Incidental Mutation 'R5120:Pnkp'
ID 392926
Institutional Source Beutler Lab
Gene Symbol Pnkp
Ensembl Gene ENSMUSG00000002963
Gene Name polynucleotide kinase 3'- phosphatase
Synonyms PNK, 1810009G08Rik
MMRRC Submission 042708-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.962) question?
Stock # R5120 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 44506563-44512416 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 44511827 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 113 (S113L)
Ref Sequence ENSEMBL: ENSMUSP00000144484 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000003044] [ENSMUST00000046575] [ENSMUST00000098478] [ENSMUST00000107876] [ENSMUST00000123015] [ENSMUST00000124168] [ENSMUST00000200892] [ENSMUST00000202646] [ENSMUST00000207363] [ENSMUST00000201882] [ENSMUST00000154968] [ENSMUST00000139003] [ENSMUST00000155050] [ENSMUST00000209018]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000003044
AA Change: S474L

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: S474L

DomainStartEndE-ValueType
PDB:1YJM|C 1 110 4e-62 PDB
SCOP:d1lgpa_ 8 114 5e-12 SMART
Blast:FHA 31 74 1e-10 BLAST
low complexity region 116 134 N/A INTRINSIC
Pfam:PNK3P 165 327 9.3e-58 PFAM
low complexity region 350 364 N/A INTRINSIC
Pfam:AAA_33 366 488 1.6e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000046575
SMART Domains Protein: ENSMUSP00000035281
Gene: ENSMUSG00000038502

DomainStartEndE-ValueType
low complexity region 10 50 N/A INTRINSIC
low complexity region 64 82 N/A INTRINSIC
Pfam:Med25 89 238 1.7e-58 PFAM
Pfam:Med25 254 399 4.2e-57 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000098478
AA Change: S438L

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: S438L

DomainStartEndE-ValueType
PDB:1YJM|C 1 110 2e-62 PDB
SCOP:d1lgpa_ 8 114 5e-12 SMART
Blast:FHA 31 74 1e-10 BLAST
low complexity region 116 134 N/A INTRINSIC
Pfam:PNK3P 165 220 2.9e-16 PFAM
Pfam:PNK3P 211 291 5.3e-27 PFAM
low complexity region 314 328 N/A INTRINSIC
Pfam:AAA_33 330 452 5.6e-26 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000107876
AA Change: S474L

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: S474L

DomainStartEndE-ValueType
PDB:1YJM|C 1 110 4e-62 PDB
SCOP:d1lgpa_ 8 114 5e-12 SMART
Blast:FHA 31 74 1e-10 BLAST
low complexity region 116 134 N/A INTRINSIC
Pfam:PNK3P 165 327 1.9e-57 PFAM
low complexity region 350 364 N/A INTRINSIC
Pfam:AAA_33 366 488 5.9e-26 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000123015
SMART Domains Protein: ENSMUSP00000143862
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
PDB:1YJ5|C 1 143 8e-72 PDB
SCOP:d1lgpa_ 8 114 7e-13 SMART
Blast:FHA 31 74 2e-10 BLAST
PDB:3U7G|A 144 165 7e-6 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000124168
SMART Domains Protein: ENSMUSP00000144330
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
PDB:1YJM|C 1 51 3e-30 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126860
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144669
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145850
Predicted Effect probably damaging
Transcript: ENSMUST00000200892
AA Change: S95L

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000144163
Gene: ENSMUSG00000002963
AA Change: S95L

DomainStartEndE-ValueType
Pfam:AAA_33 18 100 3.9e-9 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000202646
AA Change: S113L

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000144484
Gene: ENSMUSG00000002963
AA Change: S113L

DomainStartEndE-ValueType
Pfam:AAA_33 5 44 6.1e-7 PFAM
Pfam:AAA_33 37 117 4.2e-9 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000208385
Predicted Effect probably benign
Transcript: ENSMUST00000207363
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207393
Predicted Effect probably benign
Transcript: ENSMUST00000207416
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152747
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207303
Predicted Effect probably benign
Transcript: ENSMUST00000201882
SMART Domains Protein: ENSMUSP00000144690
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
PDB:1YJM|C 1 110 6e-63 PDB
SCOP:d1lgpa_ 8 114 3e-12 SMART
Blast:FHA 31 74 2e-10 BLAST
low complexity region 116 134 N/A INTRINSIC
Pfam:PNK3P 165 327 9.9e-55 PFAM
low complexity region 350 364 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000154968
Predicted Effect probably benign
Transcript: ENSMUST00000139003
SMART Domains Protein: ENSMUSP00000143904
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
PDB:1YJM|C 1 51 3e-30 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000155050
SMART Domains Protein: ENSMUSP00000144663
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
PDB:1YJM|C 1 50 9e-30 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209139
Predicted Effect probably benign
Transcript: ENSMUST00000208410
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208655
Predicted Effect probably benign
Transcript: ENSMUST00000209018
Predicted Effect probably benign
Transcript: ENSMUST00000208682
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209003
Predicted Effect probably benign
Transcript: ENSMUST00000208666
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208765
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208687
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208991
Meta Mutation Damage Score 0.2697 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.8%
  • 20x: 90.6%
Validation Efficiency 100% (97/97)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for a frame-shift allele are embryonic lethal. Homozygotes for a hypomorphic allele exhibit smaller brain (cortex and cerebellum) and defects in both single- and double-strand DNA break repair associated with increased brain apoptosis and decreased proliferation in cortical progenitors. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 84 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310033P09Rik A G 11: 59,101,061 (GRCm39) H225R probably benign Het
Abcc9 T A 6: 142,602,344 (GRCm39) I690F probably benign Het
Acp4 A T 7: 43,906,395 (GRCm39) D52E probably damaging Het
Adam17 T C 12: 21,393,020 (GRCm39) probably benign Het
Adamts15 T C 9: 30,832,872 (GRCm39) E221G probably damaging Het
Aoc2 A G 11: 101,216,540 (GRCm39) T208A probably benign Het
Apoa4 T G 9: 46,154,035 (GRCm39) I212S probably damaging Het
Bptf A T 11: 106,964,211 (GRCm39) M1598K probably damaging Het
Camsap3 G A 8: 3,650,680 (GRCm39) R209Q probably damaging Het
Ccdc171 C A 4: 83,476,763 (GRCm39) probably benign Het
Celsr2 G C 3: 108,300,436 (GRCm39) P2875A probably benign Het
Cenpb A G 2: 131,021,738 (GRCm39) V20A probably benign Het
Cfap61 A T 2: 145,985,080 (GRCm39) K975* probably null Het
Cfhr4 T C 1: 139,680,841 (GRCm39) S226G probably benign Het
Col9a2 G T 4: 120,896,969 (GRCm39) A20S unknown Het
Crnn A T 3: 93,056,203 (GRCm39) I330F probably benign Het
Csf3r C A 4: 125,929,620 (GRCm39) P381Q probably benign Het
Csmd3 G A 15: 48,536,891 (GRCm39) Q104* probably null Het
Ctnna1 G A 18: 35,315,607 (GRCm39) probably null Het
Cwf19l2 C T 9: 3,418,761 (GRCm39) Q183* probably null Het
Ddx60 T C 8: 62,398,940 (GRCm39) Y220H probably benign Het
Dhh T C 15: 98,796,038 (GRCm39) Q39R probably benign Het
Dynlrb2 T A 8: 117,242,437 (GRCm39) I89N possibly damaging Het
Dytn T C 1: 63,662,202 (GRCm39) E645G probably benign Het
Efcab7 A G 4: 99,754,688 (GRCm39) T287A probably damaging Het
Eogt A G 6: 97,111,276 (GRCm39) V195A probably benign Het
Ep400 G T 5: 110,904,224 (GRCm39) P125Q probably damaging Het
Fasn A G 11: 120,702,217 (GRCm39) V1815A probably benign Het
Gm5866 T C 5: 52,740,224 (GRCm39) noncoding transcript Het
Gm8674 C A 13: 50,055,984 (GRCm39) noncoding transcript Het
Gpat4 G T 8: 23,670,218 (GRCm39) H270Q possibly damaging Het
Grik5 A G 7: 24,710,065 (GRCm39) L890P probably damaging Het
Gsap A G 5: 21,474,934 (GRCm39) N500S probably damaging Het
H2-M10.1 T C 17: 36,636,048 (GRCm39) D173G probably benign Het
Igfn1 T A 1: 135,901,240 (GRCm39) I413F possibly damaging Het
Ighv1-52 G T 12: 115,109,406 (GRCm39) H17N probably benign Het
Kcnu1 T A 8: 26,424,516 (GRCm39) D270E possibly damaging Het
Kif16b A C 2: 142,690,259 (GRCm39) N274K probably damaging Het
Klk1b11 C T 7: 43,648,446 (GRCm39) T151I probably benign Het
Krtap13 A G 16: 88,548,458 (GRCm39) F10S probably damaging Het
Large1 A T 8: 73,585,969 (GRCm39) I379N probably damaging Het
Lhx8 T C 3: 154,017,332 (GRCm39) H301R probably damaging Het
Lrriq3 T C 3: 154,835,021 (GRCm39) V252A probably benign Het
Lysmd3 T A 13: 81,817,311 (GRCm39) I96N probably damaging Het
Mpeg1 C T 19: 12,438,793 (GRCm39) Q84* probably null Het
Myoz1 C T 14: 20,700,722 (GRCm39) G165D probably benign Het
Myt1 G A 2: 181,439,413 (GRCm39) V312I probably benign Het
Ndufb7 T C 8: 84,293,606 (GRCm39) probably benign Het
Numa1 C T 7: 101,626,644 (GRCm39) T10M probably damaging Het
Or10d1b T A 9: 39,613,366 (GRCm39) H233L probably benign Het
Or1e30 A C 11: 73,677,790 (GRCm39) I9L probably benign Het
Or2g7 A T 17: 38,378,157 (GRCm39) I32F probably damaging Het
Or4f14d A T 2: 111,960,903 (GRCm39) D84E probably damaging Het
Or4k39 T C 2: 111,239,585 (GRCm39) noncoding transcript Het
Osmr A T 15: 6,856,756 (GRCm39) S464T probably benign Het
Pak5 G A 2: 135,925,149 (GRCm39) H718Y probably damaging Het
Pan2 T A 10: 128,150,864 (GRCm39) probably null Het
Pik3r4 T C 9: 105,546,208 (GRCm39) S853P probably benign Het
Polr3gl T A 3: 96,485,795 (GRCm39) probably benign Het
Psd2 G A 18: 36,112,863 (GRCm39) R186Q possibly damaging Het
Psd4 T C 2: 24,295,450 (GRCm39) V868A probably benign Het
Ralgapa2 G T 2: 146,254,004 (GRCm39) T852K probably benign Het
Rbm43 T C 2: 51,822,435 (GRCm39) probably benign Het
Rps6kl1 C A 12: 85,186,122 (GRCm39) G329C probably damaging Het
Scaf11 T C 15: 96,317,423 (GRCm39) T714A probably benign Het
Selenoo C A 15: 88,978,508 (GRCm39) N310K possibly damaging Het
Sepsecs T C 5: 52,818,003 (GRCm39) Q258R probably damaging Het
Sgcz T C 8: 37,993,420 (GRCm39) S226G probably benign Het
Slfn5 A G 11: 82,851,754 (GRCm39) K627E probably damaging Het
Sos1 A T 17: 80,715,677 (GRCm39) F1027I probably damaging Het
Ssh1 C G 5: 114,095,459 (GRCm39) V228L possibly damaging Het
Sugp1 C A 8: 70,501,317 (GRCm39) P65T probably benign Het
Tas2r106 T A 6: 131,655,779 (GRCm39) N24I probably damaging Het
Tex10 T C 4: 48,459,272 (GRCm39) E534G possibly damaging Het
Tmem182 C T 1: 40,894,061 (GRCm39) T192I possibly damaging Het
Traf7 T A 17: 24,737,718 (GRCm39) K51* probably null Het
Trap1 C A 16: 3,861,952 (GRCm39) R604L probably damaging Het
Trim6 T A 7: 103,877,447 (GRCm39) L179Q probably damaging Het
Ubfd1 T C 7: 121,670,973 (GRCm39) S264P probably damaging Het
Upk3bl T C 5: 136,093,045 (GRCm39) probably benign Het
Wdfy3 T A 5: 102,015,972 (GRCm39) Q2601L possibly damaging Het
Wdr89 A G 12: 75,679,412 (GRCm39) Y281H probably damaging Het
Zfp286 A T 11: 62,671,551 (GRCm39) M174K probably benign Het
Zmym1 T C 4: 126,945,230 (GRCm39) probably null Het
Other mutations in Pnkp
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01886:Pnkp APN 7 44,511,631 (GRCm39) missense probably damaging 1.00
IGL02750:Pnkp APN 7 44,509,611 (GRCm39) unclassified probably benign
IGL02822:Pnkp APN 7 44,511,848 (GRCm39) missense probably damaging 1.00
R1168:Pnkp UTSW 7 44,511,961 (GRCm39) missense probably benign 0.00
R1437:Pnkp UTSW 7 44,509,826 (GRCm39) missense possibly damaging 0.87
R1953:Pnkp UTSW 7 44,512,026 (GRCm39) missense probably benign 0.02
R2879:Pnkp UTSW 7 44,508,102 (GRCm39) missense probably damaging 0.99
R4329:Pnkp UTSW 7 44,508,018 (GRCm39) missense probably benign 0.02
R4732:Pnkp UTSW 7 44,509,878 (GRCm39) unclassified probably benign
R4842:Pnkp UTSW 7 44,511,070 (GRCm39) splice site probably null
R4846:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R4861:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R4861:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R4872:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R4873:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R4875:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R5068:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R5121:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R5266:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R5267:Pnkp UTSW 7 44,511,827 (GRCm39) missense probably damaging 0.99
R6532:Pnkp UTSW 7 44,506,829 (GRCm39) start codon destroyed probably null 0.99
R6974:Pnkp UTSW 7 44,510,462 (GRCm39) missense probably damaging 1.00
R7289:Pnkp UTSW 7 44,508,114 (GRCm39) missense probably damaging 1.00
R7326:Pnkp UTSW 7 44,509,158 (GRCm39) missense probably damaging 1.00
R7394:Pnkp UTSW 7 44,508,102 (GRCm39) missense probably damaging 0.99
R7573:Pnkp UTSW 7 44,506,852 (GRCm39) missense probably damaging 1.00
R7995:Pnkp UTSW 7 44,507,960 (GRCm39) nonsense probably null
R8951:Pnkp UTSW 7 44,507,617 (GRCm39) missense possibly damaging 0.64
Predicted Primers PCR Primer
(F):5'- GTGACAGCTGTTTTGCCTCC -3'
(R):5'- CTCCTGTAACCGGAATGGAATC -3'

Sequencing Primer
(F):5'- GTACATCCAATGTGCCAAAGATG -3'
(R):5'- TCCTGTAACCGGAATGGAATCTCAAG -3'
Posted On 2016-06-15