Incidental Mutation 'R7096:Pnpt1'
ID 550499
Institutional Source Beutler Lab
Gene Symbol Pnpt1
Ensembl Gene ENSMUSG00000020464
Gene Name polyribonucleotide nucleotidyltransferase 1
Synonyms 1200003F12Rik, polynucleotide phosphorylase, PNPase
MMRRC Submission 045188-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7096 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 29080744-29111828 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 29104867 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glutamine at position 597 (R597Q)
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 probably benign
Transcript: ENSMUST00000020756
AA Change: R597Q

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464
AA Change: R597Q

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 97% (68/70)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd18 T G 3: 40,888,305 (GRCm39) M383R probably damaging Het
Acd T A 8: 106,425,121 (GRCm39) E366V possibly damaging Het
Acvr2b T A 9: 119,257,255 (GRCm39) probably null Het
Alg10b C T 15: 90,111,564 (GRCm39) T136I probably benign Het
Ankrd42 T A 7: 92,241,040 (GRCm39) K440* probably null Het
Apc T A 18: 34,449,010 (GRCm39) S1969T probably damaging Het
Arhgef25 T C 10: 127,019,897 (GRCm39) Y447C probably damaging Het
AW146154 G A 7: 41,130,867 (GRCm39) A83V probably benign Het
Bach1 G A 16: 87,516,179 (GRCm39) R240Q probably benign Het
Barhl1 T G 2: 28,799,726 (GRCm39) I300L probably benign Het
Brd1 C A 15: 88,598,138 (GRCm39) R536L probably damaging Het
Brms1 T A 19: 5,096,708 (GRCm39) I130N probably damaging Het
Ccdc68 A G 18: 70,073,241 (GRCm39) H63R probably damaging Het
Ccl28 A G 13: 120,112,429 (GRCm39) I74V probably benign Het
Cd300ld T A 11: 114,878,321 (GRCm39) I64F possibly damaging Het
Cdkl2 G A 5: 92,181,043 (GRCm39) Q199* probably null Het
Cdkn2c C T 4: 109,518,555 (GRCm39) R133Q probably benign Het
Coq2 A G 5: 100,811,586 (GRCm39) probably benign Het
Coq6 T C 12: 84,408,595 (GRCm39) probably null Het
Csmd2 C T 4: 128,356,519 (GRCm39) S1608L Het
Cyp11b2 T A 15: 74,727,837 (GRCm39) R82W probably damaging Het
Cyp2d10 T C 15: 82,289,462 (GRCm39) T217A probably benign Het
Dclk2 C T 3: 86,700,566 (GRCm39) R638H probably damaging Het
Dnah7a T C 1: 53,522,599 (GRCm39) I2880V possibly damaging Het
Dync1h1 C A 12: 110,623,512 (GRCm39) T3595K probably damaging Het
Ecscr T A 18: 35,848,478 (GRCm39) E183V probably damaging Het
Elovl6 A G 3: 129,398,755 (GRCm39) N52S probably benign Het
Eps8l1 G T 7: 4,477,190 (GRCm39) A455S probably benign Het
Gpat2 A G 2: 127,270,209 (GRCm39) N74S probably benign Het
Gstk1 C A 6: 42,226,407 (GRCm39) T172K probably damaging Het
Gtf3c1 T C 7: 125,295,731 (GRCm39) probably null Het
Gucy2c T C 6: 136,705,339 (GRCm39) D532G probably benign Het
Hoxc12 T A 15: 102,845,473 (GRCm39) N62K possibly damaging Het
Hsdl1 C A 8: 120,293,064 (GRCm39) A124S possibly damaging Het
Il11 T C 7: 4,778,995 (GRCm39) Y45C probably damaging Het
Lcat C T 8: 106,666,309 (GRCm39) M404I possibly damaging Het
Ldhb A G 6: 142,447,099 (GRCm39) F72L probably benign Het
Map10 T C 8: 126,398,662 (GRCm39) L685P probably damaging Het
Me2 A G 18: 73,927,961 (GRCm39) V174A probably benign Het
Med13l C A 5: 118,859,991 (GRCm39) Q328K possibly damaging Het
Mta2 A T 19: 8,925,139 (GRCm39) I336F probably damaging Het
Mterf1a A T 5: 3,941,769 (GRCm39) I33N probably damaging Het
Myo15b T A 11: 115,782,324 (GRCm39) probably null Het
Myof C A 19: 37,924,648 (GRCm39) G1215V probably damaging Het
Nlgn2 G A 11: 69,716,516 (GRCm39) T675M probably damaging Het
Or1e26 T A 11: 73,480,463 (GRCm39) M34L probably benign Het
Or5p61 C A 7: 107,758,848 (GRCm39) M77I probably benign Het
Or6c38 T C 10: 128,929,715 (GRCm39) I43V probably damaging Het
Padi3 T C 4: 140,527,435 (GRCm39) D122G probably damaging Het
Pcnx3 G A 19: 5,722,643 (GRCm39) R1350C probably damaging Het
Pdzrn4 C A 15: 92,295,384 (GRCm39) Q197K probably benign Het
Pitpnm2 C T 5: 124,267,324 (GRCm39) G639S possibly damaging Het
Piwil4 T A 9: 14,648,112 (GRCm39) K156* probably null Het
Pkmyt1 T A 17: 23,953,087 (GRCm39) H214Q probably damaging Het
Poteg C A 8: 27,963,595 (GRCm39) A344E probably benign Het
Rad21l A G 2: 151,509,840 (GRCm39) M87T probably benign Het
Ranbp17 T C 11: 33,424,896 (GRCm39) I487V probably benign Het
Rap1gap2 C A 11: 74,283,057 (GRCm39) R681L probably damaging Het
Rimbp2 C A 5: 128,851,333 (GRCm39) R871L probably damaging Het
Rnf135 T C 11: 80,080,051 (GRCm39) V114A probably benign Het
Skic2 T A 17: 35,060,446 (GRCm39) H849L probably benign Het
Snai2 A G 16: 14,525,028 (GRCm39) H178R possibly damaging Het
Stip1 C T 19: 6,999,178 (GRCm39) G467S possibly damaging Het
Taar1 A T 10: 23,796,809 (GRCm39) E169V possibly damaging Het
Tdrd12 G T 7: 35,187,014 (GRCm39) D625E Het
Tlr6 A G 5: 65,111,119 (GRCm39) V596A probably benign Het
Trak2 T G 1: 58,942,749 (GRCm39) N886H probably damaging Het
Tsga10 T A 1: 37,879,695 (GRCm39) D32V probably damaging Het
Vmn1r214 A G 13: 23,219,196 (GRCm39) D230G probably damaging Het
Vmn2r108 A G 17: 20,682,762 (GRCm39) L814S probably damaging Het
Zbbx T C 3: 74,989,044 (GRCm39) D353G 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
R5514:Pnpt1 UTSW 11 29,103,246 (GRCm39) missense possibly damaging 0.82
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
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'- CTGAGTCAGTCTGGAGAAGTAAGTG -3'
(R):5'- TGCTCTTCTTTCAATACACACAATG -3'

Sequencing Primer
(F):5'- GTCTGGAGAAGTAAGTGAGGAATAG -3'
(R):5'- TAGCCTAAGTTCAGTCCCCAGG -3'
Posted On 2019-05-15