Incidental Mutation 'R5514:Pnpt1'
ID 440247
Institutional Source Beutler Lab
Gene Symbol Pnpt1
Ensembl Gene ENSMUSG00000020464
Gene Name polyribonucleotide nucleotidyltransferase 1
Synonyms 1200003F12Rik, polynucleotide phosphorylase, PNPase
MMRRC Submission 043074-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5514 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 29080744-29111828 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 29103246 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 504 (S504P)
Ref Sequence ENSEMBL: ENSMUSP00000020756 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000020756]
AlphaFold Q8K1R3
PDB Structure Solution structure of the alpha-helical domain from mouse hypothetical PNPase [SOLUTION NMR]
Predicted Effect possibly damaging
Transcript: ENSMUST00000020756
AA Change: S504P

PolyPhen 2 Score 0.820 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: S504P

DomainStartEndE-ValueType
low complexity region 4 26 N/A INTRINSIC
Pfam:RNase_PH 52 183 1.9e-16 PFAM
Pfam:RNase_PH_C 186 251 3.8e-13 PFAM
Pfam:PNPase 282 363 3.7e-9 PFAM
Pfam:RNase_PH 366 501 3.4e-22 PFAM
Pfam:RNase_PH_C 504 581 7.1e-6 PFAM
KH 604 669 8e-7 SMART
S1 677 750 2.15e-4 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154924
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene belongs to the evolutionary conserved polynucleotide phosphorylase family comprised of phosphate dependent 3'-to-5' exoribonucleases implicated in RNA processing and degradation. This enzyme is predominantly localized in the mitochondrial intermembrane space and is involved in import of RNA to mitochondria. Mutations in this gene have been associated with combined oxidative phosphorylation deficiency-13 and autosomal recessive nonsyndromic deafness-70. Related pseudogenes are found on chromosomes 3 and 7. [provided by RefSeq, Dec 2012]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality and impaired mitochondrial RNA import. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam17 T C 12: 21,390,520 (GRCm39) S382G probably damaging Het
Agr2 G A 12: 36,046,090 (GRCm39) V74I probably benign Het
Aldh3a1 T C 11: 61,108,867 (GRCm39) S423P probably damaging Het
Ampd1 C T 3: 102,986,488 (GRCm39) H56Y possibly damaging Het
Arhgef2 C A 3: 88,550,304 (GRCm39) P670T probably benign Het
Blk T G 14: 63,615,930 (GRCm39) D333A probably damaging Het
Bmi1 T C 2: 18,686,714 (GRCm39) I31T probably damaging Het
Cacna1d G A 14: 30,072,790 (GRCm39) Q62* probably null Het
Ccdc88c A G 12: 100,879,698 (GRCm39) S1801P probably damaging Het
Cdkal1 C T 13: 29,961,270 (GRCm39) A100T probably damaging Het
Cfap251 G T 5: 123,425,829 (GRCm39) probably null Het
Chst4 G T 8: 110,756,606 (GRCm39) S419Y probably damaging Het
Cntn4 T C 6: 106,649,844 (GRCm39) I680T probably damaging Het
Ddx55 T C 5: 124,694,875 (GRCm39) V101A probably damaging Het
Ddx60 A T 8: 62,411,091 (GRCm39) E451V probably damaging Het
Dffa T A 4: 149,190,772 (GRCm39) probably null Het
Dgkd A G 1: 87,861,832 (GRCm39) R796G probably damaging Het
Dzank1 T A 2: 144,323,605 (GRCm39) M614L probably benign Het
Elf2 G T 3: 51,215,555 (GRCm39) Q52K probably damaging Het
Fcamr T A 1: 130,741,793 (GRCm39) L522Q probably damaging Het
Fscn2 T C 11: 120,258,858 (GRCm39) Y468H probably damaging Het
Gm12689 T C 4: 99,184,402 (GRCm39) I85T unknown Het
Gm4787 A G 12: 81,425,102 (GRCm39) V352A possibly damaging Het
Gtsf1 T C 15: 103,336,802 (GRCm39) Q13R probably benign Het
Itpkb G A 1: 180,241,474 (GRCm39) V715M probably damaging Het
Jmjd1c T A 10: 67,053,928 (GRCm39) S263T probably damaging Het
Krba1 T G 6: 48,390,429 (GRCm39) L736R probably damaging Het
Lrrc8d C G 5: 105,960,650 (GRCm39) F353L probably damaging Het
Lrrc8d G A 5: 105,960,651 (GRCm39) E354K probably benign Het
Mtor T A 4: 148,630,901 (GRCm39) V2286E probably damaging Het
Mybbp1a T A 11: 72,341,462 (GRCm39) V1100E possibly damaging Het
Myo5a G A 9: 75,061,048 (GRCm39) G518D probably damaging Het
Nalcn A T 14: 123,521,123 (GRCm39) I1594N probably benign Het
Nav1 C G 1: 135,398,299 (GRCm39) G761A probably benign Het
Ncoa2 A T 1: 13,251,445 (GRCm39) L276H probably damaging Het
Ndufaf7 T C 17: 79,245,051 (GRCm39) Y57H probably damaging Het
Nfkb2 A G 19: 46,299,847 (GRCm39) Y807C probably damaging Het
Nid2 A T 14: 19,852,535 (GRCm39) Q1081L probably damaging Het
Nkain2 T A 10: 31,827,189 (GRCm39) I134F probably damaging Het
Nmu A C 5: 76,497,979 (GRCm39) S69A probably damaging Het
Or4c15b A T 2: 89,112,817 (GRCm39) I220N probably damaging Het
Or5t7 T C 2: 86,507,225 (GRCm39) I151V probably benign Het
Pard3 A G 8: 128,153,086 (GRCm39) R886G probably damaging Het
Pde6b G T 5: 108,571,317 (GRCm39) Q423H probably benign Het
Pip5k1b A T 19: 24,327,505 (GRCm39) D450E probably damaging Het
Plcg1 T C 2: 160,595,275 (GRCm39) probably null Het
Pomt2 A T 12: 87,175,797 (GRCm39) D312E probably damaging Het
Ppp1r1b T C 11: 98,246,228 (GRCm39) L70P probably damaging Het
Prr5 C A 15: 84,587,096 (GRCm39) P282Q probably benign Het
Reln A T 5: 22,176,883 (GRCm39) W1928R possibly damaging Het
Sacm1l A T 9: 123,415,419 (GRCm39) R465* probably null Het
Sema7a A G 9: 57,863,046 (GRCm39) Y239C probably damaging Het
Slc35e2 C T 4: 155,694,483 (GRCm39) P10L probably benign Het
Svep1 T C 4: 58,044,054 (GRCm39) T3531A possibly damaging Het
Tjp1 A T 7: 65,004,609 (GRCm39) W19R probably damaging Het
Tmc2 T A 2: 130,083,564 (GRCm39) M507K possibly damaging Het
Unc13a A G 8: 72,095,795 (GRCm39) Y1241H probably damaging Het
Upp1 C T 11: 9,081,771 (GRCm39) P103S probably damaging Het
Vldlr A G 19: 27,221,624 (GRCm39) E663G probably damaging Het
Vmn2r68 G A 7: 84,886,767 (GRCm39) T49I possibly damaging Het
Xirp2 A T 2: 67,335,465 (GRCm39) M95L probably benign Het
Other mutations in Pnpt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00229:Pnpt1 APN 11 29,104,217 (GRCm39) critical splice donor site probably null
IGL00920:Pnpt1 APN 11 29,107,087 (GRCm39) splice site probably benign
IGL01358:Pnpt1 APN 11 29,088,425 (GRCm39) missense possibly damaging 0.95
IGL01454:Pnpt1 APN 11 29,087,142 (GRCm39) missense probably benign 0.19
IGL01622:Pnpt1 APN 11 29,098,272 (GRCm39) splice site probably benign
IGL01623:Pnpt1 APN 11 29,098,272 (GRCm39) splice site probably benign
IGL01674:Pnpt1 APN 11 29,105,787 (GRCm39) missense probably benign 0.00
IGL01802:Pnpt1 APN 11 29,104,306 (GRCm39) missense probably damaging 1.00
IGL02222:Pnpt1 APN 11 29,080,842 (GRCm39) missense probably benign 0.00
IGL02222:Pnpt1 APN 11 29,109,327 (GRCm39) missense possibly damaging 0.71
IGL02616:Pnpt1 APN 11 29,085,505 (GRCm39) splice site probably benign
IGL02859:Pnpt1 APN 11 29,088,162 (GRCm39) missense probably damaging 1.00
IGL02965:Pnpt1 APN 11 29,106,939 (GRCm39) missense probably damaging 0.98
IGL03121:Pnpt1 APN 11 29,082,845 (GRCm39) missense probably benign 0.03
PIT4651001:Pnpt1 UTSW 11 29,106,945 (GRCm39) critical splice donor site probably null
R1023:Pnpt1 UTSW 11 29,091,328 (GRCm39) splice site probably benign
R1477:Pnpt1 UTSW 11 29,087,102 (GRCm39) missense probably benign 0.14
R1524:Pnpt1 UTSW 11 29,080,776 (GRCm39) missense unknown
R1769:Pnpt1 UTSW 11 29,104,159 (GRCm39) missense probably benign 0.22
R1839:Pnpt1 UTSW 11 29,104,342 (GRCm39) missense possibly damaging 0.82
R1975:Pnpt1 UTSW 11 29,091,256 (GRCm39) missense probably benign 0.16
R1977:Pnpt1 UTSW 11 29,091,256 (GRCm39) missense probably benign 0.16
R1996:Pnpt1 UTSW 11 29,091,679 (GRCm39) missense probably benign 0.01
R3771:Pnpt1 UTSW 11 29,088,174 (GRCm39) missense probably benign 0.05
R4346:Pnpt1 UTSW 11 29,095,478 (GRCm39) missense probably damaging 1.00
R4423:Pnpt1 UTSW 11 29,103,375 (GRCm39) splice site probably null
R5354:Pnpt1 UTSW 11 29,104,166 (GRCm39) missense probably damaging 1.00
R5503:Pnpt1 UTSW 11 29,088,156 (GRCm39) missense probably damaging 1.00
R5908:Pnpt1 UTSW 11 29,080,887 (GRCm39) missense probably benign 0.00
R6225:Pnpt1 UTSW 11 29,095,469 (GRCm39) missense probably benign 0.38
R6605:Pnpt1 UTSW 11 29,088,567 (GRCm39) missense possibly damaging 0.69
R7096:Pnpt1 UTSW 11 29,104,867 (GRCm39) missense probably benign 0.03
R7214:Pnpt1 UTSW 11 29,087,285 (GRCm39) missense probably damaging 1.00
R7365:Pnpt1 UTSW 11 29,111,334 (GRCm39) missense probably damaging 1.00
R7492:Pnpt1 UTSW 11 29,085,522 (GRCm39) missense probably benign 0.01
R7497:Pnpt1 UTSW 11 29,080,860 (GRCm39) missense probably benign 0.00
R7686:Pnpt1 UTSW 11 29,107,070 (GRCm39) missense probably damaging 0.97
R8166:Pnpt1 UTSW 11 29,106,875 (GRCm39) missense probably benign
R8309:Pnpt1 UTSW 11 29,103,277 (GRCm39) missense probably benign 0.01
R8389:Pnpt1 UTSW 11 29,080,758 (GRCm39) start codon destroyed unknown
R8542:Pnpt1 UTSW 11 29,082,773 (GRCm39) splice site probably null
R8737:Pnpt1 UTSW 11 29,104,815 (GRCm39) critical splice acceptor site probably null
R8876:Pnpt1 UTSW 11 29,096,769 (GRCm39) intron probably benign
R9308:Pnpt1 UTSW 11 29,097,535 (GRCm39) critical splice donor site probably null
R9545:Pnpt1 UTSW 11 29,106,840 (GRCm39) missense probably benign 0.13
Z1176:Pnpt1 UTSW 11 29,095,477 (GRCm39) missense possibly damaging 0.80
Z1176:Pnpt1 UTSW 11 29,095,475 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- GATCAAAGTCTGCTTCATTGGG -3'
(R):5'- AATGAAGGTATGTGCCTGGTC -3'

Sequencing Primer
(F):5'- GCCAAGTATAGATAATTACCTGTTGC -3'
(R):5'- TGCCTGGTCTAAGCATGTAC -3'
Posted On 2016-11-08