Gene Symbol CLN6
Gene ID 54982
Chromosomal Location 15q23
Genomic RefSeqGene NG_008764.1 29751 bp
Transcript RefSeq NM_017882.2 2258 bp
Protein RefSeq NP_060352.1 311 aa
No. of mutations 70
No. of sequence variations 9
No. of changes 79
Additional notes
Identifier Location Nucleotide change Amino acid change Type of mutation Predicted functional effect Phenotype Histology No. of families  Country of origin PMID Reference Patients Notes Column1
cln6.001 Exon 1 c.7delG p.(Ala3Argfs*30) deletion late infantile 1 Greece 11727201 Wheeler et al., Am J Hum Genet., 2002 Pa-cln6-001
cln6.002 Exon 3 c.214G>T p.(Glu72*) substitution late infantile 19 Costa Rica 11727201, 11791207 Wheeler et al., Am J Hum Genet., 2002; Gao et al., Am J Hum Genet, 2002 Pa-cln6-002-007; Pa-cln6.016-028
cln6.002 Exon 3 c.214G>T p.(Glu72*) substitution late infantile 1 Costa Rica 11727201, 12815591 Wheeler et al., Am J Hum Genet., 2002; Sharp et al., Hum Mut; 2003 Pa-cln6.008
cln6.003 Exon 4 c.368G>A p.(Gly123Asp) substitution Probably damaging late infantile 1 Costa Rica 11727201 Wheeler et al., Am J Hum Genet., 2002 Pa-cln6-012
cln6.004 Exon 4 c.316dupC p.(Arg106Profs*26) insertion late infantile 2 Pakistan 11727201 Wheeler et al., Am J Hum Genet., 2002 Pa-cln6.010-011
cln6.004 Exon 4 c.316dupC p.(Arg106Profs*26) insertion late infantile 1 Pakistan 11727201 Wheeler et al., Am J Hum Genet., 2002 Pa-cln6-009
cln6.004 Exon 4 c.316dupC p.(Arg106Profs*26) insertion N.A. 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.094
cln6.004 Exon 4 c.316dupC p.(Arg106Profs*26) insertion N.A. 2 Pakistan 23735787 Guerreiro et al., Eur J Paed Neurol, 2013 Pa-cln6.126, 127
cln6.005 Exon 4 c.395_396delCT p.(Ser132Cysfs*18) deletion late infantile 1 India 11727201 Wheeler et al., Am J Hum Genet., 2002 Pa-cln6-013
cln6.005 Exon 4 c.395_396delCT p.(Ser132Cysfs*18) deletion late infantile 1 Saudi Arabia 19520283 Al-Muhaizea et al., Pediatr Neurol; 2009 Pa-cln6.048
cln6.005 Exon 4 c.395_396delCT p.(Ser132Cysfs*18) deletion late infantile 3 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.053-054, Pa-cln6.057, Pa-cln6.060
cln6.005 Exon 4 c.395_396delCT p.(Ser132Cysfs*18) deletion N.A. 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.091
cln6.006 Exon 4 c.460_462delATC p.(Ile154del) deletion late infantile 7 Portugal 11727201                             12673792 Wheeler et al., Am J Hum Genet., 2002; Teixeira et al., Hum Mutat, 2003 Pa-cln6-014, Pa-cln6-035-040
cln6.006 Exon 4 c.460_462delATC p.(Ile154del) deletion late infantile 1 Portugal 11727201                             12815591                              12673792 Wheeler et al., Am J Hum Genet., 2002; Sharp et al., Hum Mut; 2003; Teixeira et al., Hum Mutat, 2003 Pa-cln6-015, Pa-cln6.033
cln6.006 Exon 4 c.460_462delATC p.(Ile154del) deletion N.A. 1 Arabic origin 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.113
cln6.006 Exon 4 c.460_462delATC p.(Ile154del) deletion late infantile 1 Argentina in preparation Noher Halac Pa-cln6.136
cln6.007 Exon 5 c.510_512delCTA p.(Tyr172del) deletion late infantile 1 Venezuela 11791207 Gao et al., Am J Hum Genet, 2002 Pa-cln6-029
cln6.008 Exon 2 c.185G>A p.(Arg62His) substitution Probably damaging late infantile 1 Italy / Portugal 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.041
cln6.009 Intron 2 c.198+2dupT N.A. insertion late infantile 1 Italy / Portugal 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.041 splice defect?
cln6.010 Exon 6 c.662A>C p.(Tyr221Ser) substitution Possibly damaging late infantile 1 Argentina 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.043
cln6.010 Exon 6 c.662A>C p.(Tyr221Ser) substitution Possibly damaging N.A. 2 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.101-102
cln6.011 Exon 7 c.722T>C p.(Met241Thr) substitution Possibly damaging late infantile 1 Costa Rica 11727201      12815590 Wheeler et al., Am J Hum Genet., 2002; Sharp et al., Hum Mut; 2003 Pa-cln6-008
cln6.012 Exon 7 c.794_796delCCT p.(Ser265del) deletion late infantile 1 Sudan 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.044 This mutation has previously been referred to as c.793_795delTCC
cln6.012 Exon 7 c.794_796delCCT p.(Ser265del) deletion late infantile 1 Saudi Arabia 19520283 Al-Muhaizea et al., Pediatr Neurol; 2009 Pa-cln6.049 This mutation has previously been referred to as c.793_795delTCC
cln6.012 Exon 7 c.794_796delCCT p.(Ser265del) deletion late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.056 This mutation has previously been referred to as c.793_795delTCC
cln6.012 Exon 7 c.794_796delCCT p.(Ser265del) deletion N.A. 1 Czech Republic 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.087 This mutation has previously been referred to as c.793_795delTCC
cln6.012 Exon 7 c.794_796delCCT p.(Ser265del) deletion N.A. 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6-093 This mutation has previously been referred to as c.793_795delTCC
cln6.012 Exon 7 c.794_796delCCT p.(Ser265del) deletion N.A. 3 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.104-106 This mutation has previously been referred to as c.793_795delTCC
cln6.013 Exon 7 c.829_837delinsCCTG p.(Val277Profs*5) deletion-insertion late infantile 1 Portugal 12673792 Teixeira et al., Hum Mutat, 2003 Pa-cln6-015
cln6.013 Exon 7 c.829_837delinsCCTG p.(Val277Profs*5) deletion-insertion N.A. 1 Portugal 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.033, 034 was also numbered cln6.063 on previous version of this table
cln6.014 Exon 7 c.896C>T p.(Pro299Leu) substitution Probably damaging late infantile 1 Italy 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.045
cln6.014 Exon 7 c.896C>T p.(Pro299Leu) substitution Probably damaging late infantile 4 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.055, Pa-cln6.057, Pa-cln6.060, Pa-cln6.062
cln6.014 Exon 7 c.896C>T p.(Pro299Leu) substitution Probably damaging late infantile 1 Italy / Libya 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.090
cln6.015 Exon 3 c.214G>C p.(Glu72Gln) substitution Benign late infantile 1 India 12815591 Sharp et al., Hum Mut; 2003 Pa-cln6.042 Reference does not indicate if mutation is benign
cln6.016 Exon 3 c.268_271dupAACG p.(Val91Glufs*42) duplication late infantile 1 USA 12673792 Teixeira et al., Hum Mutat, 2003 Pa-cln6.030
cln6.016 Exon 3 c.268_271dupAACG p.(Val91Glufs*42) duplication late infantile 5 Canada 18684116 Moore et al., Clin Genet, 2008 Pa-cln6.065-071 Newfoundland
cln6.017 Intron 4 c.486+1G>T N.A. substitution late infantile 1 India 12673792 Teixeira et al., Hum Mutat, 2003 Pa-cln6.031-032 splice defect?
cln6.018 Exon 7 c.898T>C p.(Trp300Arg) substitution Possibly damaging late infantile 1 USA 12673792 Teixeira et al., Hum Mutat, 2003 Pa-cln6.030
cln6.019 5' upstream c.1-194_1-185dupCTCCGCTCCG N.A. duplication polymorphism N.A. N.A. N.A. 12815591 Sharp et al., Hum Mut; 2003 Not known; N.A. upstream
cln6.020 Exon 1 c.13C>T p.(Arg5Trp) substitution Probably damaging N.A. 1 USA 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.118
cln6.021 Exon 3 c.247G>C p.(Asp83His) substitution N.A. 1 USA 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.118
cln6.022 Intron 5 c.542+5G>T N.A. substitution late infantile 1 Turkey 15996215 Siintola et al., Clin Gen, 2005 Pa-cln6.074 confirmed splice defect 
cln6.023 Exon 6 c.663C>G p.(Tyr221*) substitution late infantile 1 Turkey 15996215 Siintola et al., Clin Gen, 2005 Pa-cln6.072-073
cln6.023 Exon 6 c.663C>G p.(Tyr221*) substitution N.A. 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.103
cln6.024 Exon 4 c.406C>T p.(Arg136Cys) substitution Probably damaging late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.051-052
cln6.024 Exon 4 c.406C>T p.(Arg136Cys) substitution Probably damaging N.A. 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.098
cln6.025 Exon 4 c.426C>G p.(Tyr142*) substitution late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.051-052
cln6.026 Exon 4 c.485T>G p.(Leu162Arg) substitution Probably damaging late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.056
cln6.026 Exon 4 c.485T>G p.(Leu162Arg) substitution Probably damaging N.A. 1 Czech Republic 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.087
cln6.027 Exon 2 c.184C>T p.(Arg62Cys) substitution Probably damaging late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.058-059
cln6.028 Exon 3 c.248A>T p.(Asp83Val) substitution Probably damaging N.A. 1 USA 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.120
cln6.029 Exon 4 c.360_361insATC p.(Ile119_Phe120insIle) insertion N.A. 1 USA 21990111 K Sims pers comm Pa-cln6.121 Referred to as c.357_358 insATC in former database but c.358_360insATC p.Phe120dup in Kousi et al 2012 
cln6.030 Exon 7 c.890delC p.(Pro297Leufs*53) deletion frameshift Kufs 1 Ireland 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.082-083 
cln6.030 Exon 7 c.890delC p.(Pro297Leufs*53) deletion N.A. 1 USA 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.122
cln6.031 Exon 4 c.445C>T p.(Arg149Cys) substitution Probably damaging N.A. 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.115
cln6.032 Exon 4 c.307C>T p.(Arg103Trp) substitution Probably damaging late infantile 1 Argentina 18846690 Cismondi et al 2008 Hum Genet  Pa-cln6.063
cln6.033 Exon 6 c.552dupC p.(Phe185Leufs*17) insertion late infantile 1 Argentina 18846690 Cismondi et al 2008 Hum Genet  Pa-cln6.063
cln6.033 Exon 6 c.552dupC p.(Phe185Leufs*17) insertion N.A. 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.092
cln6.034 Exon 3 c.251delA p.(Tyr84Serfs*32 deletion N.A. 1 China 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.112
cln6.035 Intron 4 c.486+8C>T N.A. substitution late infantile 1 Argentina 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.086 splice defect?
cln6.035 Intron 4 c.486+8C>T N.A. substitution N.A. 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.092 splice defect?
cln6.035 Intron 4 c.486+8C>T N.A. substitution N.A. 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.117 splice defect?
cln6.036 Exon 7 c.755G>A p.(Arg252His) substitution Probably damaging late infantile 1 Argentina 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.086
cln6.036 Exon 7 c.755G>A p.(Arg252His) substitution Probably damaging N.A. 1 UK 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.092
cln6.037 Exon 5 c.519delT p.(Asp173Glufs*33) deletion late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.055
cln6.038 Exon 7 c.715_718delTTCG p.(Phe239Profs*29) substitution late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.053-054
cln6.039 Exon 7 c.776G>T p.(Gly259Val) substitution Probably damaging late infantile 1 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.061
cln6.040 Exon 4 c.476C>T p.(Pro159Leu) substitution Probably damaging late infantile 1 Turkey 19201763 Kousi et al., Brain, 2009 Pa-cln6.064
cln6.041 Intron 1 - Intron 3 c.83+?_297+?del N.A. deletion late infantile 1 Saudi Arabia 19520283 Al-Muhaizea et al., Pediatr Neurol; 2009 Pa-cln6.046-047 splice defect?
cln6.042 Intron 2 c.198+104T>C N.A. substitution polymorphism late infantile N.A. Argentina 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.086 intronic
cln6.042 Intron 2 c.198+104T>C N.A. substitution polymorphism N.A. N.A. UK 21990111 Kousi et al., Hum Mut; 2012 N.A. intronic
cln6.043 Exon 3 c.209C>T p.(Pro70Leu) substitution Probably damaging N.A. 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.119
cln6.044 Exon 4 c.311C>T p.(Ser104Phe) substitution Possibly damaging late infantile 1 Czech Republic 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.088
cln6.045 Exon 5 c.506T>C p.(Leu169Pro) substitution Probably damaging late infantile 1 Czech Republic 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.088
cln6.046 Exon 7 c.889C>A p.(Pro297Thr) substitution Probably damaging late infantile 1 Pakistan 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.111
cln6.047 Exon 1 c.17G>C p.(Arg6Thr) substitution probably damaging Kufs type A 1 Italy 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.078
cln6.048 Exon 2 c.100G>A p.(Ala34Thr) substitution polymorphism Kufs type B 1 Italy 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.085
cln6.049 Exon 2 c.139C>T p.(Leu47Phe) substitution probably damaging Kufs type A 1 Italy 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.077
cln6.050 Exon 2 c.150C>G p.(Tyr50*) substitution truncation adult 1 USA 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.084
cln6.051 Exon 3 c.200T>C p.(Leu67Pro) substitution Probably damaging Kufs type A 1 Italy 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.075-076 
cln6.052 Exon 3 c.231C>G p.(Asn77Lys) substitution Probably damaging adult 1 USA 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.084
cln6.053 Exon 4 c.446G>A p.(Arg149His) substitution Probably damaging Kufs 1 Ireland 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.082-083 
cln6.054 Exon 7 c.712_713delinsAC p.(Phe238Thr) deletion-insertion Probably damaging Kufs type A 1 Malta 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.079-080 predicted benign, likely causative (see reference)
cln6.054 Exon 7 c.712_713delinsAC p.(Phe238Thr) deletion-insertion probably damaging Kufs 1 Italy 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.081 predicted benign, likely causative (see reference)
cln6.055 Exon 7 c.923G>C p.(Ser308Thr) substitution polymorphism Kufs 1 USA 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.084
cln6.056 Exon 3 c.308G>A p.(Arg103Gln) substitution Probably damaging Kufs 1 Italy 21549341 Arsov et al., Am J Hum Genet; 2011 Pa-cln6.075-076 
cln6.056 Exon 3 c.308G>A p.(Arg103Gln) substitution Probably damaging Kufs 1 UK 21990111 Armour pers comm Pa-cln6.119
cln6.057 Exon 6 c.662A>G p.(Tyr221Cys) substitution Probably damaging late infantile 2 Italy 19135028 Cannelli et al., Biochim Biophys Res Comm; 2009 Pa-cln6.050
cln6.058 Exon 3 c.278C>T p.(Thr93Met) substitution Probably damaging adult 1 USA N.A. K Sims pers comm Pa-cln6.122
cln6.059 Exon 4 c.382C>G p.(Leu128Val) substitution Benign adult 1 USA N.A. K Sims pers comm Pa-cln6.122
cln6.060 5' upstream c.1-214_1-195insCTCCGCTCCGCCCCGCCTCC N.A. insertion N.A. N.A. N.A. N.A. Kousi et al., unpublished data N.A upstream
cln6.061 Exon 1 c.34G>A p.(Ala12Thr) substitution Benign N.A. 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.095
cln6.062 Exon 1 c.49G>A p.(Gly17Ser) substitution Benign N.A. 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.096
cln6.064 Intron 3 c.298-13C>T N.A. substitution N.A. 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.114 splice defect?
cln6.065 Intron 3 c.298-6C>T N.A. substitution N.A. 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.097
cln6.065 Intron 3 c.298-6C>T N.A. substitution N.A. 1 Canada 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.116
cln6.066 Exon 7 c.727delG p.(Ala243Profs*26) deletion late infantile 1 Italy / Libya 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.090
cln6.067 Exon 5 c.516T>A p.(Tyr172*) substitution N.A. 1 Turkey 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.099
cln6.068 Exon 7 c.700T>C p.(Phe234Leu) substitution Possibly damaging late infantile 1 Italy 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.089
cln6.069 Exon 6 c.557T>C p.(Phe186Ser) substitution Probably damaging late infantile 1 India 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.100
cln6.070 Exon 3 c.270C>G p.(Asn90Lys) substitution Probably damaging late infantile 1 India 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.110
cln6.071 Exon 7 c.775G>A p.(Gly259Ser) substitution Probably damaging late infantile 1 India 21990111 Kousi et al., Hum Mut; 2012 Pa-cln6.107-109 Discrepancy in paper:  c.775G>A is p.(Arg252His); c.797G>A is p.(Gly259Ser).
cln6.072 Exon 7 c.768C>G p.(Asp256Glu) substitution teenage  / progressive myoclonus epilepsy  1 Afghanistan 22883287 Andrade et al., Ped Neurol 2012 Pa-cln6.123-125 no blindness
cln6.073 Exon 7 G>C p.(Asp256Glu) substitution cerebellar ataxia 1 Afghanistan 24102492 Faruq et al., Clin Genet, 2014 Pa-cln6.128-131 no blindness pos-68500646
cln6.074 Exon 3 G>C p.(Tyr84*) substitution cerebellar ataxia, no blindness 1 Afghanistan 24102492 Faruq et al., Clin Genet, 2014 Pa-cln6.128-131 pos-68506673
cln6.079 Exon 7 c.809T>C  p.(Leu270Pro)  substitution late infantile 1 India 27147172 Jain et al.,  Neurol India 2016 Pa-cln6.133 chr15:68500605 ; A>G
cln6.080 Exon 4 N.A. p.(Val148Asp) N.A. N.A. 1 Israel N.A. parent, pers comm Pa-cln6.132
cln6.075 Exon 7 c.917_918dup  p.(Val307Thrfs*24) duplication frameshift late infantile 1 Japan 27165443 Sato et al. Brain & Dev 2016 Pa-cln6.134
cln6.076 Exon 4 c.348C>A  p.(Ser116Arg) substitution probably damaging late infantile 1 Japan 27165443 Sato et al. Brain & Dev 2016 Pa-cln6.134 PolyPhen and Mutation Taster
cln6.077 Exon 5 c.509A>G p.(Tyr170Cys) substitution progressive myoclonus epilepsy  1 Turkey 25401298 Muona et al. Nat. Genet. 2015 Pa-cln6.135 adult onset with slow progression
cln6.078 Exon 3 c.250T>A p.(Tyr84Asn) substitution possibly damaging late infantile 1 Argentina in preparation Noher Halac Pa-cln6.136
cln6.063 to be assigned
Notes
Recommended Mutation nomenclature followed (http://varnomen.hgvs.org/)
Polyphen and/or SIFT used to predict functional effects
congenital - around birth, infantile (0.5-1.5y), late infantile (2-4y), juvenile (5-10y), teenage (13-19y), adult (20+) 
GROD - Granular osmiophilic deposits, CL - Curvilinear, RL- Rectilinear, FP - Fingerprint, Condensed
N.A. - not applicable, or not available
type of mutation is at the DNA-level