Incidental Mutation 'R5267:Pnkp'
ID 401771
Institutional Source Beutler Lab
Gene Symbol Pnkp
Ensembl Gene ENSMUSG00000002963
Gene Name polynucleotide kinase 3'- phosphatase
Synonyms PNK, 1810009G08Rik
MMRRC Submission 042859-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R5267 (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: 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 noncoding transcript
Transcript: ENSMUST00000126860
Predicted Effect probably benign
Transcript: ENSMUST00000207363
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: ENSMUST00000208385
Predicted Effect probably benign
Transcript: ENSMUST00000208682
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207393
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209003
Predicted Effect probably benign
Transcript: ENSMUST00000208666
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208765
Predicted Effect probably benign
Transcript: ENSMUST00000207416
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: 98.4%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency 98% (86/88)
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 T A 1: 71,374,933 (GRCm39) probably benign Het
Adam15 T G 3: 89,257,206 (GRCm39) probably benign Het
Albfm1 T C 5: 90,732,716 (GRCm39) F509S probably damaging Het
Atp12a T C 14: 56,621,668 (GRCm39) S768P probably damaging Het
Atp8a1 G A 5: 67,919,887 (GRCm39) T393I probably damaging Het
B4galnt4 T G 7: 140,650,524 (GRCm39) I3S probably damaging Het
Bfsp1 G A 2: 143,668,971 (GRCm39) T536I probably benign Het
Brsk1 G T 7: 4,707,708 (GRCm39) W284L probably damaging Het
Cadm3 A T 1: 173,164,669 (GRCm39) D370E probably damaging Het
Cadps2 A G 6: 23,626,667 (GRCm39) I207T possibly damaging Het
Calr4 A C 4: 109,101,273 (GRCm39) T52P probably damaging Het
Catsperg2 G A 7: 29,416,491 (GRCm39) T307M probably damaging Het
Ckap5 T A 2: 91,422,097 (GRCm39) N1166K probably null Het
Clca4a G A 3: 144,659,573 (GRCm39) T761I probably damaging Het
Cnksr3 A T 10: 7,076,633 (GRCm39) probably null Het
Diaph3 A G 14: 86,893,989 (GRCm39) S7P probably benign Het
Dnah7a G A 1: 53,518,851 (GRCm39) P2969S probably damaging Het
Dnai2 A T 11: 114,631,293 (GRCm39) T221S probably benign Het
Dsc2 A G 18: 20,167,640 (GRCm39) probably null Het
Eif4g1 A G 16: 20,504,283 (GRCm39) N789S probably damaging Het
Fn1 C T 1: 71,668,863 (GRCm39) R694H probably damaging Het
Gm5478 G A 15: 101,552,837 (GRCm39) R365C probably damaging Het
Gm5591 A T 7: 38,218,338 (GRCm39) M845K possibly damaging Het
Gm5800 A T 14: 51,951,294 (GRCm39) probably null Het
Gprc5c G T 11: 114,755,093 (GRCm39) V257L possibly damaging Het
H2-Q2 A T 17: 35,562,155 (GRCm39) Y134F probably benign Het
Hcfc1r1 A G 17: 23,893,648 (GRCm39) R76G possibly damaging Het
Hectd4 T C 5: 121,482,887 (GRCm39) I3146T probably benign Het
Herc1 G T 9: 66,369,091 (GRCm39) L2928F probably damaging Het
Hmx3 C T 7: 131,145,898 (GRCm39) A202V probably benign Het
Ikzf3 A T 11: 98,381,406 (GRCm39) M58K probably benign Het
Il20ra A G 10: 19,625,107 (GRCm39) T129A probably damaging Het
Il21 T C 3: 37,281,946 (GRCm39) H66R probably benign Het
Kcnh5 A T 12: 75,134,190 (GRCm39) M453K probably damaging Het
Kdf1 C G 4: 133,256,258 (GRCm39) A325G probably damaging Het
Klhl10 C T 11: 100,338,047 (GRCm39) A262V probably benign Het
Krt81 T A 15: 101,357,340 (GRCm39) N464I probably benign Het
Ksr1 A T 11: 78,911,251 (GRCm39) I698N probably damaging Het
Lrp2 A G 2: 69,379,322 (GRCm39) V130A possibly damaging Het
Mcm2 T C 6: 88,874,432 (GRCm39) T25A probably benign Het
Mrps18c T A 5: 100,950,960 (GRCm39) Y93* probably null Het
Mycl C T 4: 122,894,289 (GRCm39) A363V probably damaging Het
Mylk2 C A 2: 152,755,469 (GRCm39) A211E probably benign Het
Myo5a G A 9: 75,059,292 (GRCm39) D507N probably damaging Het
Myo7b A G 18: 32,131,787 (GRCm39) F470L probably damaging Het
Oas1a A T 5: 121,037,284 (GRCm39) C248S probably benign Het
Or2ag2b T C 7: 106,418,015 (GRCm39) S242P probably damaging Het
Or4c15b C T 2: 89,112,574 (GRCm39) W301* probably null Het
Or51aa2 T C 7: 103,188,031 (GRCm39) I137V probably benign Het
Or5b116 A G 19: 13,422,475 (GRCm39) Y33C probably damaging Het
Or5m9b T A 2: 85,905,882 (GRCm39) V266E probably benign Het
Or5p67 A G 7: 107,922,185 (GRCm39) S233P probably damaging Het
Or8d1 G A 9: 38,767,101 (GRCm39) V248M probably damaging Het
Otub1 C A 19: 7,177,357 (GRCm39) G67C probably damaging Het
Otx1 C A 11: 21,947,037 (GRCm39) A91S probably damaging Het
Paqr8 A G 1: 21,004,920 (GRCm39) I25V probably benign Het
Pcdh1 A G 18: 38,325,252 (GRCm39) Y897H probably damaging Het
Pde4d T G 13: 109,397,343 (GRCm39) probably benign Het
Pdzd8 C A 19: 59,289,458 (GRCm39) K647N probably damaging Het
Praf2 T C X: 7,596,641 (GRCm39) probably benign Het
Pramel29 A T 4: 143,939,575 (GRCm39) probably benign Het
Psg25 A T 7: 18,258,711 (GRCm39) Y322N possibly damaging Het
Rxrg A G 1: 167,463,335 (GRCm39) E402G probably damaging Het
Selenok T A 14: 29,692,022 (GRCm39) V20E probably benign Het
Sipa1 G A 19: 5,705,786 (GRCm39) T394I probably benign Het
Spag17 A T 3: 99,969,264 (GRCm39) N1247I probably damaging Het
Spata31d1c A G 13: 65,183,718 (GRCm39) D420G probably damaging Het
Syk A G 13: 52,795,962 (GRCm39) K519R probably benign Het
Syne2 A T 12: 75,985,515 (GRCm39) E1654D possibly damaging Het
Tha1 A C 11: 117,760,502 (GRCm39) S241A probably damaging Het
Thsd7a T A 6: 12,379,601 (GRCm39) E941V probably damaging Het
Tjp1 T C 7: 64,972,797 (GRCm39) T548A probably damaging Het
Tube1 C A 10: 39,020,552 (GRCm39) D210E probably benign Het
Vmn1r183 T A 7: 23,754,971 (GRCm39) I258N possibly damaging Het
Vmn1r89 A T 7: 12,954,140 (GRCm39) N292I probably damaging Het
Vmp1 C A 11: 86,554,377 (GRCm39) V79L probably benign Het
Zfp182 T A X: 20,902,605 (GRCm39) D125V possibly damaging Het
Zfp975 T G 7: 42,311,654 (GRCm39) T320P probably damaging Het
Znrf1 G A 8: 112,263,899 (GRCm39) A43T probably benign 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
R5120: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
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'- TTTGCCTCCACAGGTACATC -3'
(R):5'- GTCCAGATGCTCCTGTAACC -3'

Sequencing Primer
(F):5'- GTACATCCAATGTGCCAAAGATG -3'
(R):5'- ATGCTCCTGTAACCGGAATG -3'
Posted On 2016-07-06