Incidental Mutation 'R1562:Upf1'
ID 170682
Institutional Source Beutler Lab
Gene Symbol Upf1
Ensembl Gene ENSMUSG00000058301
Gene Name UPF1 regulator of nonsense transcripts homolog (yeast)
Synonyms B430202H16Rik, PNORF-1, Rent1
MMRRC Submission 039601-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R1562 (G1)
Quality Score 225
Status Not validated
Chromosome 8
Chromosomal Location 70331525-70353278 bp(-) (GRCm38)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 70343367 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Stop codon at position 138 (W138*)
Ref Sequence ENSEMBL: ENSMUSP00000148927 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000075666] [ENSMUST00000215817]
AlphaFold Q9EPU0
Predicted Effect probably null
Transcript: ENSMUST00000075666
AA Change: W138*
SMART Domains Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: W138*

DomainStartEndE-ValueType
low complexity region 47 67 N/A INTRINSIC
low complexity region 101 110 N/A INTRINSIC
Pfam:UPF1_Zn_bind 116 267 4.1e-78 PFAM
Pfam:ResIII 475 617 1.3e-6 PFAM
Pfam:AAA_11 476 600 4.5e-24 PFAM
Pfam:AAA_30 476 688 5.6e-13 PFAM
Pfam:AAA_19 483 559 3.8e-16 PFAM
Pfam:AAA_11 576 679 7.7e-30 PFAM
Pfam:AAA_12 686 883 3.3e-64 PFAM
low complexity region 995 1001 N/A INTRINSIC
low complexity region 1013 1028 N/A INTRINSIC
low complexity region 1066 1081 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000215817
AA Change: W138*
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.8%
  • 20x: 91.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein is located only in the cytoplasm. When translation ends, it interacts with the protein that is a functional homolog of yeast Upf2p to trigger mRNA decapping. Use of multiple polyadenylation sites has been noted for this gene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
PHENOTYPE: Mice homozygous for a targeted null mutation are viable in the pre-implantation period but resorb in the early post-implantation period. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700016K19Rik A T 11: 76,003,198 (GRCm38) I134F probably damaging Het
Abca2 A G 2: 25,446,319 (GRCm38) I2201V probably benign Het
Adam22 T C 5: 8,095,007 (GRCm38) N817S probably damaging Het
Alox12 C A 11: 70,250,165 (GRCm38) R348L probably damaging Het
Asb17 A T 3: 153,853,506 (GRCm38) T285S probably benign Het
Casp4 T C 9: 5,324,733 (GRCm38) S182P possibly damaging Het
Cenpe T C 3: 135,238,394 (GRCm38) M985T possibly damaging Het
Clcn1 C T 6: 42,300,235 (GRCm38) P420L probably benign Het
Coro2a T C 4: 46,548,917 (GRCm38) I126V probably benign Het
Cubn T C 2: 13,427,967 (GRCm38) Y1181C probably damaging Het
Cyp2d22 A T 15: 82,373,978 (GRCm38) L147Q probably damaging Het
D430042O09Rik C A 7: 125,842,848 (GRCm38) S643Y probably damaging Het
Dna2 C T 10: 62,949,187 (GRCm38) R28W probably benign Het
Ecm1 G A 3: 95,735,963 (GRCm38) R342C probably damaging Het
Fat2 T C 11: 55,309,974 (GRCm38) N758S probably damaging Het
Fbxo43 T C 15: 36,163,016 (GRCm38) D15G probably damaging Het
Flt3 T C 5: 147,344,513 (GRCm38) E803G probably damaging Het
Folr1 T G 7: 101,858,594 (GRCm38) D213A probably damaging Het
Fus T C 7: 127,979,922 (GRCm38) V359A probably damaging Het
Gabrb3 C T 7: 57,765,514 (GRCm38) R111* probably null Het
Gm17324 T C 9: 78,448,682 (GRCm38) probably benign Het
Hormad2 A T 11: 4,408,848 (GRCm38) probably null Het
Ifi27l2b T A 12: 103,456,521 (GRCm38) probably null Het
Isg20 G T 7: 78,920,143 (GRCm38) C176F probably benign Het
Krt15 C A 11: 100,133,181 (GRCm38) V346L probably benign Het
Med13l A G 5: 118,738,519 (GRCm38) K920R probably damaging Het
Mlh3 A T 12: 85,266,920 (GRCm38) F831I probably benign Het
Mtmr9 A G 14: 63,534,337 (GRCm38) S267P probably benign Het
Mybpc1 C T 10: 88,553,331 (GRCm38) A406T probably damaging Het
Myh1 T C 11: 67,211,370 (GRCm38) M829T probably benign Het
Myo10 A G 15: 25,780,411 (GRCm38) Q209R possibly damaging Het
Nceh1 T A 3: 27,239,552 (GRCm38) V153D probably damaging Het
Olfr1195 T A 2: 88,683,079 (GRCm38) I218F probably benign Het
Olfr348 A G 2: 36,786,684 (GRCm38) D53G probably damaging Het
Olfr694 C T 7: 106,688,980 (GRCm38) M250I probably benign Het
Olfr898 C A 9: 38,349,362 (GRCm38) S87* probably null Het
Oog3 A T 4: 144,162,599 (GRCm38) I3N probably damaging Het
Pcnt G A 10: 76,367,330 (GRCm38) T2646M probably benign Het
Phf10 A T 17: 14,946,250 (GRCm38) C453S probably damaging Het
Plcb4 T A 2: 135,970,447 (GRCm38) probably null Het
Plekhh1 A G 12: 79,076,708 (GRCm38) H1185R probably benign Het
Prmt3 G T 7: 49,826,854 (GRCm38) V404L probably benign Het
Ptprb T A 10: 116,339,467 (GRCm38) D1122E probably benign Het
Rars A G 11: 35,821,094 (GRCm38) probably null Het
Rasa2 G T 9: 96,545,750 (GRCm38) N687K possibly damaging Het
Rbm11 A G 16: 75,596,535 (GRCm38) T40A probably damaging Het
Rem2 T C 14: 54,476,318 (GRCm38) V16A probably benign Het
Rlf A T 4: 121,150,391 (GRCm38) M574K possibly damaging Het
Rpap3 A T 15: 97,694,217 (GRCm38) V186D possibly damaging Het
Sertad3 G A 7: 27,476,623 (GRCm38) E161K probably damaging Het
Sh3gl2 T C 4: 85,385,893 (GRCm38) S278P probably benign Het
Strn3 T C 12: 51,633,618 (GRCm38) T400A probably benign Het
Sycp2 A T 2: 178,382,385 (GRCm38) I402N probably damaging Het
Synj1 C T 16: 90,987,402 (GRCm38) V283I probably benign Het
Tas2r108 A G 6: 40,494,066 (GRCm38) probably null Het
Ttpal A G 2: 163,615,403 (GRCm38) N265S probably benign Het
Unc80 G A 1: 66,637,957 (GRCm38) G2015D probably damaging Het
Vmn1r25 T G 6: 57,978,801 (GRCm38) M168L probably benign Het
Vmn2r18 A T 5: 151,586,836 (GRCm38) F24Y probably benign Het
Vmn2r4 G T 3: 64,389,444 (GRCm38) T640N probably damaging Het
Wdr75 T A 1: 45,803,870 (GRCm38) probably null Het
Zdbf2 T G 1: 63,303,588 (GRCm38) S375R possibly damaging Het
Zfp648 A G 1: 154,204,392 (GRCm38) Q99R probably benign Het
Zfp964 C T 8: 69,663,004 (GRCm38) P85S probably benign Het
Other mutations in Upf1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01113:Upf1 APN 8 70,338,284 (GRCm38) missense probably benign
IGL01890:Upf1 APN 8 70,334,230 (GRCm38) missense possibly damaging 0.94
IGL02534:Upf1 APN 8 70,335,652 (GRCm38) critical splice donor site probably null
IGL03142:Upf1 APN 8 70,333,327 (GRCm38) missense probably benign 0.04
IGL03151:Upf1 APN 8 70,335,387 (GRCm38) missense probably damaging 0.98
Nanosphere UTSW 8 70,344,262 (GRCm38) missense probably benign 0.01
Particulate UTSW 8 70,337,025 (GRCm38) missense probably damaging 0.96
R0270:Upf1 UTSW 8 70,335,645 (GRCm38) splice site probably benign
R0477:Upf1 UTSW 8 70,334,080 (GRCm38) missense probably benign
R0755:Upf1 UTSW 8 70,334,129 (GRCm38) missense probably benign 0.01
R1018:Upf1 UTSW 8 70,338,906 (GRCm38) missense possibly damaging 0.85
R1067:Upf1 UTSW 8 70,338,403 (GRCm38) missense probably damaging 0.98
R1445:Upf1 UTSW 8 70,341,524 (GRCm38) missense probably benign 0.00
R1458:Upf1 UTSW 8 70,344,254 (GRCm38) missense probably benign 0.00
R1511:Upf1 UTSW 8 70,338,505 (GRCm38) missense probably damaging 0.99
R1552:Upf1 UTSW 8 70,333,059 (GRCm38) nonsense probably null
R1560:Upf1 UTSW 8 70,338,442 (GRCm38) missense probably damaging 1.00
R2082:Upf1 UTSW 8 70,341,572 (GRCm38) missense probably damaging 1.00
R2143:Upf1 UTSW 8 70,339,354 (GRCm38) missense probably null 1.00
R2423:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R2425:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R3031:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R3032:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R3123:Upf1 UTSW 8 70,337,483 (GRCm38) splice site probably benign
R3508:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R3747:Upf1 UTSW 8 70,333,350 (GRCm38) missense possibly damaging 0.75
R3748:Upf1 UTSW 8 70,333,350 (GRCm38) missense possibly damaging 0.75
R3750:Upf1 UTSW 8 70,333,350 (GRCm38) missense possibly damaging 0.75
R3754:Upf1 UTSW 8 70,339,814 (GRCm38) missense probably benign 0.30
R3964:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R3965:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R4152:Upf1 UTSW 8 70,338,460 (GRCm38) missense probably damaging 1.00
R4505:Upf1 UTSW 8 70,337,566 (GRCm38) missense probably damaging 1.00
R4506:Upf1 UTSW 8 70,337,566 (GRCm38) missense probably damaging 1.00
R4838:Upf1 UTSW 8 70,339,368 (GRCm38) missense probably benign 0.03
R5001:Upf1 UTSW 8 70,334,700 (GRCm38) missense probably damaging 1.00
R5715:Upf1 UTSW 8 70,352,978 (GRCm38) missense probably damaging 0.96
R5748:Upf1 UTSW 8 70,338,517 (GRCm38) missense probably damaging 1.00
R5856:Upf1 UTSW 8 70,334,762 (GRCm38) critical splice acceptor site probably null
R5930:Upf1 UTSW 8 70,344,262 (GRCm38) missense probably benign 0.01
R6010:Upf1 UTSW 8 70,337,025 (GRCm38) missense probably damaging 0.96
R6056:Upf1 UTSW 8 70,333,037 (GRCm38) missense probably damaging 0.98
R6870:Upf1 UTSW 8 70,341,561 (GRCm38) missense probably benign 0.11
R7205:Upf1 UTSW 8 70,340,045 (GRCm38) missense possibly damaging 0.94
R7385:Upf1 UTSW 8 70,340,618 (GRCm38) missense probably damaging 1.00
R7464:Upf1 UTSW 8 70,333,423 (GRCm38) missense probably benign
R7759:Upf1 UTSW 8 70,334,080 (GRCm38) missense probably benign
R7783:Upf1 UTSW 8 70,352,858 (GRCm38) missense probably benign 0.11
R8079:Upf1 UTSW 8 70,338,884 (GRCm38) critical splice donor site probably null
R8192:Upf1 UTSW 8 70,340,644 (GRCm38) missense probably benign 0.03
R8544:Upf1 UTSW 8 70,337,052 (GRCm38) missense probably damaging 1.00
R8738:Upf1 UTSW 8 70,333,323 (GRCm38) missense probably benign 0.06
R8738:Upf1 UTSW 8 70,333,322 (GRCm38) missense probably benign 0.01
R8826:Upf1 UTSW 8 70,338,280 (GRCm38) missense probably benign
R8876:Upf1 UTSW 8 70,344,268 (GRCm38) missense possibly damaging 0.92
R8906:Upf1 UTSW 8 70,334,165 (GRCm38) nonsense probably null
R8911:Upf1 UTSW 8 70,338,437 (GRCm38) missense possibly damaging 0.53
R9163:Upf1 UTSW 8 70,340,024 (GRCm38) missense probably benign
R9425:Upf1 UTSW 8 70,339,353 (GRCm38) missense probably benign 0.06
Predicted Primers PCR Primer
(F):5'- TCACACGCCACCATCTGTTTCAAG -3'
(R):5'- TGGTTGCACAGTACCTGCCTTC -3'

Sequencing Primer
(F):5'- GTTTCAAGTTACACCAGTCAAAGGG -3'
(R):5'- AGGTGCTCCCACAACCTTG -3'
Posted On 2014-04-13