Incidental Mutation 'R1023:Pnpt1'
ID 94651
Institutional Source Beutler Lab
Gene Symbol Pnpt1
Ensembl Gene ENSMUSG00000020464
Gene Name polyribonucleotide nucleotidyltransferase 1
Synonyms 1200003F12Rik, polynucleotide phosphorylase, PNPase
MMRRC Submission 039125-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1023 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 29080744-29111828 bp(+) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) T to C at 29091328 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
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
SMART Domains Protein: ENSMUSP00000020756
Gene: ENSMUSG00000020464

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: ENSMUST00000131527
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154924
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.0%
  • 10x: 95.6%
  • 20x: 90.7%
Validation Efficiency 100% (42/42)
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: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik C T 3: 137,772,632 (GRCm39) A607V probably damaging Het
4930523C07Rik A G 1: 159,905,057 (GRCm39) probably benign Het
Ap3d1 A T 10: 80,550,092 (GRCm39) L713Q probably damaging Het
Baz2a A G 10: 127,957,676 (GRCm39) T1010A possibly damaging Het
Cdh15 T C 8: 123,591,939 (GRCm39) I608T probably damaging Het
Cdkl2 A T 5: 92,187,145 (GRCm39) D40E possibly damaging Het
Col9a2 G A 4: 120,901,207 (GRCm39) G118R unknown Het
Cryge C A 1: 65,089,945 (GRCm39) C79F probably damaging Het
Dapk1 T C 13: 60,878,799 (GRCm39) L596P probably damaging Het
Dqx1 G A 6: 83,038,070 (GRCm39) C486Y probably damaging Het
Dync2i1 T C 12: 116,196,277 (GRCm39) E490G probably damaging Het
Enam A G 5: 88,649,826 (GRCm39) Q445R probably damaging Het
Gm10608 CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 9: 118,989,784 (GRCm39) probably benign Het
Gnpat A T 8: 125,597,519 (GRCm39) D27V probably benign Het
Htr5a A T 5: 28,047,996 (GRCm39) T184S possibly damaging Het
Lap3 C T 5: 45,652,553 (GRCm39) P50S probably benign Het
Mamdc2 A T 19: 23,288,271 (GRCm39) M589K probably damaging Het
Mast4 A G 13: 102,872,004 (GRCm39) S2263P probably benign Het
Mef2b C T 8: 70,618,247 (GRCm39) P109L possibly damaging Het
Meltf T A 16: 31,703,778 (GRCm39) F168L probably damaging Het
Mib2 C T 4: 155,743,917 (GRCm39) G42S probably damaging Het
Nup205 T A 6: 35,211,641 (GRCm39) F1661I probably damaging Het
Or11h4b A T 14: 50,918,473 (GRCm39) L206H probably damaging Het
Or5h19 A T 16: 58,856,178 (GRCm39) N307K probably benign Het
Plac8 A T 5: 100,704,447 (GRCm39) D83E probably benign Het
Pold2 G T 11: 5,825,140 (GRCm39) Q86K probably benign Het
Ptprt A G 2: 161,400,863 (GRCm39) L1057P probably damaging Het
Rev3l A G 10: 39,708,635 (GRCm39) H2284R probably damaging Het
Scart1 T A 7: 139,804,376 (GRCm39) C484S possibly damaging Het
Skint6 A C 4: 113,095,300 (GRCm39) S120A probably benign Het
Slc1a7 G A 4: 107,864,770 (GRCm39) V270M probably damaging Het
Spata2 A G 2: 167,327,142 (GRCm39) M85T probably benign Het
Taf1b G T 12: 24,559,558 (GRCm39) probably benign Het
Tert A G 13: 73,790,178 (GRCm39) N844S probably benign Het
Thrap3 G A 4: 126,073,882 (GRCm39) S288L possibly damaging Het
Ubap2l A G 3: 89,955,180 (GRCm39) probably benign Het
Ubtf T C 11: 102,202,276 (GRCm39) E197G possibly damaging Het
Usp20 G T 2: 30,897,825 (GRCm39) G216W probably damaging Het
Yy1 T A 12: 108,759,457 (GRCm39) V40E unknown Het
Zfp335 G A 2: 164,734,505 (GRCm39) H1254Y possibly damaging 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
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
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'- GAGCAAGCCAAATGCCTATAACTGC -3'
(R):5'- TGGGTTCCACTCTAAGTCCCACTG -3'

Sequencing Primer
(F):5'- AAATGTTTGACTGTCTCCATTGGC -3'
(R):5'- ccactctaagtcccactgaatcC -3'
Posted On 2014-01-05