Incidental Mutation 'R4329:Pnkp'
ID 324519
Institutional Source Beutler Lab
Gene Symbol Pnkp
Ensembl Gene ENSMUSG00000002963
Gene Name polynucleotide kinase 3'- phosphatase
Synonyms PNK, 1810009G08Rik
MMRRC Submission 041663-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R4329 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 44506563-44512416 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 44508018 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 114 (S114P)
Ref Sequence ENSEMBL: ENSMUSP00000143862 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000003044] [ENSMUST00000046575] [ENSMUST00000054343] [ENSMUST00000098478] [ENSMUST00000107876] [ENSMUST00000107880] [ENSMUST00000123015] [ENSMUST00000107882] [ENSMUST00000107885] [ENSMUST00000141311] [ENSMUST00000124168] [ENSMUST00000127783] [ENSMUST00000139003] [ENSMUST00000155050] [ENSMUST00000201882] [ENSMUST00000209018] [ENSMUST00000207363] [ENSMUST00000154968] [ENSMUST00000200892] [ENSMUST00000202646]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000003044
AA Change: S114P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000003044
Gene: ENSMUSG00000002963
AA Change: S114P

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: S114P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000096078
Gene: ENSMUSG00000002963
AA Change: S114P

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: S114P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000103508
Gene: ENSMUSG00000002963
AA Change: S114P

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: ENSMUST00000123015
AA Change: S114P

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000143862
Gene: ENSMUSG00000002963
AA Change: S114P

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 noncoding transcript
Transcript: ENSMUST00000145850
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126860
Predicted Effect probably benign
Transcript: ENSMUST00000142880
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144669
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152091
Predicted Effect probably benign
Transcript: ENSMUST00000107882
SMART Domains Protein: ENSMUSP00000103514
Gene: ENSMUSG00000011096

DomainStartEndE-ValueType
low complexity region 59 86 N/A INTRINSIC
low complexity region 92 127 N/A INTRINSIC
low complexity region 128 142 N/A INTRINSIC
low complexity region 187 206 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 probably benign
Transcript: ENSMUST00000141311
SMART Domains Protein: ENSMUSP00000120690
Gene: ENSMUSG00000011096

DomainStartEndE-ValueType
low complexity region 40 67 N/A INTRINSIC
low complexity region 73 108 N/A INTRINSIC
low complexity region 109 123 N/A INTRINSIC
low complexity region 168 187 N/A INTRINSIC
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: ENSMUST00000127783
SMART Domains Protein: ENSMUSP00000116149
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
Pfam:PRAS 134 247 1.3e-39 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 probably benign
Transcript: ENSMUST00000201882
AA Change: S114P

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000144690
Gene: ENSMUSG00000002963
AA Change: S114P

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 unknown
Transcript: ENSMUST00000208666
AA Change: S33P
Predicted Effect probably benign
Transcript: ENSMUST00000208385
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208687
Predicted Effect probably benign
Transcript: ENSMUST00000209018
Predicted Effect probably benign
Transcript: ENSMUST00000208410
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207303
Predicted Effect noncoding transcript
Transcript: ENSMUST00000207393
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152747
Predicted Effect probably benign
Transcript: ENSMUST00000207363
Predicted Effect probably benign
Transcript: ENSMUST00000207416
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: 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
Meta Mutation Damage Score 0.0627 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency 96% (68/71)
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2900026A02Rik C A 5: 113,243,455 (GRCm39) probably null Het
Adamts15 T C 9: 30,815,814 (GRCm39) S681G probably benign Het
Ampd2 C A 3: 107,985,103 (GRCm39) probably benign Het
Ang2 A T 14: 51,433,325 (GRCm39) I19N possibly damaging Het
Brd10 G T 19: 29,720,961 (GRCm39) T688K probably benign Het
Cacna1s A C 1: 136,046,771 (GRCm39) D1819A probably benign Het
Cand2 C A 6: 115,776,949 (GRCm39) H1112Q possibly damaging Het
Catsperd T A 17: 56,961,517 (GRCm39) I413K possibly damaging Het
Ccdc142 T A 6: 83,083,997 (GRCm39) probably benign Het
Cd55 A T 1: 130,380,220 (GRCm39) C253S probably damaging Het
Celsr3 C T 9: 108,723,248 (GRCm39) R2847C probably benign Het
Cep290 C T 10: 100,373,530 (GRCm39) S1270L probably damaging Het
Chka T C 19: 3,925,803 (GRCm39) probably benign Het
Cntnap5b T A 1: 99,999,888 (GRCm39) D215E probably damaging Het
Col13a1 T C 10: 61,699,758 (GRCm39) T476A unknown Het
Cspg4 T C 9: 56,799,749 (GRCm39) F1539L probably damaging Het
Cwf19l2 A T 9: 3,458,878 (GRCm39) I776F probably damaging Het
Dchs1 A T 7: 105,402,966 (GRCm39) I3192N probably damaging Het
Dnah7c T A 1: 46,688,441 (GRCm39) D1870E probably benign Het
Drc1 A T 5: 30,513,002 (GRCm39) I359L probably benign Het
Esp1 A G 17: 41,039,768 (GRCm39) M18V probably benign Het
Exoc1 T A 5: 76,715,822 (GRCm39) F789L probably damaging Het
Fbxw22 T A 9: 109,213,111 (GRCm39) T279S probably damaging Het
Frem1 G A 4: 82,904,774 (GRCm39) A880V probably benign Het
Gm29514 A G 1: 146,296,429 (GRCm39) noncoding transcript Het
Grm7 T C 6: 110,891,325 (GRCm39) L186P probably damaging Het
Ipo8 A T 6: 148,701,662 (GRCm39) probably benign Het
Klk4 A G 7: 43,533,830 (GRCm39) D202G probably damaging Het
Marchf6 C T 15: 31,498,887 (GRCm39) E137K probably benign Het
Mpp3 T C 11: 101,914,337 (GRCm39) probably benign Het
Mroh2b T A 15: 4,960,861 (GRCm39) Y808N probably damaging Het
Myom1 C T 17: 71,343,348 (GRCm39) L182F probably damaging Het
Nova1 A T 12: 46,767,615 (GRCm39) I102N unknown Het
Or7g34 T A 9: 19,478,318 (GRCm39) M121L possibly damaging Het
Pak3 T C X: 142,516,205 (GRCm39) probably null Het
Palm G A 10: 79,643,520 (GRCm39) G83S probably benign Het
Patl2 C T 2: 121,958,018 (GRCm39) S80N probably benign Het
Pcdhb9 A T 18: 37,534,875 (GRCm39) S290C probably benign Het
Pcdhb9 G T 18: 37,534,876 (GRCm39) S290I probably benign Het
Pdgfrb A T 18: 61,204,792 (GRCm39) I551F possibly damaging Het
Pkmyt1 T A 17: 23,951,709 (GRCm39) Y88N probably damaging Het
Rdm1 T A 11: 101,521,734 (GRCm39) V92E probably damaging Het
Sema4d T C 13: 51,857,340 (GRCm39) R631G probably benign Het
Sin3a T C 9: 57,002,642 (GRCm39) L178P probably damaging Het
Skint9 A C 4: 112,249,062 (GRCm39) L122R probably damaging Het
Slc16a13 T C 11: 70,108,723 (GRCm39) N369S probably benign Het
Strada A G 11: 106,077,999 (GRCm39) probably benign Het
Tnxb C A 17: 34,912,838 (GRCm39) S1784Y probably damaging Het
Trpc2 T C 7: 101,736,727 (GRCm39) V318A probably damaging Het
Ttc3 G A 16: 94,267,820 (GRCm39) R1589H probably damaging Het
Ttyh1 A T 7: 4,133,580 (GRCm39) D295V probably damaging Het
Unc5b A G 10: 60,618,969 (GRCm39) Y58H probably damaging Het
Xylt1 G A 7: 117,255,684 (GRCm39) G752D probably damaging Het
Yipf7 A T 5: 69,678,465 (GRCm39) L55Q probably damaging Het
Zfp827 G A 8: 79,916,463 (GRCm39) probably benign Het
Zfta A G 19: 7,398,591 (GRCm39) 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
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'- AAGTTCTGACTGGCCACACG -3'
(R):5'- TTAACTGGCTAGCCTGGGTG -3'

Sequencing Primer
(F):5'- AAATTGATTGGGAGCTAAGGTATTG -3'
(R):5'- CCTGGGTGGCAGCAGGG -3'
Posted On 2015-06-24