Incidental Mutation 'R0571:Upf3a'
ID 46460
Institutional Source Beutler Lab
Gene Symbol Upf3a
Ensembl Gene ENSMUSG00000038398
Gene Name UPF3 regulator of nonsense transcripts homolog A (yeast)
Synonyms RENT3A, 2600001C03Rik, 4930546M19Rik, UPF3
MMRRC Submission 038762-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0571 (G1)
Quality Score 221
Status Validated
Chromosome 8
Chromosomal Location 13835615-13849193 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 13842184 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Lysine at position 200 (I200K)
Ref Sequence ENSEMBL: ENSMUSP00000037354 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043767]
AlphaFold Q3ULJ3
Predicted Effect probably damaging
Transcript: ENSMUST00000043767
AA Change: I200K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: I200K

DomainStartEndE-ValueType
low complexity region 6 18 N/A INTRINSIC
Pfam:Smg4_UPF3 63 224 1.4e-54 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211724
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.7%
Validation Efficiency 100% (71/71)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd4 C T 14: 54,500,706 (GRCm39) T165I possibly damaging Het
Acsl5 A G 19: 55,277,343 (GRCm39) probably benign Het
Actl6b C A 5: 137,565,046 (GRCm39) probably benign Het
Atg13 T C 2: 91,509,063 (GRCm39) probably benign Het
Cabyr A G 18: 12,883,909 (GRCm39) E132G probably damaging Het
Cadps2 C T 6: 23,583,411 (GRCm39) V389I probably damaging Het
Capn2 C T 1: 182,298,325 (GRCm39) V647I probably benign Het
Card10 G T 15: 78,671,601 (GRCm39) P621Q possibly damaging Het
Catsperb C G 12: 101,569,033 (GRCm39) H902D possibly damaging Het
Cers3 A G 7: 66,435,805 (GRCm39) M255V possibly damaging Het
Cfh T C 1: 140,030,071 (GRCm39) probably null Het
Chd3 A C 11: 69,252,495 (GRCm39) probably null Het
Chpf2 G T 5: 24,795,425 (GRCm39) R316L probably damaging Het
Clca3a1 T A 3: 144,713,550 (GRCm39) N694Y probably damaging Het
Cplane1 A G 15: 8,289,277 (GRCm39) D2909G unknown Het
Ctbp2 G A 7: 132,616,534 (GRCm39) L44F probably damaging Het
Cttnbp2 T C 6: 18,381,102 (GRCm39) M1365V probably benign Het
D130052B06Rik G A 11: 33,573,922 (GRCm39) R173H probably benign Het
Dchs1 A G 7: 105,421,203 (GRCm39) F406L probably damaging Het
Ddx43 T A 9: 78,321,145 (GRCm39) N384K possibly damaging Het
Drd5 G A 5: 38,477,270 (GRCm39) V88M probably damaging Het
Eefsec A T 6: 88,274,881 (GRCm39) F361Y probably benign Het
Epb41 T C 4: 131,717,215 (GRCm39) D313G probably damaging Het
Etl4 T C 2: 20,748,580 (GRCm39) M104T probably damaging Het
Fabp7 A T 10: 57,661,637 (GRCm39) T37S probably benign Het
Fam186b T C 15: 99,184,834 (GRCm39) T30A probably benign Het
Fam83d G A 2: 158,627,611 (GRCm39) W433* probably null Het
Fmnl2 A T 2: 52,944,503 (GRCm39) T161S probably benign Het
Ghsr C T 3: 27,426,165 (GRCm39) R74C probably damaging Het
Gtf3c3 C T 1: 54,456,937 (GRCm39) A488T probably damaging Het
Gtpbp4 A T 13: 9,040,722 (GRCm39) probably benign Het
Hamp2 A G 7: 30,623,511 (GRCm39) L17P possibly damaging Het
Heatr1 C A 13: 12,445,121 (GRCm39) S1581R probably damaging Het
Hpf1 T C 8: 61,353,147 (GRCm39) V176A probably benign Het
Hydin T A 8: 111,240,735 (GRCm39) probably null Het
Ighg2c G A 12: 113,252,382 (GRCm39) Q57* probably null Het
Itgb4 A G 11: 115,870,594 (GRCm39) N141S possibly damaging Het
Kif13b G T 14: 64,988,977 (GRCm39) R786L probably damaging Het
Lhx3 C A 2: 26,091,136 (GRCm39) W391L probably damaging Het
Map1s T A 8: 71,365,551 (GRCm39) V152D probably damaging Het
Map4 T C 9: 109,865,834 (GRCm39) M608T probably benign Het
Mb21d2 G A 16: 28,748,324 (GRCm39) A31V probably benign Het
Mfn1 T C 3: 32,615,621 (GRCm39) I328T probably damaging Het
Mif-ps9 G A 19: 56,743,675 (GRCm39) noncoding transcript Het
Myh4 A T 11: 67,141,157 (GRCm39) I740F possibly damaging Het
Neo1 A G 9: 58,893,069 (GRCm39) V191A probably benign Het
Nfatc4 T C 14: 56,067,485 (GRCm39) V565A probably damaging Het
Nrxn2 G C 19: 6,523,563 (GRCm39) E525D probably damaging Het
Or12k8 T C 2: 36,975,346 (GRCm39) H138R probably benign Het
Pcdhb12 A T 18: 37,570,261 (GRCm39) D469V probably damaging Het
Pcdhb6 G T 18: 37,468,167 (GRCm39) V363L probably benign Het
Pkd1l2 T C 8: 117,808,957 (GRCm39) T78A probably benign Het
Primpol T G 8: 47,034,674 (GRCm39) D418A probably damaging Het
Rbm12b1 G A 4: 12,146,248 (GRCm39) S740N probably benign Het
Rpe65 T C 3: 159,305,986 (GRCm39) L15P probably damaging Het
Rxrb CGCGGCGGCGGCGGCGGCGGC CGCGGCGGCGGCGGCGGC 17: 34,251,106 (GRCm39) probably benign Het
Sectm1a A G 11: 120,959,928 (GRCm39) probably benign Het
Sft2d1 C A 17: 8,545,782 (GRCm39) probably benign Het
Slc22a18 A G 7: 143,045,598 (GRCm39) probably benign Het
Slu7 G A 11: 43,332,405 (GRCm39) probably null Het
Smc4 T C 3: 68,931,622 (GRCm39) V572A probably damaging Het
Spire2 T A 8: 124,080,855 (GRCm39) I33N probably damaging Het
Tbck T A 3: 132,458,403 (GRCm39) C678S probably damaging Het
Tnrc6b T C 15: 80,797,539 (GRCm39) V1362A probably damaging Het
Ttn T C 2: 76,570,326 (GRCm39) K25110E possibly damaging Het
Ugt2b35 A G 5: 87,148,793 (GRCm39) S15G possibly damaging Het
Vill G C 9: 118,899,701 (GRCm39) G295A possibly damaging Het
Vmn1r191 A T 13: 22,363,217 (GRCm39) V179D probably damaging Het
Vmn2r74 T C 7: 85,601,629 (GRCm39) T670A probably damaging Het
Zfp169 T C 13: 48,643,166 (GRCm39) T654A possibly damaging Het
Zfp646 A G 7: 127,481,138 (GRCm39) E1105G probably damaging Het
Zyg11b A T 4: 108,117,239 (GRCm39) Y334N probably damaging Het
Other mutations in Upf3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01398:Upf3a APN 8 13,836,221 (GRCm39) missense probably damaging 0.98
IGL01678:Upf3a APN 8 13,841,930 (GRCm39) missense probably benign 0.21
IGL02072:Upf3a APN 8 13,848,368 (GRCm39) missense probably damaging 0.99
R0309:Upf3a UTSW 8 13,845,500 (GRCm39) splice site probably null
R0564:Upf3a UTSW 8 13,845,656 (GRCm39) missense probably benign 0.42
R0826:Upf3a UTSW 8 13,848,338 (GRCm39) missense possibly damaging 0.65
R1387:Upf3a UTSW 8 13,842,118 (GRCm39) missense probably damaging 1.00
R1913:Upf3a UTSW 8 13,842,108 (GRCm39) missense probably damaging 1.00
R2072:Upf3a UTSW 8 13,835,850 (GRCm39) missense possibly damaging 0.63
R2520:Upf3a UTSW 8 13,846,443 (GRCm39) splice site probably null
R3845:Upf3a UTSW 8 13,848,238 (GRCm39) missense probably benign 0.16
R4239:Upf3a UTSW 8 13,846,591 (GRCm39) missense probably benign 0.28
R4424:Upf3a UTSW 8 13,846,573 (GRCm39) missense probably benign 0.09
R5522:Upf3a UTSW 8 13,845,497 (GRCm39) critical splice donor site probably null
R6321:Upf3a UTSW 8 13,837,466 (GRCm39) missense possibly damaging 0.53
R6922:Upf3a UTSW 8 13,841,911 (GRCm39) missense probably damaging 1.00
R7583:Upf3a UTSW 8 13,835,889 (GRCm39) splice site probably null
R7585:Upf3a UTSW 8 13,837,418 (GRCm39) missense probably damaging 1.00
R7695:Upf3a UTSW 8 13,848,279 (GRCm39) missense probably benign 0.01
R7991:Upf3a UTSW 8 13,842,166 (GRCm39) missense probably damaging 1.00
R8913:Upf3a UTSW 8 13,845,728 (GRCm39) missense possibly damaging 0.94
R9638:Upf3a UTSW 8 13,848,343 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- ATGGTGAGCCCTTTCCGAAAGC -3'
(R):5'- ACAAAGTGTCCTCTCTGAGCAGCC -3'

Sequencing Primer
(F):5'- GCCCTTTCCGAAAGCTGAATTG -3'
(R):5'- GGCCATTCTAAGCCAGGAC -3'
Posted On 2013-06-11