Incidental Mutation 'R1437:Pnkp'
ID 161296
Institutional Source Beutler Lab
Gene Symbol Pnkp
Ensembl Gene ENSMUSG00000002963
Gene Name polynucleotide kinase 3'- phosphatase
Synonyms PNK, 1810009G08Rik
MMRRC Submission 039492-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R1437 (G1)
Quality Score 192
Status Not validated
Chromosome 7
Chromosomal Location 44506563-44512416 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 44509826 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 262 (S262G)
Ref Sequence ENSEMBL: ENSMUSP00000144690 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000003044] [ENSMUST00000046575] [ENSMUST00000054343] [ENSMUST00000098478] [ENSMUST00000107876] [ENSMUST00000107880] [ENSMUST00000107885] [ENSMUST00000201882] [ENSMUST00000154968] [ENSMUST00000200892] [ENSMUST00000124168] [ENSMUST00000123015] [ENSMUST00000202646] [ENSMUST00000139003] [ENSMUST00000155050] [ENSMUST00000209018] [ENSMUST00000207363]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000003044
AA Change: S262G

PolyPhen 2 Score 0.365 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: S262G

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 probably benign
Transcript: ENSMUST00000054343
SMART Domains Protein: ENSMUSP00000049764
Gene: ENSMUSG00000011096

DomainStartEndE-ValueType
low complexity region 33 60 N/A INTRINSIC
low complexity region 66 101 N/A INTRINSIC
low complexity region 102 116 N/A INTRINSIC
low complexity region 161 180 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000098478
AA Change: S226G

PolyPhen 2 Score 0.129 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: S226G

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 benign
Transcript: ENSMUST00000107876
AA Change: S262G

PolyPhen 2 Score 0.365 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: S262G

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: ENSMUST00000107880
SMART Domains Protein: ENSMUSP00000103512
Gene: ENSMUSG00000011096

DomainStartEndE-ValueType
low complexity region 33 60 N/A INTRINSIC
low complexity region 66 101 N/A INTRINSIC
low complexity region 102 116 N/A INTRINSIC
low complexity region 161 180 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000107885
SMART Domains Protein: ENSMUSP00000103517
Gene: ENSMUSG00000011096

DomainStartEndE-ValueType
low complexity region 104 131 N/A INTRINSIC
low complexity region 137 172 N/A INTRINSIC
low complexity region 173 187 N/A INTRINSIC
Pfam:PRAS 199 323 1.2e-51 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000201882
AA Change: S262G

PolyPhen 2 Score 0.872 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000144690
Gene: ENSMUSG00000002963
AA Change: S262G

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 noncoding transcript
Transcript: ENSMUST00000145850
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126860
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152747
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152091
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207303
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144669
Predicted Effect probably benign
Transcript: ENSMUST00000154968
Predicted Effect probably benign
Transcript: ENSMUST00000200892
SMART Domains Protein: ENSMUSP00000144163
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
Pfam:AAA_33 18 100 3.9e-9 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124168
SMART Domains Protein: ENSMUSP00000144330
Gene: ENSMUSG00000002963

DomainStartEndE-ValueType
PDB:1YJM|C 1 51 3e-30 PDB
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: ENSMUST00000202646
SMART Domains Protein: ENSMUSP00000144484
Gene: ENSMUSG00000002963

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: 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 unknown
Transcript: ENSMUST00000208666
AA Change: S135G
Predicted Effect probably benign
Transcript: ENSMUST00000208385
Predicted Effect probably benign
Transcript: ENSMUST00000208682
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208765
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208991
Predicted Effect probably benign
Transcript: ENSMUST00000209018
Predicted Effect probably benign
Transcript: ENSMUST00000207416
Predicted Effect probably benign
Transcript: ENSMUST00000208410
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207393
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208687
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209139
Predicted Effect probably benign
Transcript: ENSMUST00000207363
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 94.7%
  • 20x: 87.3%
Validation Efficiency
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1b T A 5: 8,871,436 (GRCm39) V330E possibly damaging Het
Abcb5 A G 12: 118,838,497 (GRCm39) S1022P probably damaging Het
Abcc8 A G 7: 45,829,237 (GRCm39) I46T probably damaging Het
Add3 A G 19: 53,222,109 (GRCm39) R275G probably damaging Het
Akap1 C A 11: 88,735,577 (GRCm39) G362* probably null Het
Arhgef4 A G 1: 34,763,026 (GRCm39) T761A unknown Het
Asap1 A T 15: 63,991,956 (GRCm39) L751Q probably damaging Het
Atg2a C A 19: 6,300,646 (GRCm39) P741H probably damaging Het
Atxn10 T C 15: 85,243,675 (GRCm39) I46T possibly damaging Het
BC049715 C A 6: 136,817,090 (GRCm39) A110E probably damaging Het
Bltp1 C A 3: 36,996,578 (GRCm39) H1097N possibly damaging Het
Btbd7 T A 12: 102,754,349 (GRCm39) T806S possibly damaging Het
Cdk4 C A 10: 126,900,558 (GRCm39) P108H probably damaging Het
Cep290 A G 10: 100,407,963 (GRCm39) T2391A probably benign Het
Col6a3 G T 1: 90,729,098 (GRCm39) A1281E probably damaging Het
Cpa5 A T 6: 30,624,654 (GRCm39) I165F probably damaging Het
Ctdp1 G T 18: 80,493,428 (GRCm39) Q356K probably benign Het
Ddx21 A G 10: 62,434,369 (GRCm39) M130T unknown Het
Epha5 T G 5: 84,381,555 (GRCm39) D432A probably damaging Het
Esr1 ACGCCGCCGCCGCCGCCGCCGCCGCCGCC ACGCCGCCGCCGCCGCCGCCGCCGCC 10: 4,662,571 (GRCm39) probably benign Het
Fads2 A T 19: 10,069,193 (GRCm39) L77Q probably benign Het
Fbn2 A T 18: 58,186,731 (GRCm39) H1723Q possibly damaging Het
Fbxo42 C T 4: 140,895,165 (GRCm39) H43Y probably benign Het
Fry A G 5: 150,233,890 (GRCm39) T121A possibly damaging Het
Gpr156 T G 16: 37,808,904 (GRCm39) S209A probably damaging Het
Hey2 T C 10: 30,709,845 (GRCm39) T303A probably benign Het
Hivep1 T A 13: 42,310,616 (GRCm39) M952K probably benign Het
Hydin C T 8: 111,308,617 (GRCm39) Q3968* probably null Het
Jup T C 11: 100,274,402 (GRCm39) E96G probably benign Het
Kcnn1 A G 8: 71,297,195 (GRCm39) I504T probably benign Het
Klk1b9 T C 7: 43,629,114 (GRCm39) V174A probably damaging Het
Lama3 G C 18: 12,682,284 (GRCm39) M1083I possibly damaging Het
Lcmt2 A G 2: 120,969,377 (GRCm39) S569P probably benign Het
Lrfn2 T C 17: 49,378,253 (GRCm39) S445P probably damaging Het
Lrp3 C A 7: 34,912,595 (GRCm39) G31W probably damaging Het
Lrrc8b T C 5: 105,629,568 (GRCm39) L638P probably damaging Het
Mief2 C T 11: 60,621,769 (GRCm39) T113M probably benign Het
Mrps2 T C 2: 28,358,899 (GRCm39) F76S probably damaging Het
Naca A G 10: 127,878,048 (GRCm39) probably benign Het
Ndst4 C A 3: 125,355,099 (GRCm39) R336S probably damaging Het
Nr1i3 CACTCAACACTAC CAC 1: 171,044,710 (GRCm39) probably null Het
Nr5a1 T A 2: 38,600,685 (GRCm39) T29S probably benign Het
Or5ak23 T C 2: 85,245,218 (GRCm39) I2V probably benign Het
Or5as1 C T 2: 86,980,115 (GRCm39) V297M possibly damaging Het
Pald1 A G 10: 61,177,064 (GRCm39) F662S possibly damaging Het
Pdcd4 G T 19: 53,897,674 (GRCm39) A59S probably damaging Het
Pde4a T C 9: 21,103,888 (GRCm39) probably null Het
Pkd1 T A 17: 24,814,106 (GRCm39) S4159T probably damaging Het
Plaat1 C A 16: 29,046,922 (GRCm39) A147E possibly damaging Het
Plch1 C A 3: 63,604,954 (GRCm39) R1641L probably benign Het
Plec G T 15: 76,073,481 (GRCm39) P308Q probably damaging Het
Pou2f1 A G 1: 165,719,399 (GRCm39) V504A probably damaging Het
Prepl G A 17: 85,395,785 (GRCm39) R66W probably damaging Het
Rasgrf2 T C 13: 92,167,396 (GRCm39) K226E probably damaging Het
Ror1 T A 4: 100,269,306 (GRCm39) F381L probably benign Het
Sbsn C T 7: 30,452,478 (GRCm39) Q498* probably null Het
Scgb2b19 T C 7: 32,977,980 (GRCm39) I106V probably benign Het
Sf3a2 G A 10: 80,640,040 (GRCm39) probably benign Het
Sis T C 3: 72,841,475 (GRCm39) H780R probably damaging Het
Slc28a3 G T 13: 58,706,389 (GRCm39) C617* probably null Het
Slc44a1 T A 4: 53,561,006 (GRCm39) V574D probably damaging Het
Slc8a3 T A 12: 81,362,760 (GRCm39) T20S probably damaging Het
Stt3b T A 9: 115,083,995 (GRCm39) I394F probably damaging Het
Ubap1l T A 9: 65,279,337 (GRCm39) V212D possibly damaging Het
Ugt2b35 T C 5: 87,148,890 (GRCm39) V47A probably benign Het
Vmn2r114 A G 17: 23,510,185 (GRCm39) F765S probably damaging Het
Vps50 C T 6: 3,517,852 (GRCm39) Q97* probably null Het
Vsig10 A G 5: 117,489,635 (GRCm39) Q467R probably damaging Het
Wdsub1 T G 2: 59,708,477 (GRCm39) Y11S probably damaging Het
Zbtb11 T G 16: 55,811,983 (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
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
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'- CCAGAGAGAACGTGCCAATGCATC -3'
(R):5'- AAGCTCCTATCTGTGGGCCACTTC -3'

Sequencing Primer
(F):5'- TGCCAATGCATCGGGGG -3'
(R):5'- GAGCATCTCTGTTTACCTAACACTG -3'
Posted On 2014-03-14