Non-Homologous End-Joining (NHEJ) DNA Double-Strand Break Repair Gene Coding Region Polymorphisms (cSNPs)

[ PRKDC | Ku70 ]

METHOD: Segments containing indicated exons were amplified by PCR from genomic DNA obtained from approximately 96 individuals. Both strands of each amplified fragment were sequenced using the PCR primers and/or internal primers, as appropriate, and BigDye chemistry (Applied Biosystems, Inc). The sequences from each individual then were compared to a reference sequence. Genomic DNAs were from the first 96 individuals (PD0001 to PD0096) of the NIGMS polymorphism discovery set (Collins et al., 1998) and were obtained from the Coriell Institute, Camden, NJ.

Collins, F.S., Brooks, L.D. and Chakravarti, A. (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res, 8, 1229-31.

For information on non-coding polymorphisms, contact: Carl W. Anderson, Biology Department, Brookhaven National Laboratory, Upton, NY 11973 USA; phone: 631-344-3375, fax: 631-344-6398, email:

This work has been supported by Grant 1R01CA 89199-01 from the National Cancer Institute, NIH, and by Laboratory Directed Research and Development funds from Brookhaven National Laboratory.

GENE: PRKDC - catalytic subunit of the DNA-dependent protein kinase
Human Chromosomal Location: 8q11
cDNA: U47077.5, 12,509 bp, Last updated 27 Aug, 2001
Number of Exons: 86
Protein: 4128 amino acids
OMIM Entry: 600899

Description: PRKDC encodes the catalytic subunit (DNA-PKcs) of the DNA-dependent protein kinase, DNA-PK. The two other subunits of the enzyme are Ku70 and Ku80. DNA-PK is activated when bound to DNA ends. The enzyme is required for the efficient repair of DNA double-strand breaks by the NHEJ pathway, and also for the site-specific V(D)J recombination and class switching of immunoglobulin genes. Mice and horses lacking DNA-PK activity exhibit severe combined immunodeficiencies. DNA-PK is a member of a family of phosphotidylinositol-3-kinase related protein kinases that includes ATM, ATR, and FRAP. DNA-PK is found in vertebrates but a true homologue has not been identified in yeast, Drosophila, or C. elegans.

LAST UPDATED: April 6, 2002
Exon U47077.5
nucleotides		 cDNA
Position		 amino
acid #		 Codon Maj
Nt		 Maj
AA		 Min
nt		 Min
AA		 No.
Ind.		 Minor
Allele
Freq.		 Ref. Last
Update
12 1,170-1,335 None - - - - - - 76 0/152 = 0% 1 10/21/01
32 3,905-4,128 None - - - - - - 87 0/174 = 0% 1 10/21/01
48 6,403-6,522 None - - - - - - 91 0/182 = 0% UP 10/21/01
73 10,355-10,515 10,358 3434 ATT T Ile C Thr 95 45/190 = 23.7% UP 10/21/01
81 11,547-11,636 11,564 3836 CCG C Pro T Leu 87 1/174 = 0.006 UP 10/21/01
85 12,100-12,239 None - - - - - - 88 0/176 UP 10/22/01
86 12,240-12,444 None - - - - - - 96 0/192 UP 10/21/01

NOTES:
Exon 32 - Only known human mutation in DNA-PKcs that affects activity is a single nucleotide deletion in exon 32 in the glioma-derived cell line M059J.

Exon 48 - The mouse BALB/c DNA-PKcs cDNA has a variant nucleotide at the positon equivalent to nucleotide 6464 in Genbank U47077.5; the change of C to T in the first position of a conserved Arg codon (CGT) changes DNA-PKcs amino acid 3843 from Met (mouse) to Val (Yu et al., 2001). Human predominantly have Thr (ACA) at this position. This change is associated with increased sensitivity to ionizing radiation and susceptibility to radiation-induced breast cancer in BALB/c mice compared to most other mouse strains, but it is not believe to be the cause of the increased sensitivity (see note for exon 48).

Exon 81 - The mouse BALB/c DNA-PKcs cDNA has a variant nucleotide at the positon equivalent to nucleotide 11,587 in Genbank U47077.5; the change of A to G in the first position of a non-conserved Met codon (ATG) (mouse) changes DNA-PKcs amino acid 2143 to Val (GTG). This change is associated with increased sensitivity to ionizing radiation and susceptibility to radiation-induced breast cancer in BALB/c mice compared to most other mouse strains (Yu et al., 2001).

Exon 86 - Includes only the coding region for the C-terminus of DNA-PKcs; see 3'UTR for non-coding segment of exon 86.

References:                                                           
UP = Anderson et al., unpublished

1. Anderson, C. W., J. J. Dunn, P. Freimuth, A. M. Galloway and M. J. Allalunis-Turner. Frameshift mutation in PRKDC, the gene for DNA-PKcs, in the human, DNA repair-defective, glioma-derived cell line M059J. Radiat. Res. 156, 2-9 (2001).

2. Yu, Okayasu, Weil, Silver, McCarthy, Zabriskie, Cox, and Ullrich. Elevated breast cancer risk in irradiated BALB/c mice associated with unique functional polymorphism of the Prkdc (DNA-PKcs) gene. Cancer Res. 61 (2001) 1820-4.


GENE: KU70 - DNA end binding protein; targeting subunit of the DNA-dependent protein kinase; forms heterodimer with Ku80
         Literature Aliases: G22P1
Human Chromosomal Location: 22q13.2-q13.31
cDNA: >XM_086818.1, 2119 bp, Last updated 07 Feb. 2002 = Predicted Model REFSEQ
Number of Exons: 13
Protein: 609 amino acids
OMIM Entry: 152690

Description: Ku70 forms a heterodimer with Ku80 that binds to DNA ends and serves as the targeting subunit of the DNA-dependent protein kinase, DNA-PK. Mice and murine cells deficient in Ku70 are sensitive to ionizing radiation and deficient in the repair of DNA double-strand breaks and in V(D)J recombination. Ku70 homologues have been found in all eukaryotic species that have been examine, including yeast.

Ku70 cSNPs: LAST UPDATED: March 23, 2002
Exon >XM_086819
nucleotides		 cDNA
Position		 amino
acid #		 Codon Maj
Nt		 Maj
AA		 Min
nt		 Min
AA		 No.
Ind.		 Minor
Allele
Freq.		 Ref. Last
Updated
1 1-51 Not Done                    
2 52-148 None - - - - - - - 0/192 - 3/23/02
3 149-261 None - - - - - - - 0/190 - 3/16/02
4 262-400 None - - - - - - - 0/190 - 3/16/02
5 401-655 None - - - - - - - 0/184 - 3/16/02
6 656-839 None - - - - - - - 0/190 - 3/16/02
7 840-1026 None - - - - - - - 0/192 - 3/15/02
8 1027-1195 None - - - - - - - 0/190 - 3/16/02
9 1196-1357 None - - - - - - - 0/192 - 3/15/02
10 1358-1486 None - - - - - - - 0/190 - 3/16/02
11 1487-1588 None - - - - - - - 0/192 - 3/15/02
12 1589-1702 None - - - - - - - 0/192 - 3/15/02
13 1703-2119 1830
1845		 587
592		 TAC
GGG		 C
G		 Tyr
Gly		 T
T		 Tyr
Gly		 1
26		 1/192 = ~0.5%
29192 = 15.1%		   3/23/02
3/16/02

NOTES:
Exon 1 is a non-coding exon predicted from a ``full length'', alternatively spliced, Ku70 cDNA clone (Genbank AK055786) which is predicted to encode a 586 amino acid product that is missing most of exon 4.

Exon 13 encodes the C-terminal 64 amino acids. Individual PD0005 is heterozygous the third base of codon for Tyr587 and has both C and T in this position; the polymorphism does not change the encoded amino acid. Twenty three of 96 individuals are heterogeneous the third position base of the codon for Gly592 and have G and T in this position; 3 individuals are homozygous for T at this position. The polymorphism is silent and does not change the encoded amino acid.