Gene Symbol CLN5
Gene ID 1203
Chromosomal Location 13q21.1-32
Genomic RefSeqGene NG_009064.1 17594 bp
Transcript RefSeq NM_006493 2816 bp
Protein RefSeq 5729772 407 aa
No. of mutations 35
No. of sequence variations 10
Total No. of changes 45
Additional notes cln5.031& cln5.036 no longer used
Identifier 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
cln5.037 3' UTR c.1224+33A>G downstream polymorphism Sequence variant 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.041
cln5.002 B: Exon 1 c.225G>A r.(225g>a) g.77566311G>A rs104894385, CM980371 p.(Trp75*) Nonsense classic 1 Sweden 20157158 , 10953198 Xin et al., Neurology, 2010, Holmberg et al., Neurology, 2000 Pa-cln5.043
cln5.002 B: Exon 1 c.225G>A r.(225g>a) g.77566311G>A rs104894385, CM980371 p.(Trp75*) Nonsense classic 1 Finland 9662406 Savukoski et al., Nature Genet, 1998 Pa-cln5.019
cln5.002 B: Exon 1 c.225G>A r.(225g>a) g.77566311G>A rs104894385, CM980371 p.(Trp75*) Nonsense classic 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.073
cln5.012 Exon 1 c.4C>T p.Arg2Cys Sequence variant classic 6 n.a.,                           Argentina 20157158 , 21990111 Kousi et al., Hum Mut; 2012
cln5.012 Exon 1 c.4C>T p.Arg2Cys Sequence variant classic 13 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.053, 054-060, Pa-cln6-064, 105, Pa-cln7.009, 059, 006
cln5.012 Exon 1 c.4C>T p.Arg2Cys Sequence variant classic 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.049
cln5.012 Exon 1 c.4C>T p.Arg2Cys Sequence variant classic 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.076, 081
cln5.012 Exon 1 c.4C>T p.Arg2Cys Sequence variant classic n.a. Czech Republic 21990111 Kousi et al., Hum Mut; 2012
cln5.012 B: Exon 1 c.4C>T r.(4c>u) g.77566090C>T rs77416795 p.(Arg2Cys) Sequence variant classic 6 n.a.,                           Argentina 20157158 , 21990111 Kousi et al., Hum Mut; 2012
cln5.012 B: Exon 1 c.4C>T r.(4c>u) g.77566090C>T rs77416795 p.(Arg2Cys) Sequence variant classic 13 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.053, 054-060, Pa-cln6-064, 105, Pa-cln7.009, 059, 006
cln5.012 B: Exon 1 c.4C>T r.(4c>u) g.77566090C>T rs77416795 p.(Arg2Cys) Sequence variant classic 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.049
cln5.012 B: Exon 1 c.4C>T r.(4c>u) g.77566090C>T rs77416795 p.(Arg2Cys) Sequence variant classic 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.076, 081
cln5.012 B: Exon 1 c.4C>T r.(4c>u) g.77566090C>T rs77416795 p.(Arg2Cys) Sequence variant classic n.a. Czech Republic 21990111 Kousi et al., Hum Mut; 2012
cln5.019 B: Exon 1 c.291dupC r.(291dup) g.77566377dup HI070015 p.(Ser98Leufs*13) 1-bp insertion early onset (4 mo) 1 Argentina 20960661 Cismondi et al., Hum Genet, 2008 Pa-cln5.030
cln5.023 Exon 1 c.72A>G p.Gly24Gly Sequence variant 2 USA,                             Argentina 20157158                                    21990111 Xin et al., Neurology, 2010, Kousi et al., Hum Mut; 2011 Pa-cln5.041
cln5.024 Exon 1 c.234C>G p.Ala78Ala Sequence variant 1=0.5% chr USA 20157158 Xin et al., Neurology, 2010
cln5.023 B: Exon 1 c.72A>G r.(72a>g) g.77566158A>G rs7987664 p.(=) Sequence variant 2 USA,                             Argentina 20157158                                    21990111 Xin et al., Neurology, 2010, Kousi et al., Hum Mut; 2011 Pa-cln5.041
cln5.024 B: Exon 1 c.234C>G r.(234c>g) g.77566320C>G rsS138037471 p.(=) Sequence variant 1=0.5% chr USA 20157158 Xin et al., Neurology, 2010
cln5.038 B: Exon 1 c.61C>T r.(61c>u) g.77566147C>T p.(Pro21Ser) Missense Possibly damaging 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.061
cln5.038 B: Exon 1 c.61C>T r.(61c>u) g.77566147C>T p.(Pro21Ser) Missense Possibly damaging congenital/infantile GROD, CL, FP (lymphocytes and skin) 1 22727047 Staropoli et al 2012 BMC Med Genet. 13:50 Pa-cln5.084 also found as an isolated change in a teenage boy with progressive neurological decline
cln5.039 B: Exon 1 c.223T>C r.(223u>c) g.77566309T>C p.(Trp75Arg) Missense Probably damaging 3 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.060
cln5.006 C: Exon 2 c.335G>A r.(335g>a) g.77569212G>A rs104894386 p.(Arg112His) Missense Probably damaging later onset 1 Colombia 15728307 Pineda-Trujillo et al., Neurology; 2005 Pa-cln5.022-023
cln5.006 C: Exon 2 c.335G>A r.(335g>a) g.77569212G>A rs104894386 p.(Arg112His) Missense Probably damaging later onset 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.051
cln5.008 C: Exon 2 c.335G>C r.(335g>c) g.77569212G>C CM050199 p.(Arg112Pro) Missense Probably damaging classic 1 Portugal 16814585 Bessa et al., Mol Genet Metab, 2006 Pa-cln5.024 Found on same maternal allele as p.Asp279Asn
cln5.021 C: Exon 2 c.377G>A r.(377g>a) g.77569254G>A CM063906 p.(Cys126Tyr) Missense Probably damaging Late onset (age 17) 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.040
cln5.040 C: Exon 2 c.433C>T r.(433c>u) g.77569310C>T COSM196447 p.(Arg145*) Nonsense 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.052
cln5.005  D: Exon 3 c.669dupC r.(669dup) g.77570219dup CI003728 p.(Trp224Leufs*30) 1-bp insertion classic 1 Sweden 20157158                                               10953198 Xin et al., Neurology, 2010, Holmberg et al., Neurology, 2000 Pa-cln5.043 classic in combination with Y392X
cln5.005  D: Exon 3 c.669dupC r.(669dup) g.77570219dup CI003728 p.(Trp224Leufs*30) 1-bp insertion mild 1 Finland 10953198 Holmberg et al., Neurology, 2000 Pa-cln5.021  mild in combination with Y75X
cln5.005  D: Exon 3 c.669dupC r.(669dup) g.77570219dup CI003728 p.(Trp224Leufs*30) 1-bp insertion classic/mild 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.073
cln5.007 D: Exon 3 c.565C>T r.(565c>u) g.77570115C>T CM063905 p.(Gln189*) Nonsense classic 1 Portugal 16814585 Bessa et al., Mol Genet Metab, 2006 Pa-cln5.024
cln5.009 D: Exon 3 c.671G>A r.(671g>a) g.77570221G>A p.(Trp224*) Nonsense 2 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.038, Pa-cln5.039
cln5.009 D: Exon 3 c.671G>A r.(671g>a) g.77570221G>A p.(Trp224*) Nonsense 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.048
cln5.015 D: Exon 3 c.619T>C r.(619u>c) g.77570169T>C rs147065248 p.(Trp207Arg) Missense Probably damaging 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.051
cln5.027 D: Exon 3 c.527_528insA r.(527_528insa g.77570077_77570078insA p.(Gly177Trpfs*10) 1-bp insertion vLINCL 1 Pakistan / USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.047
cln5.029 D: Exon 3 c.575A>G r.(575a>g) g.77570125A>G p.(Asn192Ser) Missense Probably damaging 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.045
cln5.030 D: Exon 3 c.620G>C r.(620g>c) g.77570170G>C p.(Trp207Ser) Missense Probably damaging 1 China / USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.044
cln5.042 D: Exon 3 c.524T>G r.(524u>g) g.77570074T>G p.(Leu175*) Nonsense 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.067
cln5.028 Exon 3 c.528T>G p.Thr176Thr Sequence variant 1 Sweden 20157158 Xin et al., Neurology, 2010 Pa-cln5.043
cln5.028 Exon 3 c.528T>G p.Thr176Thr Sequence variant Argentina 21990111 Kousi et al., Hum Mut; 2012
cln5.028 D: Exon 3 c.528T>G r.(528u>g) g.77570078T>G rs34481987 p.(=) Sequence variant 1 Sweden 20157158 Xin et al., Neurology, 2010 Pa-cln5.043 p.Thr176Thr
cln5.028 D: Exon 3 c.528T>G r.(528u>g) g.77570078T>G rs34481987 p.(=) Sequence variant Argentina 21990111 Kousi et al., Hum Mut; 2012 p.Thr176Thr
cln5.043 D: Exon 3 c.593T>C r.(593u>c) g.77570143T>C p.(Leu198Pro) Missense Probably damaging 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln7.068
cln5.044 D: Exon 3 c.613C>T r.(613c>u) g.77570163C>T p.(Pro205Ser) Missense Probably damaging 2 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.074, 075
cln5.044 D: Exon 3 c.613C>T r.(613c>u) g.77570163C>T p.(Pro205Ser) Missense Probably damaging 1 Arab (Qatar and Yemen) 21447811 Al-Kowari et al., 2011 Pa-cln5.036, 037
cln5.045 D: Exon 3 c.486+139_712+2132del r.(487_712del) g.77569502_77572394del p.(Lys163Glufs*11) Frameshift congenital/infantile GROD, CL, FP (lymphocytes and skin) 22727047 Staropoli et al 2012 BMC Med Genet. 13:50 Pa-cln5.084 de novo mutation in patient of 2.8 kb del
cln5.046 D: Exon 3 c.694C>T r.(694c>u) g.77570244C>T p.(Gln232*) Nonsense 1 Serbia 23160995 Haddad et al., 2012 Pa-cln5.085
cln5.001 E: Exon 4 c.1175_1176delAT r.(1175_1176del) g.77575055_77575056delAT p.(Tyr392*) 2-bp deletion classic 19 Finland 9662406                                                          10953198 Savukoski et al., Nature Genet, 1998, Holmberg et al., Neurology, 2000 Pa-cln5.001-18, Pa-cln5.021 Finnish major mutation
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.041
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant n.a. Finland 9662406 Savukoski et al., Nature Genet, 1998 Pa-cln5.019 nearly 20% carrier freq in Finland, linked to FINmin mutation p.Trp75X
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant n.a. Argentina 21990111 Kousi et al., Hum Mut; 2012
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant 4 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.063, Pa-cln7.066,Pa-cln5- 069-071
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant 5 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.077, 078, 079, 080, 082
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant 1 India 21990111 Kousi et al., Hum Mut; 2012 Pa-cln7.004
cln5.004 Exon 4 c.1103A>G p.Lys368Arg Sequence variant 1 Hispanic 21990111 Xin et al., 2010 Pa-cln4.041
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.041 A common polymorphisms
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant n.a. Finland 9662406 Savukoski et al., Nature Genet, 1998 Pa-cln5.019 nearly 20% carrier freq in Finland, linked to FINmin mutation p.Trp75X
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant n.a. Argentina 21990111 Kousi et al., Hum Mut; 2012
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant 4 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.063, Pa-cln7.066,Pa-cln5- 069-071
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant 5 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.077, 078, 079, 080, 082
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant 1 India 21990111 Kousi et al., Hum Mut; 2012 Pa-cln7.004
cln5.004 E: Exon 4 c.1103A>G r.(1103a>g) g.77574983A>G rs1800209 p.(Lys368Arg) Sequence variant 1 Hispanic 21990111 Xin et al., 2010 Pa-cln4.041
cln5.003 E: Exon 4 c.835G>A r.(835g>a) g.77574715G>A rs28940280, CM980372 p.(Asp279Asn) Missense Probably damaging classic 1 The Netherlands 9662406                                      10953198 Savukoski et al., Nature Genet, 1998, Holmberg et al., Neurology, 2000 Pa-cln5.020
cln5.003 E: Exon 4 c.835G>A r.(835g>a) g.77574715G>A rs28940280, CM980372 p.(Asp279Asn) Missense Probably damaging classic 1 Portugal 16814585 Bessa et al., Mol Genet Metab, 2006 Pa-cln5.024 Found on same maternal allele as p.Arg112Pro
cln5.010 E: Exon 4 c.955_970del16 r.(955_970del) g.77574835_77574850del16 p.(Gly319Phefs*12) 16-bp del 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.048
cln5.011 E: Exon 4 c.772T>G r.(772u>g) g.77574652T>G CM076117 p.(Tyr258Asp) Missense Probably damaging vJNCL, seizures lateer 1 Italy 17607606 Cannelli et al., Neuropediatrics; 2007 Pa-cln5.025-026
cln5.013 E: Exon 4 c.726C>A r.(726c>a) g.77574606C>A rs138611001 p.(Asn242Lys) Missense SNP at 1.4% in European Americans 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.049
cln5.013 E: Exon 4 c.726C>A r.(726c>a) g.77574606C>A rs138611001 p.(Asn242Lys) Missense SNP at 1.4% in European Americans 2 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.058, 068
cln5.016 E: Exon 4 c.1026C>A r.(1026c>a) g.77574906C>A p.(Tyr342*) Nonsense 1 Roma from the former Czechoslovakia 19201763 Kousi et al., Brain; 2009 Pa-cln5.031
cln5.017 E: Exon 4 c.1054G>T r.(1054g>u g.77574934G>T rs121908292, CM083489 p.(Glu352*) Nonsense 1 Newfoundland / UK 18684116 Moore et al., Clin Genet; 2008 Pa-cln5.027-028
cln5.018 E: Exon 4 c.1137G>T r.(1137g>u) g.77575017G>T CM093057 p.(Trp379Cys) Missense Probably damaging 1 Afghanistan 19309691 Lebrun et al., Hum Mut; 2009 Pa-cln5.034-35
cln5.022 E: Exon 4 c.1121A>G r.(1121a>g) g.77575001A>G rs148862100 p.(Tyr374Cys) Missense Probably damaging Late onset (age 17) 2 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.040, Pa-cln5.042 Probably milder mutation
cln5.032 E: Exon 4 c.907_1094del188 r.(907_1094del) g.77574787_77574974del188 p.(Thr303Cysfs*10) deletion 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.039
cln5.032 E: Exon 4 c.907_1094del188 r.(907_1094del) g.77574787_77574974del188 p.(Thr303Cysfs*10) deletion 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.042
cln5.033 E: Exon 4 c.919delA r.(919del) g.77574799delA p.(Arg307Glufs*29 1-bp deletion 1 Egypt / USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.046
cln5.033 E: Exon 4 c.919delA r.(919del) g.77574799delA   p.(Arg307Glufs*29 1-bp deletion       1 Egypt 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.083  
cln5.034 E: Exon 4 c.1071_1072delCT r.(1071_1072del) g.77574951_77574952delCT   p.(Leu358Alafs*4) 2-bp deletion       1 China / USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.044  
cln5.014 E: Exon 4 c.1072_1073delTT r.(1072_1073del) g.77574952_77574953delTT CD093058 p.(Leu358Alafs*4) 2-bp deletion 1 Pakistan 19309691 Lebrun et al., Hum Mut; 2009 Pa-cln5.032-33
cln5.014 E: Exon 4 c.1072_1073delTT r.(1072_1073del) g.77574952_77574953delTT CD093058 p.(Leu358Alafs*4) 2-bp deletion 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.050
cln5.020 E: Exon 4 c.1103_1106delAACA r.(1103_1106del) g.77574983_77574986delAACA HD070030 p.(Lys368Serfs*15) 4-bp deletion   vLINCL, vJNCL   1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.038  
cln5.025 Intron 1 c.320+8C>T intronic polymorphism Sequence variant 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5-041
cln5.025 Intron 1 c.320+8C>T intronic polymorphism Sequence variant 4 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.063-066
cln5.025 Intron 1 c.320+8C>T intronic polymorphism Sequence variant 1 Cook Islands 21990111 Kousi et al., Hum Mut; 2012 Pa-cln7.055
cln5.025 Intron 1 c.320+8C>T intronic polymorphism Sequence variant 4 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.077, 079, 080, 082
cln5.026 Intron 1 c.320+18C>T intronic polymorphism Sequence variant n.a. USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.041
cln5.041 Intron 2 c.486+5G>C splice defect / polymorphism?? Sequence variant 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.076
cln5.020 E: Exon 4 c.1103_1106delAACA r.(1103_1106del) g.77574983_77574986delAACA HD070030 p.(Lys368Serfs*15) 4-bp deletion vLINCL, vJNCL 1 Spain 20960652 Kohan et al., Hum Genet, 2008 Pa-cln5.029
cln5.025 B: Intron 1 c.320+8C>T r.(=) g.77566414C>T rs9565308 p.(=) Sequence variant 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5-041
cln5.025 B: Intron 1 c.320+8C>T r.(=) g.77566414C>T rs9565308 p.(=) Sequence variant 4 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.063-066
cln5.025 B: Intron 1 c.320+8C>T r.(=) g.77566414C>T rs9565308 p.(=) Sequence variant 1 Cook Islands 21990111 Kousi et al., Hum Mut; 2012 Pa-cln7.055
cln5.025 B: Intron 1 c.320+8C>T r.(=) g.77566414C>T rs9565308 p.(=) Sequence variant 4 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.077, 079, 080, 082
cln5.026 B: Intron 1 c.320+18C>T r.(=) g.77566424C>T rs112141862 p.(=) Sequence variant n.a. USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.041
cln5.041 B: Intron 1 c.486+5G>C r.spl? g.77569368G>C p.? Sequence variant 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln5.076
cln5.035 E: Exon 4 c.1083delT r.(1083del) g.77574963delT p.(Phe361Leufs*4) 1-bp deletion 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5-041
cln5.037 3' UTR c.*33A>G r.(1224+33a>g g.77575137A>G rs9573974 p.(=) Sequence variant 1 USA 20157158 Xin et al., Neurology, 2010 Pa-cln5.041 formerly c.1224+33A>G
? ? 1 Pakistan 24082928 Setty et al. J. Pediatr Neurosci. 2013 Pa-cln5.086-087
                                 
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
cln5.020=cln2.036