Incidental Mutation 'R5522:Upf3a'
ID 431617
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 043081-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5522 (G1)
Quality Score 225
Status Not validated
Chromosome 8
Chromosomal Location 13835615-13849193 bp(+) (GRCm39)
Type of Mutation critical splice donor site (2 bp from exon)
DNA Base Change (assembly) T to A at 13845497 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000037354 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043767] [ENSMUST00000043767]
AlphaFold Q3ULJ3
Predicted Effect probably null
Transcript: ENSMUST00000043767
SMART Domains Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398

DomainStartEndE-ValueType
low complexity region 6 18 N/A INTRINSIC
Pfam:Smg4_UPF3 63 224 1.4e-54 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000043767
SMART Domains Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398

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
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 97.4%
  • 10x: 93.9%
  • 20x: 85.3%
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrl1 T C 8: 84,649,704 (GRCm39) Y121H possibly damaging Het
Agbl5 G A 5: 31,051,247 (GRCm39) probably null Het
Atp13a2 T A 4: 140,731,671 (GRCm39) probably null Het
Cd69 A T 6: 129,248,379 (GRCm39) S36T probably damaging Het
Ceacam5 A T 7: 17,449,005 (GRCm39) I124L probably benign Het
Cerkl T C 2: 79,223,328 (GRCm39) H131R probably benign Het
Cfap57 A T 4: 118,453,085 (GRCm39) N539K probably benign Het
Cyp4x1 C A 4: 114,979,174 (GRCm39) W141L probably damaging Het
Dlgap1 T C 17: 70,823,993 (GRCm39) probably null Het
Dnaaf9 G A 2: 130,656,222 (GRCm39) probably benign Het
Dst T C 1: 34,296,954 (GRCm39) I5781T possibly damaging Het
Epha2 T A 4: 141,035,867 (GRCm39) V101E probably damaging Het
Exph5 T C 9: 53,285,613 (GRCm39) F898S possibly damaging Het
Fyco1 G A 9: 123,623,836 (GRCm39) R1398* probably null Het
Gemin6 T G 17: 80,535,178 (GRCm39) V46G probably damaging Het
Grb10 T C 11: 11,886,746 (GRCm39) I508V probably benign Het
Igf1r C A 7: 67,833,258 (GRCm39) Q473K probably damaging Het
Ighv1-66 T A 12: 115,556,755 (GRCm39) D109V probably damaging Het
Ipmk C A 10: 71,199,304 (GRCm39) T55K probably benign Het
Kdm2b A G 5: 123,087,225 (GRCm39) Y192H probably damaging Het
Krt32 A T 11: 99,977,497 (GRCm39) probably null Het
Kti12 T A 4: 108,705,620 (GRCm39) L178Q possibly damaging Het
Mchr1 A T 15: 81,122,211 (GRCm39) K320N possibly damaging Het
Mdn1 T C 4: 32,685,783 (GRCm39) L858S probably damaging Het
Myo3a T A 2: 22,464,353 (GRCm39) F198Y probably damaging Het
Ncam2 C T 16: 81,231,766 (GRCm39) R77* probably null Het
Nfatc1 T C 18: 80,696,744 (GRCm39) T647A probably benign Het
Nuf2 A G 1: 169,326,453 (GRCm39) Y433H probably damaging Het
Nup210l T C 3: 90,061,972 (GRCm39) V717A probably benign Het
Or3a1b A G 11: 74,012,484 (GRCm39) Y123C probably damaging Het
Or5h17 A T 16: 58,820,268 (GRCm39) L73F probably benign Het
Or6c35 A T 10: 129,168,798 (GRCm39) D16V probably damaging Het
Pbrm1 A G 14: 30,811,520 (GRCm39) Y1210C probably damaging Het
Pcdhb6 A G 18: 37,467,402 (GRCm39) I108V probably benign Het
Plac8 T A 5: 100,710,584 (GRCm39) T6S probably benign Het
Plbd1 A T 6: 136,594,298 (GRCm39) V317E probably benign Het
Rars1 A T 11: 35,708,195 (GRCm39) Y406* probably null Het
Scamp3 T C 3: 89,084,929 (GRCm39) F11L possibly damaging Het
Sctr A G 1: 119,964,146 (GRCm39) N142S probably benign Het
Sh2d4a T C 8: 68,749,349 (GRCm39) S128P probably benign Het
Snrnp70 C T 7: 45,026,601 (GRCm39) probably benign Het
Taf3 T C 2: 9,945,816 (GRCm39) K596R probably damaging Het
Tango6 T C 8: 107,422,230 (GRCm39) probably null Het
Taok3 A G 5: 117,411,822 (GRCm39) T414A probably benign Het
Tmem104 G A 11: 115,079,149 (GRCm39) probably null Het
Tmem231 T A 8: 112,645,042 (GRCm39) S155C possibly damaging Het
Tssk3 G A 4: 129,383,343 (GRCm39) R110W possibly damaging Het
Ugt2b37 T C 5: 87,388,759 (GRCm39) T485A probably benign Het
Unc5b T C 10: 60,613,974 (GRCm39) K292E possibly damaging Het
Usp24 T A 4: 106,229,918 (GRCm39) V797E probably damaging Het
Vcan T C 13: 89,839,929 (GRCm39) T1872A possibly damaging Het
Vmn1r195 A G 13: 22,463,120 (GRCm39) M197V probably damaging Het
Vmn2r40 T A 7: 8,911,203 (GRCm39) T697S probably benign Het
Xab2 A T 8: 3,661,718 (GRCm39) D578E probably benign Het
Xpo7 A T 14: 70,909,090 (GRCm39) Y810* probably null Het
Zcchc2 A G 1: 105,951,426 (GRCm39) N587S probably benign Het
Zfp189 C T 4: 49,529,739 (GRCm39) R281* probably null Het
Zranb1 T C 7: 132,585,678 (GRCm39) *735R probably null 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
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'- CGGTGCACACTCACACTTTAG -3'
(R):5'- AGACACTTGGGTGGAGTTACG -3'

Sequencing Primer
(F):5'- GGTGCACACTCACACTTTAGAGATC -3'
(R):5'- GATGGATAATACTGTTTCCGCACTC -3'
Posted On 2016-10-05