1. Spectrum of BTK gene mutations in a single-centre cohort of
X-linked agammaglobulinemia from North India
Surjit Singh1, Amit Rawat1, Deepti Suri1, Anju Gupta1, Ravinder Garg1, Biman Saikia2, Ranjana Walker Minz2, Shobha Sehgal2, Koon-Wing Chan3, Yu Lung Lau3, Chikako Kamae4, Kenichi Honma4, Noriko Nakagawa4, Kohsuke Imai4, Shigeaki Nonoyama4, Koichi Oshima5, Noriko Mitsuiki5, Osamu Ohara5
1Pediatric Allergy and Immunology Unit, Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh
2Department of Immunopathology, Postgraduate Institute of Medical Education and Research, Chandigarh
3 Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
4Department of Pediatrics, National Defense Medical College, Tokorozawa, Saitama, Japan
5 Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
Introduction
Topology of BTK gene mutations at PGIMER, Chandigarh
X-linked agammaglobulinemia (XLA) is the prototypic humoral immunodeficiency resulting BTK gene mutations
BTK gene (Chromosome X; Xq22.1-Xq22) spans 19 exons & 37.5 kilobases
BTKbase; version BTK: shows 1374 public variants with 713 unique variants
We follow a large cohort of 56 children with XLA and BTK gene mutations in 34 at Advanced Pediatrics Centre, PGIMER, Chandigarh, India
Materials and Methods
Comprehensive analysis of 34 BTK gene mutations in our cohort of XLA patients
BTK gene sequencing was performed at Kazusa DNA Research, Chiba, Japan and Department of Pediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong
Effect of missense mutations was assessed using in-silico prediction tools
Table 1. BTK gene mutations in XLA cohort at Chandigarh
Patient
Exon/Intro n
Domain
Nucleotide change
Codon Change
Type of mutation 1
Exon 10
SH2
8842G>A
W281X
Point mutation (Nonsense mutation) 2
Intron 5 PH
IVS5-1G>C
Point mutation (Intronic/splice site) 3
Exon 16 TK
1771C>A
N526K
Point mutation (Missense mutation) 4
Intron 8~9
SH3
Deletion 5
Intron 17
c ,T>C
Point mutation (Intronic/splice site ) 6
Exon 1-3 7
Exon 2
83G>A
R28H
Point mutation (Missense) 8
Intron 18
IVS18-8 G>A
p.53GlyfsX5 9 10
Exon 15
1514 T>A
V505D
Point mutation (Missense mutation) 11
Exon 12
1064 T>A
I355N 12
Exon 19
1921C>T
R641C 13
126 T>A
Y42X
Point mutation (Nonsense) 14
Exon 3
insG
G53fsX5
Frameshift mutation (Insertion 15
Frameshift mutation (Insertion) 16
Exon 2-3 17
1594 C>T
Gln532>X
Point mutation (Nonsense ) 18
1002T>G
Tyr(Y)334X 19
Intron 1
IVS1+1 G>A
Point mutation (Splice site) 20
1589 T>C
L486P 21
Exon 17
1828C>T
P566S
Point mutation (Missense ) 22
169C>T
R13X 23
Exon 18
2013_2014delTA
Y627fsX635
Frameshift mutation (Deletion) 24
Exon8
895C>T
R255X 25
Exon 6 TH
c.461G>A
C154Y 26
1863delA
C577fsX586 27
1713_1716delTTTG
C527fsX528 28 29
Exon 8-9 30
c.1696C>T 31
c. 1732C>T
S578P 32
c. 1573C>G
R525G 33
Exon 9
803_804delAT
Y268fsX270 34
Exon 14
c.1325dupT
p.F442fsX44 4
Results
Single nucleotide substitutions (missense, nonsense and splice-site mutations) most common (65%; 22/34)
Frame-shift mutations resulting from small deletions and insertions accouted for 23% of mutations (8/34)
Large deletions accounted for 12% of all mutations
Of single nucleotide substitutions, missense 50%, nonsense 27% and splice-site 23%
Fifty (50%) of mutations in exons encoding for the SH1 or TYK3 domain, followed by those in PH domain (34%)
Distribution of mutations across different domains similar to previously reported cohorts
Five novel mutations were identified in our cohort
Figure 1. BTK mutation spectrum
Figure 2. Types of misense mutations
Table 2. Prediction of effect of missesnse mutations
S. No.
Nucleotide
Change
Codon
Prediction by various in-silico bioinformatic tools
SIFT
PMut
PolpPhen
Condel 1.
83G>A
R28H
Damaging
Pathological
Probably
Deleterious 2.
1771C>A
N526K 3.
1828C>T
P566S
Neutral 4.
1514T>A
V505D 5.
1064T>A
I355N 6.
1921C>T
R641C 7.
1589 T>C
L486P 8.
461G>A
C154Y 9.
c. 1732C>T
S578P
10.
c. 1573C>G
R525G
References
Buckley CR. Agammaglobulinemia, by Col. Ogden C. Bruton, MC, USA, Pediatrics, 1952;9: Pediatrics. 1998;102:213e215.
Vetrie D, Vorechovsky I, Sideras P, et al. The gene involved in X-linked agammaglobulinaemia is a member of the src family of protein-tyrosine kinases. Nature. 1993;361:226e233.
Suri D, Rawat A, Singh S. X-linked Agammaglobulinemia. Indian J Pediatr. 2016;83:331-7.
Bhattad S, Vignesh P, Rawat A, et al. Spondylodiscitis in a Boy with X-linked Agammaglobulinemia: an Unusual Occurrence. J Clin Immunol. 2016;36:360-2
Contact: Dr Amit Rawat, Additional Professor of Pediatric Allergy and Immunology, Advanced Pediatrics Centre, PGIMER, Chandigarh, INDIA.