Incidental Mutation 'R7695:Upf3a'
ID 593608
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 045758-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7695 (G1)
Quality Score 225.009
Status Not validated
Chromosome 8
Chromosomal Location 13835615-13849193 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 13848279 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 358 (S358R)
Ref Sequence ENSEMBL: ENSMUSP00000037354 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043767]
AlphaFold Q3ULJ3
Predicted Effect probably benign
Transcript: ENSMUST00000043767
AA Change: S358R

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: S358R

DomainStartEndE-ValueType
low complexity region 6 18 N/A INTRINSIC
Pfam:Smg4_UPF3 63 224 1.4e-54 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrb1 T C 15: 74,415,487 (GRCm39) V689A possibly damaging Het
Casp12 A G 9: 5,353,641 (GRCm39) E225G probably damaging Het
Ccdc39 A G 3: 33,868,668 (GRCm39) L806P probably damaging Het
Ccnd3 T A 17: 47,908,421 (GRCm39) I164N probably damaging Het
Cd209b A G 8: 3,976,005 (GRCm39) V52A probably benign Het
Celsr2 G A 3: 108,310,069 (GRCm39) R1554W probably damaging Het
Cnot1 A T 8: 96,497,260 (GRCm39) I239N probably benign Het
Csmd3 A T 15: 47,683,777 (GRCm39) V948D Het
Dnmt1 C A 9: 20,825,281 (GRCm39) G1061V probably null Het
Dpysl4 A G 7: 138,666,039 (GRCm39) M1V probably null Het
Elp5 T C 11: 69,860,327 (GRCm39) T227A probably benign Het
Exosc1 G A 19: 41,916,519 (GRCm39) H86Y possibly damaging Het
Foxn4 G T 5: 114,394,648 (GRCm39) D426E probably damaging Het
Gabbr2 A G 4: 46,875,687 (GRCm39) L145P probably damaging Het
Gkn3 A G 6: 87,361,422 (GRCm39) Y126H probably damaging Het
Gm16506 A G 14: 43,962,463 (GRCm39) F148S Het
Gm3558 A G 14: 19,121,623 (GRCm39) I76T probably benign Het
Gm49359 A G 13: 62,604,558 (GRCm39) F45S possibly damaging Het
Gpc5 A T 14: 115,330,026 (GRCm39) H63L unknown Het
H2bl1 T C 13: 99,120,766 (GRCm39) T87A probably damaging Het
Hbs1l A T 10: 21,175,116 (GRCm39) D28V possibly damaging Het
Ide G A 19: 37,306,435 (GRCm39) H113Y Het
Igkv3-3 A T 6: 70,664,295 (GRCm39) S46C probably damaging Het
Igsf10 A T 3: 59,233,612 (GRCm39) V1707D probably damaging Het
Kcna5 A T 6: 126,511,174 (GRCm39) V318E probably damaging Het
Kdm3b T C 18: 34,927,612 (GRCm39) F158S possibly damaging Het
Lrrc14b T A 13: 74,511,297 (GRCm39) D261V possibly damaging Het
Lrrc71 T A 3: 87,646,769 (GRCm39) I485F probably damaging Het
Map6 C T 7: 98,985,499 (GRCm39) L671F possibly damaging Het
Mast1 A G 8: 85,647,557 (GRCm39) V560A probably damaging Het
Mfap4 A T 11: 61,376,545 (GRCm39) probably null Het
Myh9 A G 15: 77,650,936 (GRCm39) I1637T probably benign Het
Neo1 A T 9: 58,810,212 (GRCm39) F1080I possibly damaging Het
Or1e17 T A 11: 73,831,720 (GRCm39) V216E possibly damaging Het
Or4k48 A G 2: 111,475,970 (GRCm39) V124A probably damaging Het
Or4x6 A G 2: 89,949,207 (GRCm39) V245A probably benign Het
Or51a25 T C 7: 102,372,866 (GRCm39) H277R probably benign Het
Pax2 A G 19: 44,821,638 (GRCm39) Y318C probably damaging Het
Pcnx4 A T 12: 72,588,350 (GRCm39) M53L probably benign Het
Pkd2l2 T A 18: 34,561,298 (GRCm39) D435E possibly damaging Het
Plec G A 15: 76,068,055 (GRCm39) Q1117* probably null Het
Ppp2r2c T C 5: 37,104,526 (GRCm39) L302P probably damaging Het
Prex2 T C 1: 11,232,497 (GRCm39) F855L probably benign Het
Reg3d A T 6: 78,354,119 (GRCm39) W103R probably benign Het
Rnf216 A C 5: 143,071,659 (GRCm39) H440Q possibly damaging Het
Scn2a A G 2: 65,542,251 (GRCm39) T785A probably damaging Het
Sh3pxd2a T A 19: 47,256,270 (GRCm39) Y844F probably damaging Het
Sp110 G A 1: 85,506,813 (GRCm39) R417C probably benign Het
Spp1 T C 5: 104,583,009 (GRCm39) probably benign Het
Tacc2 T A 7: 130,330,633 (GRCm39) S196T probably benign Het
Thrap3 G A 4: 126,073,891 (GRCm39) S285L probably damaging Het
Ttn T A 2: 76,666,305 (GRCm39) R11584* probably null Het
Ubap2 A G 4: 41,211,740 (GRCm39) S341P probably damaging Het
Zdbf2 T A 1: 63,346,529 (GRCm39) I1636N possibly damaging Het
Zfp946 C A 17: 22,674,002 (GRCm39) T252N probably benign 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
R0571:Upf3a UTSW 8 13,842,184 (GRCm39) missense probably damaging 0.98
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
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'- ATGGGCTCAATTCTCACACAC -3'
(R):5'- ACATCAACAGGGACGATGGC -3'

Sequencing Primer
(F):5'- CCACTCAGGGTAGAAAGGAGAC -3'
(R):5'- ACGATGGCCCATGGTCTACTG -3'
Posted On 2019-11-12