,839 (GRCm39) T27685S probably damaging Het
Ttn T C 2: 76,573,466 (GRCm39) E25809G probably damaging Het
Uvssa G A 5: 33,566,191 (GRCm39) G445S probably benign Het
Zfp326 T C 5: 106,058,141 (GRCm39) S427P probably damaging Het
Zfp592 A G 7: 80,674,637 (GRCm39) T534A possibly damaging Het
Zfp672 A G 11: 58,207,173 (GRCm39) S383P possibly damaging Het
Zfp799 A G 17: 33,039,700 (GRCm39) S188P possibly damaging Het
Zyg11b A C 4: 108,129,450 (GRCm39) V54G possibly damaging Het
Other mutations in Cln3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01084:Cln3 APN 7 126,174,426 (GRCm39) missense probably damaging 1.00
IGL01603:Cln3 APN 7 126,174,526 (GRCm39) missense probably benign 0.30
IGL02216:Cln3 APN 7 126,174,514 (GRCm39) critical splice donor site probably null
IGL02440:Cln3 APN 7 126,181,954 (GRCm39) missense probably benign 0.01
IGL03118:Cln3 APN 7 126,174,569 (GRCm39) missense probably null 0.00
R0610:Cln3 UTSW 7 126,179,361 (GRCm39) missense probably damaging 1.00
R1256:Cln3 UTSW 7 126,182,208 (GRCm39) missense probably damaging 0.98
R2136:Cln3 UTSW 7 126,181,971 (GRCm39) missense probably benign 0.00
R2202:Cln3 UTSW 7 126,178,390 (GRCm39) missense probably benign 0.11
R3977:Cln3 UTSW 7 126,179,308 (GRCm39) splice site probably benign
R4563:Cln3 UTSW 7 126,171,730 (GRCm39) missense probably damaging 0.98
R4690:Cln3 UTSW 7 126,174,565 (GRCm39) missense possibly damaging 0.61
R4936:Cln3 UTSW 7 126,174,393 (GRCm39) missense probably damaging 1.00
R5668:Cln3 UTSW 7 126,171,558 (GRCm39) missense probably benign 0.01
R5726:Cln3 UTSW 7 126,174,673 (GRCm39) missense probably null 0.00
R6385:Cln3 UTSW 7 126,174,207 (GRCm39) missense probably null 1.00
R6591:Cln3 UTSW 7 126,178,606 (GRCm39) missense possibly damaging 0.82
R6691:Cln3 UTSW 7 126,178,606 (GRCm39) missense possibly damaging 0.82
R6891:Cln3 UTSW 7 126,181,975 (GRCm39) missense possibly damaging 0.88
R7173:Cln3 UTSW 7 126,178,589 (GRCm39) missense probably damaging 1.00
R7214:Cln3 UTSW 7 126,181,942 (GRCm39) missense probably damaging 1.00
R7426:Cln3 UTSW 7 126,180,912 (GRCm39) missense probably benign 0.31
R7520:Cln3 UTSW 7 126,180,852 (GRCm39) missense probably damaging 1.00
R7556:Cln3 UTSW 7 126,174,242 (GRCm39) missense probably damaging 0.97
R7761:Cln3 UTSW 7 126,180,886 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCATTCTTCCAAAGGACACTCCGAC -3'
(R):5'- TCGTGTATAGCAGACAGCGGAACC -3'

Sequencing Primer
(F):5'- TCCGACTATCCAACCGAGGG -3'
(R):5'- AGCGGAACCTGGGACTG -3'
Posted On 2013-04-16