Gene Symbol CLN3
Gene ID 1201
Chromosomal Location 16p12.1
Genomic RefSeqGene NG_008654.2 32641 bp
Transcript RefSeq NM_001042432.1 1915 bp NM_000086.2 1879 bp
Protein RefSeq NP_001035897.1 438 aa NP_000077.1 438 aa
No. of mutations 57
No. of sequence variations 13
Total No. of changes 70
Additional notes
Identifier Mutation Location cDNA Change RNA change Genomic DNA change hg19 dbSNP Protein Change Type of mutation Predicted functional effect Phenotype Histology No. of families Country of origin PMID References Patients Notes
cln3.056 A: Promoter c.-1101C>T r.(=) g.28504365G>A p.(=) Sequence variant n.a. n.a. 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.366 c.1-1101C>T; polymorphism
cln3.057 A: Promoter c.-681_-676delTGAAGC r.(?) g.28503756_28503761delGCTTCA p.(?) Sequence variant n.a. n.a. 21990111 Kousi et al., Hum Mutat, 2012 n.a c.1-676_1-675delTGAAGC; polymorphism?
cln3.058 B: Exon 1 c.1A>C r.(1a>c) g.28503080T>G p.? Missense or aberrant start 1 The Netherlands 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.342
cln3.036 C: Exon 2 c.105G>A r.(105g>a) g.28502823C>T CM052841 p.(Trp35*) nonsense 1 Germany 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.280
cln3.036 C: Exon 2 c.105G>A r.(105g>a) g.28502823C>T CM052841 p.(Trp35*) nonsense 1 USA 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.377
cln3.044 C: Exon 2 c.49G>T r.(49g>u) g.28502879C>A HM040128 p.(Glu17*) Nonsense 1 USA 16087292 Kwon et al., Neurosci Lett., 2005 Pa-cln3.253
cln3.059 C: Intron 2 c.125+5G>A r.spl? g.28502798C>T p.? splice defect 1 Belgium 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.346
cln3.030 C: Intron 2 c.126-1G>A                 IVS2-1G>A r.spl? g.28500708C>T CS011836 p.? Splice site   JNCL   1 Turkey 11589012 Mole et al.,Eur J Pediatr Neurol.,2001 (Taschner pers comm) Pa-cln3.394  
cln3.030 C: Intron 2 c.126-1G>A r.spl? g.28500708C>T CS011836 p.? splice defect 2 Turkey 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.322, 395
cln3.045 D: Exon 3 c.214C>T r.(214c>u) g.28500619G>A p.(Gln72*) Nonsense JNCL 1 USA 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.378
cln3.046 D: Intron 3 c.222+2T>G r.spl? g.28500609A>C p.? Splice site eJNCL/vLINCL 1 Greece 21990111 Santorelli and Michelakakis pers comm; Kousi et al., 2012 (Basinger personal communication to NCL database) Pa-cln3.392 originally IVS3+2T>G
cln3.053 D: Intron 3 c.222+5G>C r.spl? g.28500606C>G p.? Splice site JNCL 1 Germany 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.280
cln3.061 E: Exon 4 c.233_234insG r.(233_234insg) g.28499972_28499973insC p.(Thr80Asnfs*12) Frameshift       1 Turkey 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.323  
cln3.062 E: Exon 4 c.265C>T r.(265c>u) g.28499941G>A p.(Arg89*) Nonsense 1 Spain 21499717 Prez-Poyato et al., J Inherit Metab Dis 2011 Pa-cln3.271
cln3.062 E: Exon 4 c.265C>T r.(265c>u) g.28499941G>A p.(Arg89*) Nonsense 1 Norway 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.344
cln3.033 E: Intron 4 c.294-58G>A                 r.(=) g.28499970C>T p.(=) Sequence variant 1 The Netherlands 11589012 Mole et al 2001 (Taschner pers comm) Pa-cln3.398 orignally IVS4-59G>A
cln3.034 E: Intron 4 c.294-80G>A                  r.(=) g.28499992C>T p.(=) Sequence variant n.a. n.a. 11589012 Mole et al 2001 (Taschner pers comm) Pa-cln3.399 originally IVS-81G>A
cln3.005 F: Exon 5 c.302T>C r.(302u>c g.28499055A>G CM970329 p.(Leu101Pro) Missense Possibly damaging 1 The Netherlands 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.143
cln3.037 F: Exon 5 c.370dupT r.(370dupu) g.28498987dup CI053015 p.(Tyr124Leufs*36) Frameshift, introducing a premature stop codon 1 Spain 21499717 Prez-Poyato et al., J Inherit Metab Dis 2011 Pa-cln3.273
cln3.037 F: Exon 5 c.370dupT r.(370dupu) g.28498987dup CI053015 p.(Tyr124Leufs*36) Frameshift, introducing a premature stop codon 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Sims pers comm to NCL database) Pa-cln3.379 Formerly c.370insT
cln3.064 F: Exon 5 c.374G>A r.[374g>a, spl?] g.28498983C>T p.[Ser125Asn, ?] Missense a/affects splice site 2 Spain 21499717 Prez-Poyato et al., J Inherit Metab Dis 2011 Pa-cln3.262-263 formerly p.Ser125Asn / splice-site affecting
cln3.006 G: Exon 6  c.378_379dupCC r.(378_379dupcc) g.28498856_28498857dup CI972579 p.(Arg127Profs*55) 2-bp insertion 1 UK 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.144 formerly c.374-375insCC in Munroe et al 1997, and described as p.Val128GlyfsX54 in Kousi et al 2012, 
cln3.007 G: Exon 6 c.424delG r.(424delg) g.28498813delC CD972140 p.(Val142Leufs*39) 1-bp deletion 3 The Netherlands 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.167-169 described as p.Val142LeufsX39 in Kousi et al 2012
cln3.007 G: Exon 6 c.424delG r.(424delg) g.28498813delC CD972140 p.(Val142Leufs*39) 1-bp deletion       4 USA 9311735, 10964839, 21990111 Munroe et al., Am J Hum Genet; 1997, Bensaoula et al., 2000,  Kousi et al., Hum Mutat, 2012 Pa-cln3.170-171, Pa-cln3.237  
cln3.007 G: Exon 6 c.424delG r.(424delg) g.28498813delC CD972140 p.(Val142Leufs*39) 1-bp deletion       1 The Netherlands 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.337  
cln3.007 G: Exon 6 c.424delG r.(424delg) g.28498813delC CD972140 p.(Val142Leufs*39) 1-bp deletion       2 Belgium 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.338  
cln3.007 G: Exon 6 c.424delG r.(424delg) g.28498813delC CD972140 p.(Val142Leufs*39) 1-bp deletion       1 n.a. 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.339  
cln3.050 G: Exon 6 c.379delC r.(379delc) g.28498858delG p.(Arg127Glyfs*54) 1-bp deletion 1 Russia 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.379
cln3.065 G: Exon 6 c.400T>C r.(400u>c) g.28498837A>G p.(Cys134Arg) Missense Possibly damaging 1 Italy 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.285
cln3.008 G: Intron 6 c.461-13G>C r.[=, 461_533del] g.28497984C>G CS971664 p.[=, Val155Profs*2] Aberrant splicing that removes exon 7 1 USA 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.145 splice defect (confirmed by RT-PCR).  Sometimes aberrant splicing to give truncated protein p.Gly154fsX2; IVS6-13G>C: two transcripts: normal and one with exon 7 missing 
cln3.048 G: Intron 6 c.461-1G>C r.spl? g.28497972C>G p.? Splice defect 2 Canada 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.350
cln3.048 G: Intron 6 c.461-1G>A r.spl? g.28497972C>T p.? Intron change       1 USA 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.381 A Basinger???
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 151 Multiple 7553855, 9311735 The International Batten Disease Consortium, 1995     Munroe et al., 1997                                            Pa-cln3.001-80, Pa-cln3.081-139, Pa-cln3.178-190, There may be some overlap of families between these groups, p.Gly154_Ser438delinsGluGlyArgLeuGlyTrpLeuArgCys or 1 kb deletion; c.461-280_677+382del
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 35 Morocco, The Netherlands, UK, USA, Sweden, Denmark, Italy, Finland, Norway,  Germany, Iceland 9932957                                         16087292                                             9311735                                                              10964839                                9490299                                                        15991331                                             10916181                             9450775                                         21990111 The International Batten Disease Consortium, 1995     Munroe et al., 1997 Pa-cln3.142-177
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 2 Finland 7553855, 9311735, 9932957 The International Batten Disease Consortium, 1995     Munroe et al., 1997                                           Lauronen et al., 1999 Pa-cln3.140, Pa-cln3.141
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)       12 Spain 21499717 Prez-Poyato et al., 2011, Kousi et al., Hum Mutat, 2012 Pa-cln3.262-265, Pa-cln3.267-269, Pa-cln3.272  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)       6 Portugal 12796825 Texeira et al., J Neurol; 2003 Pa-cln3.240-247  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)       2 Portugal 12796825 Texeira et al., J Neurol; 2003 Pa-cln3.248-250  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)       1 Portugal 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.279  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Newfoundland 18684116 Moore et al., Clin Genet, 2008 Pa-cln3.254-256
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 USA 15032383 de los Reyes et al., J Child Neurol, 2004 Pa-cln3.251
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 USA 15991331 Leman et al., 2005 Pa-cln3.252
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 USA 16087292 Kwon et al., 2005 Pa-cln3.253
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Brazil 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.274
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)       3 Argentina 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.275-277  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 3 Czech Republic 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.281-283
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)     1 USA 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.284, 357, 367  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion)     2 Italy 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.285-286  
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 33 UK 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.287-321, Pa-cln3.347, 366
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 13 n.a. 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.324-336, Pa-cln3.339
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 5 The Netherlands 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.337, Pa-cln3.340-342, Pa-cln3.345
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Belgium 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.360
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Sweden 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.343, 370
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 2 Canada 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.348-349, Pa-cln3.350
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 France 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.358, Pa-cln3.364
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Germany 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.361
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Ireland 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.362
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 1 Italy 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.363, 365
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 2 Norway 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.368-369
cln3.001 G: Intron 6 - Intron 8 c.461-280_677+382del966 r.[461_677del, 461_790del] g.28497286_28498251del CG952287 p.[Gly154Alafs*29, Val155_Gly264del] (966 b deletion) 4 Russia 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.371-374
cln3.009 H: Exon 7 c.482C>G r.(482c>g) g.28497950G>C CM970330 p.(Ser161*) Nonsense 1 Sweden 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.146
cln3.010 H: Exon 7 c.485C>G r.(485c>g) g.28497947G>C CM970331 p.(Ser162*) Nonsense 1 Denmark 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.147
cln3.011 H: Exon 7 c.509T>C r.(509u>c) g.28497923A>G CM970332 p.(Leu170Pro) Missense Possibly damaging 1 UK 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.148-149
cln3.038 H: Exon 7 c.472G>C r.(472g>c) g.28497960C>G CM052839 p.(Ala158Pro) Missense Possibly damaging 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Sims pers comm to NCL database) Pa-cln3.382
cln3.004=c.3.043 H: Intron 7 c.533+1G>C r.spl? g.28497898C>G CS951380 p.? Splice site 1 Finland 7553855, 9311735, 9932957 The International Batten Disease Cosortium, 1995, Munroe et al., Am J Hum Genet; 1997 Pa-cln3.141 670+1G>C; c.533+1G>C splice defect
cln3.004=c.3.043 H: Intron 7 c.533+1G>A r.spl? g.28497898C>T CS052954 p.? Splice site 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Sims pers comm to NCL database) Pa-cln3.383 c.533+1G>A splice defect
cln3.012 I: Exon 8 c.558_559delAG r.(558_559delag) g.28497786_28497787delCT CD972141 p.(Gly187Aspfs*48) 2-bp deletion 1 Italy 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.172
cln3.013 I: Exon 8 c.586dupG or c.586-587insG r.(586dupg) g.28497759dup CI972580 p.(Ala196Glyfs*40) 1-bp insertion 1 UK 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.173
cln3.014 I: Exon 8 c.631C>T r.(631c>u) g.28497714G>A CM970333 p.(Gln211*) Nonsense  1 Italy 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.150
cln3.031 I: Exon 8 c.560G>C r.(560g>c) g.28497785C>G CM011758 p.(Gly187Ala) Missense Benign JNCL 1 Spain 21990111 Kousi et al., Hum Mutat, 2011 Pa-cln3.278
cln3.031 I: Exon 8 c.560G>C r.(560g>c) g.28497785C>G CM011758 p.(Gly187Ala) Missense JNCL 1 The Netherlands 11589012 Mole et al.,Eur J Pediatr Neurol.,2001 (Taschner pers comm) Pa-cln3.384
cln3.049 I: Exon 8 c.569delG r.(569delg) g.28497776delC p.(Gly190Glufs*65) 1-bp deletion JNCL 2 Portugal 16814585 Texeira et al., J Neurol; 2003, Bessa et al., Mol Genet Metab, 2006 Pa-cln3.249-250 previously described as c.568delG
cln3.054 I: Exon 8 c.565G>C r.(565g>c) g.28497780C>G p.(Gly189Arg) Missense Possibly damaging JNCL 1 Portugal 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.279
cln3.066 I: Exon 8 c.582G>T r.(582g>u) g.28497763C>A p.(=) Sequence variant 1 Lebanon 19489875 Sarpong et al., Clin Genet, 2009 N.A p.Leu194Leu
cln3.029 I: Exon 8 c.597C>A r.(597c>a) g.28497748G>T CM011759 p.(Tyr199*) Nonsense Protracted 1 Lebanon 19489875 Sarpong et al., Clin Genet, 2009 Pa-cln3.257-261
cln3.029 I: Exon 8 c.597C>A r.(597c>a) g.28497748G>T CM011759 p.(Tyr199*) Nonsense 1 Italy 21990111 Kousi et al., Hum Mutat, 2012, Stone pers comm to Mutation Database Pa-cln3.385
cln3.025 I: Exon 8 c.622dupT r.(622dupu) g.28497723dup CI983055 p.(Ser208Phefs*28) Frameshift, introducing a premature stop codon 1 Spain 21499717 Prez-Poyato et al., J Inherit Metab Dis 2011 Pa-cln3.266 Also c.622-623insT; Originally M Mil pers comm.
cln3.025 I: Exon 8 c.622dupT r.(622dupu) g.28497723dup CI983055 p.(Ser208Phefs*28) Frameshift, introducing a premature stop codon 1 Spain 21499717 Prez-Poyato et al., J Inherit Metab Dis 2011 Pa-cln3.270
cln3.025 I: Exon 8 c.622dupT r.(622dupu) g.28497723dup CI983055 p.(Ser208Phefs*28) Frameshift, introducing a premature stop codon 1 Spain 21990111 Kousi et al., Hum Mutat, 2012  Pa-cln3.278
cln3.063 I: Exon 8 c.575G>A r.(575g>a) g.28497770C>T p.(Gly192Glu) Missense Possibly damaging 1 Spain 21499717 Prez-Poyato et al., J Inherit Metab Dis 2011 Pa-cln3.270
cln3.052 I: Intron 8 c.678-?_1317+?del r.spl? g.28488837-?_28495439+?del p.? partly characterised deletion 1 Portugal 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.375-376 frameshift / premature truncation
cln3.067 J: Intron 9 c.790+3A>C r.spl? g.28495324T>G p.? Sequence Variant 1 Canada 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.353 frameshift / premature truncation
cln3.002 J: Intron 9 - Intron 13 c.791-802_1056+1445del2815 r.(791_1056del) g.28491981_28494795del2815 p.(Gly264Valfs*29) 2.8-kb deletion 1 Finland 9311735, 9932957 The International Batten Disease Consortium, 1995, Munroe et al., Am J Hum Genet; 1997 Pa-cln3.140 2.8 kb deletion or p.Gly264_Gln352delinsValfsX29 or p.Gly264_Leu437delinsAlaSerAspSerProAlaSerAlaSerArgValAlaGlyThrThrGly
cln3.027 J: Intron 9 - Intron 13 c.791-?_1056-?del, deletion breakpoints not defined r.791_1056del g.28493426-?_28493993+?del CG994841 p.Gly264Valfs*29 2.8 kb deletion where D16S298 not deleted 3 Finland 9932957 Lauronen et al., Neurology, 1999 Pa-cln3.192-197 2.8-kb genomic deletion of exons 10-13: a truncated protein of 291 amino acids, 28 of which are new; 2.8 kb deletion or p.Gly264_Gln352delinsValfsX29
cln3.024 K: Exon 10 c.831G>A r.[461_790del, 838_906del] g.28493953C>T rs1142183 p.[Val155_Gly264del, Gly280_Leu302del] Sequence variant n.a. n.a. 9490299 Mitchison et al., 1996, Zhong et al Hum Genet 102:57-62 1998                                               66.7% G, 33.3% A; nt 968G>A polymorphism: two normal RNA splicing alternative isoforms, one spliced-out exons
7, 8, and 9, and second spliced-out exon 11; c.831G>A:p.Val277Val
cln3.015 L: Exon 11 c.883G>A r.(883g>a) g.28493821C>T rs121434286, CM970334 p.(Glu295Lys) Missense Possibly damaging 1 Finland The International Batten Disease Cosortium, 1995     9311735                                          9932957 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.151 nt 1020G>A
cln3.015 L: Exon 11 c.883G>A r.(883g>a) g.28493821C>T rs121434286, CM970334 p.Glu295Lys Missense Possibly damaging     2 USA 9490299 Zhong et al.,Hum Genet, 1998 Pa-cln3.221-222  
cln3.015 L: Exon 11 c.883G>A r.(883g>a) g.28493821C>T rs121434286, CM970334 p.Glu295Lys Missense Possibly damaging     1 German/Dutch 9450775 Wisniewski et al., Ann Neurol, 1998 Pa-cln3.230-231  
cln3.035 L: Exon 11 c.883G>T r.(883g>u) g.28493821C>A CM003663 p.Glu295X nonsense JNCL 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Zhong pers comm to NCL mutation database) Pa-cln3.386
cln3.047 L: Intron 11 c.906+5G>A r.spl? g.28493793C>T CS003697 splice defect Splice site JNCL 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Zhong pers comm to NCL mutation database) Pa-cln3.387
cln3.039 L: Intron 11 c.906+49del r.(spl?) g.28493749del CG053041 polymorphism / possible splice defect 34 bp deletion 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Sims pers comm to NCL database) Formerly IVS11+49del
cln3.016 M: Exon 12 c.944dupA r.(944dupa) g.28493666dup CI972581 p.His315GlnfsX67 1-bp insertion 2 Italy 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.174-175 c.944-945insA
cln3.016 M: Exon 12 c.944dupA r.(944dupa) g.28493666dup CI972581 p.His315GlnfsX67 1-bp insertion 1  Iceland 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.176 c.944-945insA
cln3.016 M: Exon 12 c.944dupA r.(944dupa) g.28493666dup CI972581 p.His315GlnfsX67 1-bp insertion 1 USA 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.177 c.944-945insA
cln3.003 Minimum deletion of exon 8-15; maximum deletion of intron 5-15 c.432+?_1350-?del r.? g.28488804_28498805del CG952289 6-kb deletion 1 Morocco 7887419 Mitchison et al., Am J Hum Genet, 1995 Pa-cln3.142 deletion of 6 kb that starts between F2 and F4 and ends between GF1 and R3 primers; i08 - 3' region, unknown 6 kb deletion; Truncated protein
cln3.017 N: Exon 13 c.979C>T r.(979c>u) g.28493503G>A CM970335 p.Gln327X Nonsense 1 Denmark 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.152
cln3.018 N: Exon 13 c.988G>T r.(988g>u) g.28493494C>A CM970336 p.Val330Phe Missense Possibly damaging 1 Norway 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.153
cln3.019 N: Exon 13 c.1000C>T r.(1000c>u) g.28493482G>A CM970338 p.Arg334Cys Missense Possibly damaging 4 The Netherlands 9311735                            21990111 Munroe et al., Am J Hum Genet; 1997, Kousi et al., Hum Mutat, 2012 Pa-cln3.154-155-156, Pa-cln3.345
cln3.019 N: Exon 13 c.1000C>T r.(1000c>u) g.28493482G>A CM970338 p.Arg334Cys Missense Possibly damaging 1 Argentina 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.277
cln3.020 N: Exon 13 c.1001G>A r.(1001g>a) g.28493481C>T CM970337 p.Arg334His Missense Possibly damaging     1 Finland N.A. The International Batten Disease CosortiumMunroe et al., Am J Hum Genet; 1997 Pa-cln3.157  
cln3.020 N: Exon 13 c.1001G>A r.(1001g>a) g.28493481C>T CM970337 p.Arg334His Missense Possibly damaging 1 UK 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.158
cln3.020 N: Exon 13 c.1001G>A r.(1001g>a) g.28493481C>T CM970337 p.Arg334His Missense Possibly damaging 1 Germany 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.159
cln3.020 N: Exon 13 c.1001G>A r.(1001g>a) g.28493481C>T CM970337 p.Arg334His Missense Possibly damaging 1 USA 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.160
cln3.020 N: Exon 13 c.1001G>A r.(1001g>a) g.28493481C>T CM970337 p.Arg334His Missense Possibly damaging 1 Spain 21499717 Prez-Poyato et al., 2011 Pa-cln3.273
cln3.020 N: Exon 13 c.1001G>A r.(1001g>a) g.28493481C>T CM970337 p.Arg334His Missense Possibly damaging 2 Canada 21990111 Kousi et al., Hum Mutat, 2011 Pa-cln3.351-352
cln3.021 N: Exon 13 c.1054C>T r.(1054c>u) g.28493428G>A CM970339 p.Gln352X Nonsense 3 The Netherlands 9311735                                  21990111 Munroe et al., Am J Hum Genet; 1997, Kousi et al., Hum Mutat, 2012 Pa-cln3.161. Pa-cln3.340-341
cln3.021 N: Exon 13 c.1054C>T r.(1054c>u) g.28493428G>A CM970339 p.Gln352X Nonsense 1 USA 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.162
cln3.021 N: Exon 13 c.1054C>T r.(1054c>u) g.28493428G>A CM970339 p.Gln352X Nonsense 1 France 21990111 Kousi et al., Hum Mutat, 2011 Pa-cln3.358
cln3.042 N: Exon 13 c.1056G>C r.(1056g>c) g.28493426C>G HM040085 p.Gln352His / splice defect Missense Possibly damaging 1 USA 15991331 Leman et al., Hum Genet, 2005 Pa-cln3.252 p.Gln352His / splice defect
cln3.051 N: Exon 13 c.1048delC r.(1048delc) g.28493434delG p.Leu350CysfsX27 1-bp deletion 1 Russia 21990111 Kousi et al., Hum Mutat, 2012  (Burkina personal communication to NCL database) Pa-cln3.391
cln3.068 N: Exon 12 c.954_962+18del27 r.spl? g.28493630_28493656del27 p.Leu313_Trp321del / splice defect Splice defect       1 Sweden 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.343 p.Leu313_Trp321del / splice defect
cln3.068 N: Exon 12 c.954_962+18del27 r.spl? g.28493630_28493656del27 p.Leu313_Trp321del / splice defect Splice defect 1 Norway 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.344 p.Leu313_Trp321del / splice defect
cln3.068 N: Exon 12 c.954_962+18del27 r.spl? g.28493630_28493656del27 p.Leu313_Trp321del / splice defect Splice defect 1 The Netherlands 11589012 Mole et al 2001 (Taschner pers comm) Pa-cln3.390 p.Leu313_Trp321del / splice defect
cln3.026 N: Intron 13 n.a. D16S298 microsatellite marker Sequence variant n.a. n.a. N.A. Thompson et al. Genomics 13:402-408 1992  Mitchison et al. Genomics 40:346-350 1997
cln3.040 N: Intron 13 c.1056+3A>C r.spl? g.28493423T>G CS052953 p.? Splice site 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Drury personal communication to NCL database) Pa-cln3.388
cln3.060 N: Intron 13 c.963-1G>T r.spl? g.28493520C>A p.? Splice defect 1 UK 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.347
cln3.032 O: Exon 14 c.1195G>T r.(1195g>u) g.28489060C>A p.(Glu399*) 27-bp deletion JNCL 1 Italy 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.286
cln3.022 O: Intron 14 c.1198-1G>T r.1198_1202del g.28488957C>A CS971665 p.Thr400* Splice site 1 USA 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.163-165 splice defect (confirmed by RT-PCR)
cln3.022 O: Intron 14 c.1198-1G>T r.1198_1202del g.28488957C>A CS971665 p.Thr400* Splice site 1 UK 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.389 splice defect (confirmed by RT-PCR)
cln3.023 P: Exon 15 c.1272delG r.(1272delg) g.28488882delC CD972142 p.(Leu425Serfs*87) 1-bp deletion 1 UK 9311735 Munroe et al., Am J Hum Genet; 1997 Pa-cln3.166
cln3.028 P: Exon 15 c.1211A>G r.(1211a>g) g.28488943T>C rs77595156 p.(His404Arg) Sequence variant 2 Sweden, UK 10916181 Munroe et al., Am J Hum Genet; 1997, Eksandh et al, Ophthalmic Genet 2000 Pa-cln3_190, Pa-cln3.235-236 10/94 chr Sweden
cln3.028 P: Exon 15 c.1211A>G r.(1211a>g) g.28488943T>C rs77595156 p.(His404Arg) Sequence variant 4 Turkey 21990111 Kousi et al., Hum Mutat, 2011 Pa-cln3.398-402
cln3.028 P: Exon 15 c.1211A>G r.(1211a>g) g.28488943T>C rs77595156 p.(His404Arg) Sequence variant 3 Canada 21990111 Kousi et al., Hum Mutat, 2012 Pa-cln3.354-355-356
cln3.041 P: Exon 15 c.1247A>G r.(1247a>g) g.28488907T>C CM052840 p.(Asp416Gly) Missense Possibly damaging 1 USA 21990111 Kousi et al., Hum Mutat, 2012 (Sims personal communication to NCL database) Pa-cln3.388
cln3.055 P: Exon 15 c.1268C>A r.(1268c>a) g.28488886G>T p.(Ser423*) Nonsense 1 Portugal 21990111 Kousi et al., 2012 (Laranjeira personal communication to NCL database) Pa-cln3.393
Notes
Recommended mutation nomenclature followed (http://www.hgvs.org/rec.html)
Polyphen and/or SIFT used to predict functional effects
C - around birth, I -  infantile (6-18 mo), LI - late infantile (2-4 yr), vLI - variant late infantile, J - juvenile (5-10 yr), A - adult 
GROD - Granular osmiophilic deposits, CL - Curvilinear, RL- Rectilinear, FP - Fingerprint, condensed
See dbSNP for more short genetic variations