Incidental Mutation 'R0826:Upf3a'
ID 78236
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 039006-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0826 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 13835615-13849193 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to C at 13848338 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Alanine at position 378 (G378A)
Ref Sequence ENSEMBL: ENSMUSP00000037354 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043767]
AlphaFold Q3ULJ3
Predicted Effect possibly damaging
Transcript: ENSMUST00000043767
AA Change: G378A

PolyPhen 2 Score 0.647 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000037354
Gene: ENSMUSG00000038398
AA Change: G378A

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 0.1244 question?
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 98.6%
  • 10x: 95.7%
  • 20x: 86.3%
Validation Efficiency 100% (69/69)
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930433I11Rik A T 7: 40,642,480 (GRCm39) T141S probably benign Het
4931406C07Rik T C 9: 15,203,292 (GRCm39) probably null Het
Adamts16 T A 13: 70,916,811 (GRCm39) D727V possibly damaging Het
Anxa10 A C 8: 62,529,318 (GRCm39) L133* probably null Het
Arfgef3 G A 10: 18,465,414 (GRCm39) T2143I probably damaging Het
Arhgef17 T C 7: 100,579,950 (GRCm39) T333A probably benign Het
Arhgef40 A G 14: 52,238,450 (GRCm39) T1310A probably benign Het
Atg10 C T 13: 91,084,705 (GRCm39) probably null Het
Atp1a1 A G 3: 101,492,169 (GRCm39) F569S probably damaging Het
Baiap3 A G 17: 25,464,203 (GRCm39) W849R possibly damaging Het
Baz1a A T 12: 54,977,097 (GRCm39) Y9* probably null Het
Catsperg2 C T 7: 29,405,049 (GRCm39) D702N possibly damaging Het
Clasrp G T 7: 19,318,226 (GRCm39) probably benign Het
Col11a1 G A 3: 113,932,414 (GRCm39) R113H unknown Het
Col19a1 T C 1: 24,565,467 (GRCm39) K288R unknown Het
Ctnnbl1 C T 2: 157,641,337 (GRCm39) probably benign Het
Cttnbp2 A G 6: 18,405,177 (GRCm39) probably benign Het
Dnah1 T A 14: 31,025,864 (GRCm39) I828F probably benign Het
Dpf2 G T 19: 5,957,155 (GRCm39) Q23K probably damaging Het
Dsc3 T A 18: 20,114,229 (GRCm39) I342F probably damaging Het
Enpp3 A G 10: 24,671,614 (GRCm39) L460P probably damaging Het
Epb41l2 A G 10: 25,380,090 (GRCm39) E871G probably damaging Het
Exoc2 T C 13: 31,040,780 (GRCm39) probably null Het
Fam243 G A 16: 92,118,075 (GRCm39) S71L probably benign Het
Fpr-rs7 A T 17: 20,333,888 (GRCm39) S201T probably benign Het
Gtf2ird2 T C 5: 134,245,797 (GRCm39) F685S probably damaging Het
Helz2 C T 2: 180,882,646 (GRCm39) R49H possibly damaging Het
Ica1 A G 6: 8,667,375 (GRCm39) probably benign Het
Ift56 A G 6: 38,402,049 (GRCm39) probably null Het
Iqca1 C A 1: 90,070,453 (GRCm39) G133V probably null Het
Kif21a A G 15: 90,881,744 (GRCm39) probably null Het
Lamb3 T A 1: 193,013,216 (GRCm39) C480* probably null Het
Lamc2 A G 1: 153,027,828 (GRCm39) S199P probably damaging Het
Lrfn3 T C 7: 30,059,676 (GRCm39) N183S probably benign Het
Lsm14a C A 7: 34,070,470 (GRCm39) probably benign Het
Mest C A 6: 30,742,813 (GRCm39) H146Q probably damaging Het
Mmp27 T C 9: 7,579,010 (GRCm39) V339A probably damaging Het
Myo16 T C 8: 10,426,285 (GRCm39) probably benign Het
Myoz1 C T 14: 20,703,679 (GRCm39) probably benign Het
Nlrp5 A G 7: 23,117,133 (GRCm39) M286V probably benign Het
Optc T C 1: 133,832,893 (GRCm39) K69R probably benign Het
Or13c3 C T 4: 52,855,566 (GRCm39) V316I probably benign Het
Or2y1c A T 11: 49,361,158 (GRCm39) Y60F probably damaging Het
Or4a77 A C 2: 89,487,181 (GRCm39) N201K possibly damaging Het
Or8g18 C T 9: 39,149,725 (GRCm39) M1I probably null Het
Osbpl3 A T 6: 50,323,357 (GRCm39) M242K probably damaging Het
Pdzd9 T A 7: 120,267,624 (GRCm39) S64C probably damaging Het
Pik3cg A G 12: 32,245,672 (GRCm39) S859P possibly damaging Het
Ppp1r12a G T 10: 108,066,414 (GRCm39) A202S possibly damaging Het
Rab32 A T 10: 10,426,611 (GRCm39) F112I possibly damaging Het
Ror2 T C 13: 53,267,253 (GRCm39) Y394C probably damaging Het
Rtn3 A G 19: 7,445,245 (GRCm39) probably benign Het
Sbk1 C T 7: 125,891,007 (GRCm39) P147L probably damaging Het
Shpk T A 11: 73,094,857 (GRCm39) M91K probably damaging Het
Slco6c1 C T 1: 97,055,826 (GRCm39) S25N probably benign Het
Snx2 A T 18: 53,327,594 (GRCm39) T107S probably benign Het
Tle2 G A 10: 81,422,148 (GRCm39) V397I possibly damaging Het
Tmem131l T C 3: 83,805,724 (GRCm39) D1573G probably damaging Het
Tnfrsf8 A G 4: 145,011,708 (GRCm39) probably benign Het
Tpmt T C 13: 47,194,965 (GRCm39) E36G probably benign Het
Trim30c T A 7: 104,032,688 (GRCm39) T257S probably benign Het
Tsc2 A G 17: 24,815,932 (GRCm39) L150P probably benign Het
Yeats2 A T 16: 20,011,966 (GRCm39) K514* probably null Het
Zfp11 A G 5: 129,734,589 (GRCm39) Y291H probably benign Het
Zfp457 T C 13: 67,441,378 (GRCm39) D399G possibly 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
R0571:Upf3a UTSW 8 13,842,184 (GRCm39) missense probably damaging 0.98
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'- TGACTCACAGGCTACAGGATACCAG -3'
(R):5'- TGAAATTCAGCCCACATGGGAAGAC -3'

Sequencing Primer
(F):5'- CTACAGGATACCAGTGATAAAGAGCC -3'
(R):5'- CACAAGGCAGATTGTTCTTATCTAGC -3'
Posted On 2013-10-16