Incidental Mutation 'R9163:Upf1'
ID 695846
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
Accession Numbers
Essential gene? Probably essential (E-score: 0.970) question?
Stock # R9163 (G1)
Quality Score 225.009
Status Validated
Chromosome 8
Chromosomal Location 70331525-70353278 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 70340024 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 345 (T345A)
Ref Sequence ENSEMBL: ENSMUSP00000075089 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000075666] [ENSMUST00000215817]
AlphaFold Q9EPU0
Predicted Effect probably benign
Transcript: ENSMUST00000075666
AA Change: T345A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000075089
Gene: ENSMUSG00000058301
AA Change: T345A

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 benign
Transcript: ENSMUST00000215817
AA Change: T345A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency 99% (69/70)
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik T C 13: 77,245,281 S351P possibly damaging Het
4930558K02Rik A G 1: 161,949,605 S128P probably benign Het
Adam17 C T 12: 21,351,587 V136I probably benign Het
Adam19 A G 11: 46,127,349 T413A probably benign Het
Adam28 T C 14: 68,629,082 K443E probably damaging Het
Adgrv1 T A 13: 81,419,422 T5211S probably benign Het
Adnp2 A T 18: 80,128,985 N736K possibly damaging Het
Agtpbp1 C T 13: 59,462,070 W1082* probably null Het
Ap3b2 T G 7: 81,463,798 M888L unknown Het
Arhgap35 C A 7: 16,561,624 R1172L possibly damaging Het
Arrdc3 T A 13: 80,893,387 D402E probably benign Het
Ccdc14 T C 16: 34,690,748 F31L possibly damaging Het
Ccdc173 A T 2: 69,776,166 I302K probably benign Het
Cd5l T G 3: 87,367,625 L157R probably benign Het
Cdc14a G T 3: 116,328,564 D251E possibly damaging Het
Chmp2a T A 7: 13,032,718 Q91L possibly damaging Het
Col12a1 A G 9: 79,641,447 probably null Het
Ctdsp1 G T 1: 74,394,967 R201L possibly damaging Het
Dhx15 C T 5: 52,184,856 R40H probably damaging Het
Dnph1 A G 17: 46,498,934 Y134C probably damaging Het
Foxo1 T A 3: 52,345,880 V488D probably benign Het
Gcn1l1 C A 5: 115,604,885 N1538K probably benign Het
Gldc T A 19: 30,134,286 E500V probably benign Het
Hhip G A 8: 79,975,114 T597I probably benign Het
Hmgn1 A G 16: 96,127,309 probably null Het
Ifi205 A T 1: 174,017,422 S265T possibly damaging Het
Igkv1-131 T C 6: 67,766,769 M2V probably benign Het
Irgm2 T G 11: 58,220,454 S324A probably damaging Het
Jarid2 C G 13: 44,911,251 D937E possibly damaging Het
Jrkl A T 9: 13,245,399 W86R probably damaging Het
Kbtbd3 A G 9: 4,330,584 I319M probably benign Het
Klhl7 T C 5: 24,159,467 Y500H probably damaging Het
Lats1 C T 10: 7,702,288 A392V probably benign Het
Llgl1 G T 11: 60,709,576 A584S probably benign Het
Macf1 G T 4: 123,509,893 S560Y probably damaging Het
Olfr1206 C T 2: 88,865,451 P282L possibly damaging Het
Olfr250 T A 9: 38,368,082 C169S probably damaging Het
Pde10a G A 17: 8,962,959 C498Y possibly damaging Het
Pde4dip A G 3: 97,751,807 probably null Het
Pdhx G A 2: 103,022,216 P434L probably damaging Het
Pdlim3 T C 8: 45,885,674 probably null Het
Pik3c3 T C 18: 30,294,430 probably null Het
Prkag1 T C 15: 98,814,019 K242R possibly damaging Het
Rap1b A G 10: 117,818,486 S150P possibly damaging Het
Scn4a A G 11: 106,326,250 S1102P probably damaging Het
Scrib A G 15: 76,049,259 Y1332H probably damaging Het
Sim1 A G 10: 50,896,069 E58G probably benign Het
Slc13a1 C T 6: 24,097,579 probably null Het
Slc17a8 A G 10: 89,589,582 V380A probably damaging Het
Slc5a4b G T 10: 76,081,331 Y290* probably null Het
Slco4c1 A G 1: 96,836,908 F480L probably damaging Het
Srcap T C 7: 127,521,990 V146A unknown Het
Ssc5d T A 7: 4,933,433 D559E probably damaging Het
Sstr5 A C 17: 25,491,610 I215S probably damaging Het
Stambpl1 G A 19: 34,235,234 C268Y probably benign Het
Stard3nl C A 13: 19,376,639 probably benign Het
Sycp3 T C 10: 88,463,872 probably null Het
Syne2 A T 12: 75,962,575 M2417L possibly damaging Het
Tenm4 T G 7: 96,823,873 Y959D probably damaging Het
Tmem132d T A 5: 127,792,506 D588V possibly damaging Het
Tnfrsf26 T C 7: 143,618,393 E60G possibly damaging Het
Topbp1 A G 9: 103,328,568 R802G probably benign Het
Trmu T C 15: 85,896,895 V360A probably benign Het
Tshz2 G A 2: 169,884,642 C386Y probably damaging Het
Ttn A T 2: 76,870,427 D61E Het
Vmn2r23 T A 6: 123,741,823 C712S probably damaging Het
Vmn2r44 C T 7: 8,368,092 V652I probably benign Het
Wfdc1 T C 8: 119,666,563 V8A probably benign Het
Xrn1 A G 9: 95,998,221 Y738C probably benign Het
Zfp618 T G 4: 63,133,274 V764G probably damaging Het
Znfx1 A T 2: 167,056,341 M221K probably damaging Het
Other mutations in Upf1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01113:Upf1 APN 8 70338284 missense probably benign
IGL01890:Upf1 APN 8 70334230 missense possibly damaging 0.94
IGL02534:Upf1 APN 8 70335652 critical splice donor site probably null
IGL03142:Upf1 APN 8 70333327 missense probably benign 0.04
IGL03151:Upf1 APN 8 70335387 missense probably damaging 0.98
Nanosphere UTSW 8 70344262 missense probably benign 0.01
Particulate UTSW 8 70337025 missense probably damaging 0.96
R0270:Upf1 UTSW 8 70335645 splice site probably benign
R0477:Upf1 UTSW 8 70334080 missense probably benign
R0755:Upf1 UTSW 8 70334129 missense probably benign 0.01
R1018:Upf1 UTSW 8 70338906 missense possibly damaging 0.85
R1067:Upf1 UTSW 8 70338403 missense probably damaging 0.98
R1445:Upf1 UTSW 8 70341524 missense probably benign 0.00
R1458:Upf1 UTSW 8 70344254 missense probably benign 0.00
R1511:Upf1 UTSW 8 70338505 missense probably damaging 0.99
R1552:Upf1 UTSW 8 70333059 nonsense probably null
R1560:Upf1 UTSW 8 70338442 missense probably damaging 1.00
R1562:Upf1 UTSW 8 70343367 nonsense probably null
R2082:Upf1 UTSW 8 70341572 missense probably damaging 1.00
R2143:Upf1 UTSW 8 70339354 missense probably null 1.00
R2423:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R2425:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R3031:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R3032:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R3123:Upf1 UTSW 8 70337483 splice site probably benign
R3508:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R3747:Upf1 UTSW 8 70333350 missense possibly damaging 0.75
R3748:Upf1 UTSW 8 70333350 missense possibly damaging 0.75
R3750:Upf1 UTSW 8 70333350 missense possibly damaging 0.75
R3754:Upf1 UTSW 8 70339814 missense probably benign 0.30
R3964:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R3965:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R4152:Upf1 UTSW 8 70338460 missense probably damaging 1.00
R4505:Upf1 UTSW 8 70337566 missense probably damaging 1.00
R4506:Upf1 UTSW 8 70337566 missense probably damaging 1.00
R4838:Upf1 UTSW 8 70339368 missense probably benign 0.03
R5001:Upf1 UTSW 8 70334700 missense probably damaging 1.00
R5715:Upf1 UTSW 8 70352978 missense probably damaging 0.96
R5748:Upf1 UTSW 8 70338517 missense probably damaging 1.00
R5856:Upf1 UTSW 8 70334762 critical splice acceptor site probably null
R5930:Upf1 UTSW 8 70344262 missense probably benign 0.01
R6010:Upf1 UTSW 8 70337025 missense probably damaging 0.96
R6056:Upf1 UTSW 8 70333037 missense probably damaging 0.98
R6870:Upf1 UTSW 8 70341561 missense probably benign 0.11
R7205:Upf1 UTSW 8 70340045 missense possibly damaging 0.94
R7385:Upf1 UTSW 8 70340618 missense probably damaging 1.00
R7464:Upf1 UTSW 8 70333423 missense probably benign
R7759:Upf1 UTSW 8 70334080 missense probably benign
R7783:Upf1 UTSW 8 70352858 missense probably benign 0.11
R8079:Upf1 UTSW 8 70338884 critical splice donor site probably null
R8192:Upf1 UTSW 8 70340644 missense probably benign 0.03
R8544:Upf1 UTSW 8 70337052 missense probably damaging 1.00
R8738:Upf1 UTSW 8 70333322 missense probably benign 0.01
R8738:Upf1 UTSW 8 70333323 missense probably benign 0.06
R8826:Upf1 UTSW 8 70338280 missense probably benign
R8876:Upf1 UTSW 8 70344268 missense possibly damaging 0.92
R8906:Upf1 UTSW 8 70334165 nonsense probably null
R8911:Upf1 UTSW 8 70338437 missense possibly damaging 0.53
R9425:Upf1 UTSW 8 70339353 missense probably benign 0.06
Predicted Primers PCR Primer
(F):5'- TTGTACCGCAGACAGATCTCATC -3'
(R):5'- ACAGCACAGACATGGCCTTC -3'

Sequencing Primer
(F):5'- GATCTCATCACCCTGCATGAG -3'
(R):5'- ACAGACATGGCCTTCCTAGAGG -3'
Posted On 2022-02-07