DNAJ mutations are rare in Chinese Parkinson’s disease patients and controls
Jia Nee Fooa, Herty Lianya, Louis C. Tanb, Wing-Lok Aub, Kumar-M. Prakashb, Jianjun Liua,
Eng-King Tanb,c *
a. Human Genetics, Genome Institute of Singapore, A*STAR, Singapore 138672.
b. Departments of Neurology, Singapore General Hospital, National Neuroscience Institute,
Singapore 169108
c. Duke-NUS Graduate Medical School, Singapore
Corresponding author:
Eng-King Tan, Department of Neurology, National Neuroscience Institute, Duke-National
University of Singapore Graduate Medical School, Singapore General Hospital, Singapore
169108; tan.eng.king@sgh.com.sg ; +65-63214006
1
Abstract
Mutations in DNAJC13, DNAJC6 and DNAJC5 have been implicated in Parkinson’s
disease (PD). To determine if rare coding variants in these genes play a role in PD risk in the
Chinese population, we sequenced all coding exons of the three genes in 99 early-onset PD cases
and 99 controls, and genotyped 8 missense variants in another 711 PD cases and 539 controls.
Besides two common missense variants that did not show association with PD, the remaining
missense variants were extremely rare (<0.5%), found in healthy population controls and did not
show enrichment in PD cases. Our results suggest that missense mutations in DNAJC13,
DNAJC5 and DNAJC6 do not play a major role in PD in the Chinese population.
1. Introduction
DNAJC13 has recently been identified as a novel gene implicated in late-onset Lewy
body Parkinson’s disease (PD). The rare missense mutation p.Asn855Ser was identified through
linkage analysis and exome sequencing of a large Saskatchewan Mennonite family, in which
twelve out of 57 members had previously been diagnosed with PD (Trinh & Farrer 2013). Other
genes in the DNAJ family have previously been implicated in familial neurodegenerative
disorders, including DNAJC6 in recessive juvenile Parkinsonism (Edvardson et. al. 2012) and
DNAJC5 in dominant adult-onset neuronal ceroid lipofuscinosis (Kufs disease) (Cadieux-Dion et.
al. 2012).
2. Methods
To study if rare coding variants in these genes play a role in PD risk in the Chinese
population, we sequenced all coding exons of the three genes in 99 early-onset (<55 years; age
54.7 ± 7.1 years, onset 48.3 ± 5.8 years, 67% male) and familial (23%) PD cases and 99 elderly,
healthy controls (age 71.9 ± 10.8 years, 61% male) from Singapore. We further analyzed
2
recurrent missense variants that were genotyped as part of the Illumina HumanExome BeadChip
Exome_Asian array in an additional 711 cases with typical late-onset PD (>55 years; age 69.4 ±
9.2 years, onset 65.3 ± 9.2 years, 51% male) and 539 healthy controls (age 51.7 ± 11.6 years,
57% males) from Singapore. Patients were diagnosed with PD using the UK Brain Bank Criteria
and population controls were recruited. Cases and controls were confirmed to be well-matched in
a principal components analysis using genome-wide SNPs from the Illumina array. All subjects
gave informed consent and the study received approval from the institutional ethics committee.
Allele frequencies in cases and controls were compared using Fisher’s exact tests. We used the
SIFT algorithm to predict the effects of missense variants (Ng & Henikoff 2003).
3. Results & Discussion
None of the reported disease causing mutations was identified in any of the three genes in
the sequencing analysis of 198 samples. In DNAJC13 (NM_015268.3), we identified three
missense mutations and six silent mutations. Of the three missense mutations, one was common
(p.Ala1463Ser; >20% frequency in 1000 genomes populations and 99 controls), one was rare
(p.Gly368Cys; predicted damaging) and found in one control subject, and one was rare
(p.Met2225Ile; predicted tolerated) and found in only one case subject (Supplementary Table 1).
p.Met2225Ile is also present in 1000 genomes populations, with frequencies ranging from 0.7%
(Asians) to 6% (Americans).
In DNAJC6 (NM_014787.2), we identified three missense variants and seven silent
mutations (Supplementary Table 1). Two of the missense variants were rare (<5% in 99 controls
and 1000 genomes populations), with one found in two control subjects (p.Asn469Ser; predicted
tolerated) and one found in a single case subject (p.Gly597Asp; predicted damaging). No
nonsense, splice-site or frameshift mutations in DNAJC6 were identified in our samples, and
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none of the PD cases were homozygotes or compound heterozygotes for missense variants. In
DNAJC5 (NM_025219.2), no missense variants and only two silent mutations were identified
(Supplementary Table 1). None were located near splice sites.
We further genotyped p.Met2225Ile, p.Ala1463Ser and five other missense mutations
(present on the Illumina exome chip) in DNAJC13, as well as p.Ser671Asn and p.Asn469Ser in
DNAJC6 in 711 late-onset/sporadic cases and 539 healthy controls. Neither of the two common
variants (p.Ala1463Ser, p.Ser671Asn) showed association with PD, even though we had >75%
power to detect a variant with a frequency of 10% and odds ratio of 1.4 at the significance
threshold of alpha=0.05. All the other variants were extremely rare (<0.5%), found in healthy
controls and none showed evidence of enrichment in PD cases (Supplementary Table 2).
Our results suggest that missense mutations in DNAJC13, DNAJC5 and DNAJC6 are not
major causes of early- or late-onset PD in the Chinese population.
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Disclosure Statement
The authors have no conflicts of interest.
All subjects gave informed consent and the study received approval from the institutional ethics
committee.
Acknowledgement
We thank National Medical Research Council, Duke Graduate Medical School and Singapore
Millennium Foundation for their support.
References
Trinh J, Farrer M. Advances in the genetics of Parkinson disease. Nat Rev Neurol. 2013
Aug;9(8):445-54. Epub 2013 Jul 16.
Edvardson, S. et al. A deleterious mutation in DNAJC6 encoding the neuronal-specific clathrinuncoating co-chaperone auxilin, is associated with juvenile parkinsonism. PLoS ONE 7, e36458
(2012).
Cadieux-Dion M, Andermann E, Lachance-Touchette P, Ansorge O, Meloche C, Barnabé A,
Kuzniecky RI, Andermann F, Faught E, Leonberg S, Damiano JA, Berkovic SF, Rouleau GA,
Cossette P. Recurrent mutations in DNAJC5 cause autosomal dominant Kufs disease. Clin
Genet. 2013 Jun;83(6):571-5. Epub 2012 Nov 7.
Ng, PC and Henikoff S. SIFT: Predicting amino acid changes that affect protein function.
Nucleic Acids Res 2013 31(13): 3812-4.
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Supplementary Table 1. Coding variants identified in 99 early onset/familial PD cases and 99
controls. Missense variants are shown in bold font.
Position
Amino Acid
Substitution
SIFT
prediction
Allele
Freq
Control
Allele
Freq
Case
No. of
controls
No. of
cases
chr3
132175347
p.Gly368Cys
Damaging
0.00505
0
1
0
chr3
132218623
p.Ala1463Ser
Tolerated
0.904
0.879
-
-
chr3
chr3
132257069
132153442
p.Met2225Ile
p.Thr16Thr
Tolerated
-
0
0
0.00505
0.00505
0
0
1
1
chr3
132166266
p.Thr82Thr
-
0.0960
0.121
-
-
chr3
132166302
p.Leu94Leu
-
0
0
0
0
chr3
132172463
p.Leu255Leu
-
0
0.00505
0
1
chr3
132175602
p.Leu425Leu
-
0.00505
0
1
0
chr3
132230036
p.Pro1747Pro
-
0.00505
0
1
0
chr1
65858222
p.Asn469Ser
Tolerated
0.0101
0
2
0
chr1
65860638
p.Gly597Asp
Damaging
0
0.00505
0
1
chr1
chr1
65867519
65852546
p.Ser671Asn
p.Val292Val
Tolerated
-
0.631
0.00505
0.535
0
1
0
chr1
65855095
p.Ser393Ser
-
0.00505
0.0101
1
2
chr1
65858145
p.Glu443Glu
-
0.167
0.217
-
-
chr1
65858151
p.His445His
-
0.616
0.505
-
-
chr1
65860660
p.Ser604Ser
-
0.611
0.500
-
-
chr1
65860687
p.Pro613Pro
-
0.803
0.753
-
-
chr1
65871623
p.Ser709Ser
-
0.00505
0
1
0
chr20
62559773
p.Asn25Asn
-
0.00505
0.00505
1
1
chr20
62560701
p.Pro48Pro
-
0.0303
0.0303
6
6
chr
DNAJC13
DNAJC6
DNAJC5
Supplementary Table 2. Missense variants genotyped in 711 late onset/sporadic PD cases and
539 controls
position
Amino Acid
Substitution
SIFT
prediction
Allele
Freq
Control
Allele
Freq
Case
No. of
controls
No. of
cases
Pvalue
chr3
132196651
p.Ala822Thr
Tolerated
0.00278
0.00211
3
3
1.000
chr3
132196920
p.Gly882Val
Damaging
0.00278
0.00211
3
3
1.000
chr3
132215496
p.Arg1382His
Damaging
0.000928
0.00141
1
2
1.000
chr3
132226100
p.Tyr1673Cys
Tolerated
0.000928
0
1
0
0.431
chr3
132257069
p.Met2225Ile
Tolerated
2
1.000
132218623
p.Ala1463Ser
Tolerated
0.00141
0.892
1
chr3
0.000928
0.890
-
-
0.642
chr1
65858222
p.Asn469Ser
Tolerated
0.00278
0.00356
3
5
1.000
chr1
65867519
p.Ser671Asn
Tolerated
0.5843
0.568
-
-
0.114
chr
DNAJC13
DNAJC6
6