Incidental Mutation 'R7173:Cln3'
ID 558428
Institutional Source Beutler Lab
Gene Symbol Cln3
Ensembl Gene ENSMUSG00000030720
Gene Name CLN3 lysosomal/endosomal transmembrane protein, battenin
Synonyms battenin
MMRRC Submission 045265-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7173 (G1)
Quality Score 225.009
Status Validated
Chromosome 7
Chromosomal Location 126170571-126184991 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 126178589 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 173 (T173A)
Ref Sequence ENSEMBL: ENSMUSP00000032962 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032962] [ENSMUST00000084589] [ENSMUST00000098036] [ENSMUST00000116269] [ENSMUST00000125508] [ENSMUST00000128970] [ENSMUST00000147086] [ENSMUST00000150311] [ENSMUST00000150587] [ENSMUST00000150917]
AlphaFold Q61124
Predicted Effect probably damaging
Transcript: ENSMUST00000032962
AA Change: T173A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000032962
Gene: ENSMUSG00000030720
AA Change: T173A

DomainStartEndE-ValueType
Pfam:CLN3 37 438 3.5e-215 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000084589
AA Change: T173A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000081636
Gene: ENSMUSG00000030720
AA Change: T173A

DomainStartEndE-ValueType
Pfam:CLN3 37 438 3.5e-215 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000098036
AA Change: T149A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000095644
Gene: ENSMUSG00000030720
AA Change: T149A

DomainStartEndE-ValueType
Pfam:CLN3 37 414 4.3e-191 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000116269
AA Change: T173A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000111973
Gene: ENSMUSG00000030720
AA Change: T173A

DomainStartEndE-ValueType
Pfam:CLN3 39 437 1.6e-140 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000125508
AA Change: T149A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000117561
Gene: ENSMUSG00000030720
AA Change: T149A

DomainStartEndE-ValueType
Pfam:CLN3 37 76 1.2e-17 PFAM
Pfam:CLN3 73 151 2.8e-38 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000128970
AA Change: T173A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000114901
Gene: ENSMUSG00000030720
AA Change: T173A

DomainStartEndE-ValueType
Pfam:CLN3 37 196 1.2e-87 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000147086
Predicted Effect probably benign
Transcript: ENSMUST00000150311
SMART Domains Protein: ENSMUSP00000116160
Gene: ENSMUSG00000030720

DomainStartEndE-ValueType
Pfam:CLN3 37 69 1.5e-14 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000150587
SMART Domains Protein: ENSMUSP00000118054
Gene: ENSMUSG00000030720

DomainStartEndE-ValueType
Pfam:CLN3 37 70 4.1e-15 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000150917
SMART Domains Protein: ENSMUSP00000138688
Gene: ENSMUSG00000030720

DomainStartEndE-ValueType
Pfam:CLN3 37 77 1.6e-18 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (79/79)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5031439G07Rik C T 15: 84,833,848 (GRCm39) V403I possibly damaging Het
Actn1 G A 12: 80,224,033 (GRCm39) R475C possibly damaging Het
Adam11 T C 11: 102,662,757 (GRCm39) L191P possibly damaging Het
Adam21 G T 12: 81,606,008 (GRCm39) Q585K probably benign Het
Akap3 T C 6: 126,841,729 (GRCm39) V116A probably benign Het
Alpk1 A T 3: 127,478,024 (GRCm39) Y74* probably null Het
Alx4 G T 2: 93,473,202 (GRCm39) G67C possibly damaging Het
Ankrd17 A T 5: 90,407,976 (GRCm39) C1414S possibly damaging Het
Ankrd44 T C 1: 54,805,550 (GRCm39) D170G probably damaging Het
Arpc2 T A 1: 74,303,531 (GRCm39) M266K probably damaging Het
Atp12a A T 14: 56,621,837 (GRCm39) N794I probably damaging Het
Cabin1 A G 10: 75,582,396 (GRCm39) L340P probably benign Het
Ccer1 A T 10: 97,529,217 (GRCm39) probably benign Het
Cfap73 A T 5: 120,772,279 (GRCm39) Y8N probably damaging Het
Cfhr4 C A 1: 139,659,415 (GRCm39) E705* probably null Het
Cxcl3 A T 5: 90,934,008 (GRCm39) probably benign Het
Cyp2c66 G C 19: 39,159,401 (GRCm39) C284S probably benign Het
Dnajc22 T C 15: 98,999,187 (GRCm39) V124A probably benign Het
Dync1h1 C G 12: 110,568,173 (GRCm39) D45E probably benign Het
Elmod3 A T 6: 72,554,235 (GRCm39) probably null Het
Enpp3 A C 10: 24,649,945 (GRCm39) V827G probably damaging Het
Esyt2 T C 12: 116,327,154 (GRCm39) I574T probably benign Het
Ext2 A T 2: 93,643,957 (GRCm39) I108N probably damaging Het
Fam186a T C 15: 99,843,531 (GRCm39) I904M unknown Het
Fmnl2 T C 2: 53,004,202 (GRCm39) I638T unknown Het
Fndc3c1 G C X: 105,478,679 (GRCm39) L724V possibly damaging Het
Fras1 G T 5: 96,925,937 (GRCm39) A3714S probably damaging Het
Fsd1 C A 17: 56,303,696 (GRCm39) R479S possibly damaging Het
Gaa C T 11: 119,169,817 (GRCm39) L624F probably damaging Het
Galnt2 G A 8: 125,032,292 (GRCm39) V86I probably benign Het
Gdap1l1 T G 2: 163,280,608 (GRCm39) V48G probably damaging Het
Gm10549 A G 18: 33,597,462 (GRCm39) T83A unknown Het
Gm11437 T G 11: 84,055,374 (GRCm39) T81P probably benign Het
Gm16253 T C 3: 96,487,979 (GRCm39) probably null Het
Gprc6a A T 10: 51,504,595 (GRCm39) M83K probably benign Het
Grik5 T C 7: 24,767,587 (GRCm39) D31G probably damaging Het
Hcrtr2 A G 9: 76,167,013 (GRCm39) L108P probably damaging Het
Herc2 T A 7: 55,853,575 (GRCm39) L3689Q probably damaging Het
Igf2bp1 T C 11: 95,859,290 (GRCm39) M407V probably benign Het
Irgq A T 7: 24,233,185 (GRCm39) E342V probably damaging Het
Itih2 A T 2: 10,109,974 (GRCm39) I593N probably damaging Het
Ivd G T 2: 118,701,870 (GRCm39) G101C probably damaging Het
Jakmip1 G A 5: 37,248,708 (GRCm39) G123S probably damaging Het
Kif14 T A 1: 136,406,908 (GRCm39) I580N probably damaging Het
Kmt2e A T 5: 23,669,855 (GRCm39) Y114F probably damaging Het
Ly6g5b C A 17: 35,333,680 (GRCm39) C99F probably damaging Het
Map3k20 C T 2: 72,271,758 (GRCm39) P629S probably benign Het
Mpl A G 4: 118,305,741 (GRCm39) probably null Het
Muc4 T C 16: 32,582,862 (GRCm39) F476L probably damaging Het
Mup18 T C 4: 61,590,199 (GRCm39) T110A probably benign Het
Nlrp9a A G 7: 26,257,603 (GRCm39) D407G probably benign Het
Nmur1 G A 1: 86,314,190 (GRCm39) R359C probably benign Het
Or5ac24 T C 16: 59,165,510 (GRCm39) T185A probably benign Het
Or5p64 C T 7: 107,854,955 (GRCm39) C130Y possibly damaging Het
Panx3 A T 9: 37,572,596 (GRCm39) M318K probably damaging Het
Pcnx1 T C 12: 81,999,777 (GRCm39) probably null Het
Pcsk5 T C 19: 17,455,241 (GRCm39) Y1063C possibly damaging Het
Psme3ip1 A T 8: 95,315,486 (GRCm39) F15L probably damaging Het
Rere G A 4: 150,553,195 (GRCm39) R129H probably damaging Het
Rpgrip1 A G 14: 52,349,633 (GRCm39) Y7C possibly damaging Het
Serpina6 T C 12: 103,613,253 (GRCm39) N349S possibly damaging Het
Slc10a1 T G 12: 81,002,750 (GRCm39) E296A probably damaging Het
Slc2a9 A T 5: 38,610,214 (GRCm39) probably null Het
Sptan1 T A 2: 29,873,221 (GRCm39) M138K probably benign Het
Tbl3 T C 17: 24,924,233 (GRCm39) T175A probably benign Het
Tbrg4 T C 11: 6,570,810 (GRCm39) T221A possibly damaging Het
Tenm2 T C 11: 35,932,378 (GRCm39) T1739A probably damaging Het
Tmed5 T C 5: 108,280,187 (GRCm39) D35G probably benign Het
Tnfsf15 A T 4: 63,647,889 (GRCm39) S250R probably damaging Het
Tnpo2 G T 8: 85,781,707 (GRCm39) V830F probably benign Het
Ttbk2 G T 2: 120,570,592 (GRCm39) S1187Y probably damaging Het
Ttn G A 2: 76,625,029 (GRCm39) T15183M possibly damaging Het
Tubgcp3 T C 8: 12,689,259 (GRCm39) probably null Het
Vmn1r38 T C 6: 66,753,278 (GRCm39) I279M possibly damaging Het
Vmn1r49 A T 6: 90,049,250 (GRCm39) Y251N possibly damaging Het
Vmn1r66 C T 7: 10,008,482 (GRCm39) V184I probably benign Het
Vmn2r26 T A 6: 124,038,255 (GRCm39) M610K probably benign Het
Xrn2 C T 2: 146,884,013 (GRCm39) P591S probably 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
R0326:Cln3 UTSW 7 126,182,217 (GRCm39) start codon destroyed probably damaging 0.96
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
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'- CATAGAAAGTAGGGTGTGCTGC -3'
(R):5'- AGACCCTAGCCTGTCTGTTC -3'

Sequencing Primer
(F):5'- GCCAGCCTGGGTGAGTC -3'
(R):5'- TCAGTGACAGATCTGTTCTTAGC -3'
Posted On 2019-06-26