Incidental Mutation 'R2072:Upf3a'
ID 227232
Institutional Source Beutler Lab
Gene Symbol Upf3a
Ensembl Gene ENSMUSG00000038398
Gene Name UPF3 regulator of nonsense transcripts homolog A (yeast)
Synonyms 2600001C03Rik, RENT3A, 4930546M19Rik, UPF3
MMRRC Submission 040077-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2072 (G1)
Quality Score 107
Status Not validated
Chromosome 8
Chromosomal Location 13785615-13799193 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 13785850 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 56 (K56R)
Ref Sequence ENSEMBL: ENSMUSP00000037354 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043767] [ENSMUST00000043962]
AlphaFold Q3ULJ3
Predicted Effect possibly damaging
Transcript: ENSMUST00000043767
AA Change: K56R

PolyPhen 2 Score 0.627 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: K56R

low complexity region 6 18 N/A INTRINSIC
Pfam:Smg4_UPF3 63 224 1.4e-54 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000043962
SMART Domains Protein: ENSMUSP00000047950
Gene: ENSMUSG00000038416

Pfam:TPR_9 11 63 1.8e-3 PFAM
Pfam:ANAPC3 15 95 3.5e-23 PFAM
TPR 130 163 1.17e1 SMART
Blast:TPR 299 333 2e-8 BLAST
Blast:TPR 334 367 1e-14 BLAST
TPR 368 401 1.48e1 SMART
Blast:TPR 402 435 7e-15 BLAST
TPR 445 478 6.68e-6 SMART
TPR 479 512 1.74e-4 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137360
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211643
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211724
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.3%
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. The encoded protein is one of two functional homologs to yeast Upf3p. 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 binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome 13. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: The gene product protects against mRNA transcript degradation. Homozygous constitutive KO is embryonic lethal. Homozygous conditional KO in testes leads to reduced male fertility. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik G C 5: 63,898,737 (GRCm38) R272P possibly damaging Het
9130011E15Rik A T 19: 45,965,381 (GRCm38) I188K probably damaging Het
Ablim3 A T 18: 61,857,088 (GRCm38) D83E possibly damaging Het
Aco1 G A 4: 40,183,605 (GRCm38) G508S probably damaging Het
Adamts13 C A 2: 27,005,425 (GRCm38) T1176N probably benign Het
Adgre5 T C 8: 83,727,804 (GRCm38) T357A probably benign Het
Akap8l C T 17: 32,332,483 (GRCm38) R511H probably damaging Het
Ankrd33 T C 15: 101,119,636 (GRCm38) V310A probably benign Het
Bnipl C T 3: 95,244,211 (GRCm38) G232E probably damaging Het
Btbd17 A T 11: 114,791,952 (GRCm38) probably null Het
Cacna1s G A 1: 136,079,504 (GRCm38) V173I probably benign Het
Ccdc122 T C 14: 77,068,951 (GRCm38) probably null Het
Ces1a T A 8: 93,048,075 (GRCm38) N12Y probably benign Het
Chrdl1 T C X: 143,303,418 (GRCm38) I231V probably benign Het
Ciita C T 16: 10,518,353 (GRCm38) T958I probably benign Het
Cnot1 G T 8: 95,739,833 (GRCm38) T1592K possibly damaging Het
Dcaf15 T C 8: 84,101,741 (GRCm38) D240G probably damaging Het
Ddx58 A T 4: 40,224,069 (GRCm38) probably null Het
Dlgap1 C T 17: 70,662,770 (GRCm38) R524C probably damaging Het
Dmd G C X: 84,312,483 (GRCm38) A2257P probably benign Het
Dsg1c A G 18: 20,275,252 (GRCm38) M453V probably benign Het
Ednrb G T 14: 103,817,099 (GRCm38) N432K probably benign Het
Fcgbp G A 7: 28,120,389 (GRCm38) G2514S probably damaging Het
Fez1 A G 9: 36,867,945 (GRCm38) K306R probably benign Het
Fmo4 A G 1: 162,809,887 (GRCm38) V12A probably benign Het
Fpgt T C 3: 155,087,874 (GRCm38) Y172C probably damaging Het
Fsip2 T A 2: 83,008,815 (GRCm38) F6976I possibly damaging Het
Galnt12 C T 4: 47,108,477 (GRCm38) R205* probably null Het
Grik5 A T 7: 25,015,313 (GRCm38) M752K possibly damaging Het
Herc2 A G 7: 56,226,964 (GRCm38) N4516S probably damaging Het
Ifrd2 A T 9: 107,592,545 (GRCm38) D439V probably damaging Het
Igsf3 A G 3: 101,439,515 (GRCm38) T609A probably benign Het
Kif5a T C 10: 127,245,369 (GRCm38) D232G probably damaging Het
Lgi2 A G 5: 52,538,505 (GRCm38) S371P probably damaging Het
March3 A T 18: 56,811,853 (GRCm38) V56E possibly damaging Het
Mib2 T C 4: 155,659,701 (GRCm38) D168G probably damaging Het
Nhs T A X: 161,842,721 (GRCm38) H544L probably damaging Het
Nlrp2 A G 7: 5,325,006 (GRCm38) S683P probably damaging Het
Olfr1260 C A 2: 89,978,213 (GRCm38) T145K probably benign Het
Olfr1454 A T 19: 13,063,680 (GRCm38) M90L probably benign Het
Olfr527 T C 7: 140,336,653 (GRCm38) S264P possibly damaging Het
Onecut3 T G 10: 80,495,014 (GRCm38) L3V unknown Het
Otogl C T 10: 107,781,043 (GRCm38) C1791Y probably damaging Het
Paip1 T C 13: 119,430,262 (GRCm38) V128A possibly damaging Het
Pcnx2 A T 8: 125,761,742 (GRCm38) C1688S possibly damaging Het
Pdzd2 A G 15: 12,385,819 (GRCm38) L955P probably damaging Het
Phlpp2 T C 8: 109,928,492 (GRCm38) S605P possibly damaging Het
Pkhd1l1 G T 15: 44,558,639 (GRCm38) A3102S probably damaging Het
Plxnb2 G T 15: 89,158,451 (GRCm38) R1545S probably damaging Het
Ppp4c T C 7: 126,787,348 (GRCm38) probably null Het
Prune1 C T 3: 95,255,408 (GRCm38) R318Q probably benign Het
Psg27 A G 7: 18,565,009 (GRCm38) L129P probably benign Het
Psg27 T C 7: 18,560,417 (GRCm38) D355G probably damaging Het
Psmc6 A G 14: 45,329,866 (GRCm38) K7E possibly damaging Het
Reln A T 5: 21,919,177 (GRCm38) V2777E probably damaging Het
Scn11a G T 9: 119,811,208 (GRCm38) A207E possibly damaging Het
Slc5a5 C T 8: 70,892,439 (GRCm38) G75R possibly damaging Het
Smarcd2 A T 11: 106,265,307 (GRCm38) L42* probably null Het
Smg1 T C 7: 118,163,166 (GRCm38) probably benign Het
Smurf2 T A 11: 106,841,769 (GRCm38) Q335L probably benign Het
Sspo A T 6: 48,473,517 (GRCm38) H2580L probably benign Het
Stk3 T C 15: 34,959,049 (GRCm38) M256V possibly damaging Het
Syt1 A G 10: 108,583,972 (GRCm38) I276T probably damaging Het
Syt10 C T 15: 89,790,776 (GRCm38) D456N probably damaging Het
Taar9 A T 10: 24,108,979 (GRCm38) C186S probably damaging Het
Tnrc6b C T 15: 80,882,965 (GRCm38) P977L possibly damaging Het
Trp53bp2 A G 1: 182,458,867 (GRCm38) T1091A probably benign Het
Ttn G T 2: 76,937,776 (GRCm38) T2947N probably damaging Het
Ube2q1 T C 3: 89,779,571 (GRCm38) probably null Het
Ube3c A G 5: 29,635,640 (GRCm38) E671G probably benign Het
Vmn2r15 A T 5: 109,286,753 (GRCm38) M695K possibly damaging Het
Vmn2r3 A T 3: 64,275,072 (GRCm38) M402K possibly damaging Het
Zfp354b T A 11: 50,922,452 (GRCm38) R549* probably null Het
Zfp37 A T 4: 62,191,708 (GRCm38) M411K probably damaging Het
Zfp747 T A 7: 127,373,970 (GRCm38) T343S possibly damaging Het
Zfp853 T A 5: 143,289,382 (GRCm38) Q161L unknown Het
Other mutations in Upf3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01398:Upf3a APN 8 13,786,221 (GRCm38) missense probably damaging 0.98
IGL01678:Upf3a APN 8 13,791,930 (GRCm38) missense probably benign 0.21
IGL02072:Upf3a APN 8 13,798,368 (GRCm38) missense probably damaging 0.99
R0309:Upf3a UTSW 8 13,795,500 (GRCm38) splice site probably null
R0564:Upf3a UTSW 8 13,795,656 (GRCm38) missense probably benign 0.42
R0571:Upf3a UTSW 8 13,792,184 (GRCm38) missense probably damaging 0.98
R0826:Upf3a UTSW 8 13,798,338 (GRCm38) missense possibly damaging 0.65
R1387:Upf3a UTSW 8 13,792,118 (GRCm38) missense probably damaging 1.00
R1913:Upf3a UTSW 8 13,792,108 (GRCm38) missense probably damaging 1.00
R2520:Upf3a UTSW 8 13,796,443 (GRCm38) splice site probably null
R3845:Upf3a UTSW 8 13,798,238 (GRCm38) missense probably benign 0.16
R4239:Upf3a UTSW 8 13,796,591 (GRCm38) missense probably benign 0.28
R4424:Upf3a UTSW 8 13,796,573 (GRCm38) missense probably benign 0.09
R5522:Upf3a UTSW 8 13,795,497 (GRCm38) critical splice donor site probably null
R6321:Upf3a UTSW 8 13,787,466 (GRCm38) missense possibly damaging 0.53
R6922:Upf3a UTSW 8 13,791,911 (GRCm38) missense probably damaging 1.00
R7583:Upf3a UTSW 8 13,785,889 (GRCm38) splice site probably null
R7585:Upf3a UTSW 8 13,787,418 (GRCm38) missense probably damaging 1.00
R7695:Upf3a UTSW 8 13,798,279 (GRCm38) missense probably benign 0.01
R7991:Upf3a UTSW 8 13,792,166 (GRCm38) missense probably damaging 1.00
R8913:Upf3a UTSW 8 13,795,728 (GRCm38) missense possibly damaging 0.94
R9638:Upf3a UTSW 8 13,798,343 (GRCm38) missense probably benign
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2014-09-17