Incidental Mutation 'R7922:Tsen54'
ID 648472
Institutional Source Beutler Lab
Gene Symbol Tsen54
Ensembl Gene ENSMUSG00000020781
Gene Name tRNA splicing endonuclease subunit 54
Synonyms 0610034P02Rik
MMRRC Submission 045969-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.953) question?
Stock # R7922 (G1)
Quality Score 225.009
Status Not validated
Chromosome 11
Chromosomal Location 115705550-115713920 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 115711608 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Stop codon at position 342 (Q342*)
Ref Sequence ENSEMBL: ENSMUSP00000021134 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021134] [ENSMUST00000103032] [ENSMUST00000106481] [ENSMUST00000133250] [ENSMUST00000136343] [ENSMUST00000154304] [ENSMUST00000177736]
AlphaFold Q8C2A2
Predicted Effect probably null
Transcript: ENSMUST00000021134
AA Change: Q342*
SMART Domains Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: Q342*

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 16 30 N/A INTRINSIC
Pfam:tRNA_int_end_N2 63 130 1.4e-21 PFAM
low complexity region 196 208 N/A INTRINSIC
low complexity region 219 232 N/A INTRINSIC
low complexity region 314 324 N/A INTRINSIC
coiled coil region 338 360 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000103032
SMART Domains Protein: ENSMUSP00000099321
Gene: ENSMUSG00000020782

DomainStartEndE-ValueType
WD40 24 60 9.17e1 SMART
WD40 62 101 7.96e0 SMART
Blast:WD40 112 157 6e-20 BLAST
WD40 181 217 3.96e1 SMART
WD40 221 258 5.7e1 SMART
Pfam:LLGL 268 372 3.2e-47 PFAM
WD40 411 451 1.38e0 SMART
Blast:WD40 489 532 3e-12 BLAST
low complexity region 536 547 N/A INTRINSIC
Blast:WD40 576 615 2e-10 BLAST
low complexity region 649 668 N/A INTRINSIC
Blast:WD40 830 879 2e-10 BLAST
Predicted Effect probably null
Transcript: ENSMUST00000106481
AA Change: Q342*
SMART Domains Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: Q342*

DomainStartEndE-ValueType
low complexity region 2 13 N/A INTRINSIC
low complexity region 16 30 N/A INTRINSIC
Pfam:tRNA_int_end_N2 62 132 1.9e-23 PFAM
low complexity region 196 208 N/A INTRINSIC
low complexity region 219 232 N/A INTRINSIC
low complexity region 314 324 N/A INTRINSIC
coiled coil region 338 360 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000133250
SMART Domains Protein: ENSMUSP00000118344
Gene: ENSMUSG00000020782

DomainStartEndE-ValueType
Blast:WD40 13 60 2e-20 BLAST
SCOP:d1gxra_ 19 118 5e-8 SMART
Blast:WD40 62 101 4e-22 BLAST
Blast:WD40 112 146 1e-15 BLAST
Predicted Effect probably null
Transcript: ENSMUST00000136343
AA Change: Q186*
SMART Domains Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781
AA Change: Q186*

DomainStartEndE-ValueType
low complexity region 63 76 N/A INTRINSIC
low complexity region 158 168 N/A INTRINSIC
coiled coil region 182 204 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000154304
AA Change: Q25*
SMART Domains Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: Q25*

DomainStartEndE-ValueType
coiled coil region 21 43 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000157061
Predicted Effect probably benign
Transcript: ENSMUST00000177736
SMART Domains Protein: ENSMUSP00000136054
Gene: ENSMUSG00000020782

DomainStartEndE-ValueType
WD40 24 60 5.9e-1 SMART
WD40 62 101 5.2e-2 SMART
Blast:WD40 112 157 6e-20 BLAST
WD40 181 217 2.5e-1 SMART
WD40 221 258 3.6e-1 SMART
Pfam:LLGL 271 372 6.2e-41 PFAM
WD40 411 451 8.8e-3 SMART
Blast:WD40 489 532 3e-12 BLAST
low complexity region 536 547 N/A INTRINSIC
Blast:WD40 576 615 2e-10 BLAST
low complexity region 649 668 N/A INTRINSIC
Blast:WD40 854 903 2e-10 BLAST
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700049A03Rik C T 12: 71,211,180 (GRCm39) T638M possibly damaging Het
4930546C10Rik A G 18: 69,083,067 (GRCm39) probably null Het
Abi3 A T 11: 95,723,619 (GRCm39) Y342N unknown Het
Adk G A 14: 21,368,111 (GRCm39) V195I probably benign Het
Ago2 C T 15: 72,998,375 (GRCm39) V268M possibly damaging Het
Apaf1 T C 10: 90,835,615 (GRCm39) I1077V probably benign Het
Arap1 A T 7: 101,053,621 (GRCm39) K1317* probably null Het
Auts2 T A 5: 131,469,211 (GRCm39) D493V Het
Baz1b A T 5: 135,260,533 (GRCm39) Q1110L probably damaging Het
Brsk2 T A 7: 141,546,957 (GRCm39) S467T possibly damaging Het
Btbd9 A T 17: 30,493,858 (GRCm39) M511K probably benign Het
Cdh23 T A 10: 60,218,485 (GRCm39) Y1385F probably benign Het
Cfap100 A C 6: 90,380,962 (GRCm39) L427V unknown Het
Cnga1 A G 5: 72,762,225 (GRCm39) F430L possibly damaging Het
Csnk2a1-ps3 A T 1: 156,352,562 (GRCm39) L254F probably damaging Het
Dnhd1 A T 7: 105,317,721 (GRCm39) D472V probably damaging Het
Dock2 T A 11: 34,598,154 (GRCm39) E339V probably benign Het
Eif3a A T 19: 60,764,280 (GRCm39) V379E probably damaging Het
Erich4 T A 7: 25,315,168 (GRCm39) N36Y probably damaging Het
Frem2 T C 3: 53,560,725 (GRCm39) T1261A probably damaging Het
Fzd6 A T 15: 38,894,503 (GRCm39) D223V probably damaging Het
Gabra2 A T 5: 71,165,315 (GRCm39) Y218* probably null Het
Gcn1 G T 5: 115,752,527 (GRCm39) M2177I probably benign Het
Ghr G A 15: 3,370,556 (GRCm39) T103I possibly damaging Het
Gipc1 T C 8: 84,387,857 (GRCm39) V79A probably benign Het
Gm13272 T A 4: 88,698,577 (GRCm39) V164D probably damaging Het
Gramd4 C A 15: 86,016,159 (GRCm39) H503Q probably benign Het
Gstm4 A T 3: 107,951,987 (GRCm39) M1K probably null Het
Heatr5b T A 17: 79,067,988 (GRCm39) Q1800L probably benign Het
Hectd1 T A 12: 51,836,978 (GRCm39) K826* probably null Het
Hoxa9 T C 6: 52,201,289 (GRCm39) I251V possibly damaging Het
Il2ra A T 2: 11,679,177 (GRCm39) I46F possibly damaging Het
Ints2 T A 11: 86,135,453 (GRCm39) R320S probably benign Het
Iscu A T 5: 113,912,343 (GRCm39) N46I probably damaging Het
Iscu G A 5: 113,912,410 (GRCm39) R60Q unknown Het
Kcnk3 A T 5: 30,745,875 (GRCm39) H72L probably damaging Het
Kmt2a T G 9: 44,754,157 (GRCm39) S1228R unknown Het
Mbl2 T A 19: 30,216,638 (GRCm39) L150Q probably damaging Het
Med13 A T 11: 86,161,831 (GRCm39) F2166Y probably damaging Het
Mterf4 A C 1: 93,229,275 (GRCm39) L246* probably null Het
Muc16 T C 9: 18,496,121 (GRCm39) Q6690R probably benign Het
Myh10 T A 11: 68,699,719 (GRCm39) L1722Q possibly damaging Het
Neurod2 T C 11: 98,218,454 (GRCm39) M237V probably benign Het
Olfml1 A G 7: 107,170,356 (GRCm39) Y81C probably damaging Het
Or4q3 A G 14: 50,583,872 (GRCm39) V9A probably benign Het
Pcdhga7 A T 18: 37,849,226 (GRCm39) N411I probably benign Het
Pcdhgb8 T C 18: 37,897,002 (GRCm39) F691L probably benign Het
Pik3c2a A G 7: 115,990,517 (GRCm39) V481A probably damaging Het
Pik3r6 A T 11: 68,424,701 (GRCm39) R435S probably benign Het
Pkd1l1 G A 11: 8,799,013 (GRCm39) H2250Y Het
Pkd1l1 A G 11: 8,859,857 (GRCm39) S1034P Het
Plcd1 C A 9: 118,903,720 (GRCm39) R400L possibly damaging Het
Ppp2r1a A G 17: 21,174,879 (GRCm39) T58A probably benign Het
Ppp5c T C 7: 16,761,725 (GRCm39) E5G possibly damaging Het
Pradc1 A C 6: 85,424,950 (GRCm39) F82L probably benign Het
Prkag3 A T 1: 74,780,416 (GRCm39) S416R probably benign Het
Rab3gap2 T C 1: 184,982,117 (GRCm39) C390R probably benign Het
Rhot1 A G 11: 80,156,629 (GRCm39) T655A probably benign Het
Rorc A G 3: 94,298,495 (GRCm39) I348V probably damaging Het
Ryr1 A T 7: 28,796,649 (GRCm39) V1051E probably benign Het
Sema5b GCAC GC 16: 35,478,626 (GRCm39) probably null Het
Serpinb3c G A 1: 107,199,744 (GRCm39) T259I probably damaging Het
Sh3gl1 A T 17: 56,326,438 (GRCm39) M70K probably damaging Het
Sinhcaf T A 6: 148,827,644 (GRCm39) T125S probably benign Het
Slc7a4 C T 16: 17,391,230 (GRCm39) V607I probably benign Het
Spop A T 11: 95,362,154 (GRCm39) N62Y probably damaging Het
Spout1 A G 2: 30,066,823 (GRCm39) F130S probably benign Het
Tab1 A G 15: 80,043,066 (GRCm39) H420R possibly damaging Het
Tecpr2 CA C 12: 110,899,076 (GRCm39) probably null Het
Tnxb G C 17: 34,933,577 (GRCm39) K2332N probably damaging Het
Togaram1 T C 12: 65,014,512 (GRCm39) Y588H probably damaging Het
Trim71 G A 9: 114,342,153 (GRCm39) R710C probably damaging Het
Ube2r2 T A 4: 41,190,812 (GRCm39) N235K unknown Het
Utrn C A 10: 12,543,271 (GRCm39) K1792N possibly damaging Het
Vmn1r122 A G 7: 20,867,587 (GRCm39) I156T possibly damaging Het
Vmn1r94 T C 7: 19,901,636 (GRCm39) T223A possibly damaging Het
Vmn2r120 G A 17: 57,831,683 (GRCm39) R369W probably damaging Het
Vwa7 G T 17: 35,243,409 (GRCm39) A717S possibly damaging Het
Zc3h4 T A 7: 16,159,647 (GRCm39) C398S unknown Het
Zc3hc1 T A 6: 30,390,874 (GRCm39) E43V possibly damaging Het
Zfp101 A T 17: 33,600,511 (GRCm39) V415D possibly damaging Het
Zfp553 A G 7: 126,835,768 (GRCm39) H441R probably damaging Het
Other mutations in Tsen54
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01327:Tsen54 APN 11 115,712,538 (GRCm39) missense possibly damaging 0.90
PIT4486001:Tsen54 UTSW 11 115,713,422 (GRCm39) missense probably damaging 1.00
R0179:Tsen54 UTSW 11 115,712,856 (GRCm39) missense probably damaging 1.00
R0255:Tsen54 UTSW 11 115,706,234 (GRCm39) missense probably damaging 1.00
R0380:Tsen54 UTSW 11 115,713,423 (GRCm39) missense probably damaging 1.00
R0619:Tsen54 UTSW 11 115,705,890 (GRCm39) missense probably damaging 1.00
R0653:Tsen54 UTSW 11 115,705,887 (GRCm39) missense probably damaging 1.00
R1120:Tsen54 UTSW 11 115,705,839 (GRCm39) missense probably damaging 0.98
R2109:Tsen54 UTSW 11 115,706,549 (GRCm39) missense probably damaging 1.00
R2248:Tsen54 UTSW 11 115,706,232 (GRCm39) missense probably damaging 1.00
R2300:Tsen54 UTSW 11 115,712,904 (GRCm39) missense probably damaging 1.00
R3081:Tsen54 UTSW 11 115,710,990 (GRCm39) missense probably benign 0.08
R3763:Tsen54 UTSW 11 115,711,237 (GRCm39) missense probably benign 0.22
R4179:Tsen54 UTSW 11 115,711,678 (GRCm39) missense probably damaging 0.99
R4521:Tsen54 UTSW 11 115,707,932 (GRCm39) critical splice donor site probably null
R4618:Tsen54 UTSW 11 115,706,247 (GRCm39) unclassified probably benign
R5485:Tsen54 UTSW 11 115,706,048 (GRCm39) missense probably benign 0.15
R6111:Tsen54 UTSW 11 115,710,956 (GRCm39) missense possibly damaging 0.82
R6238:Tsen54 UTSW 11 115,711,513 (GRCm39) missense probably benign 0.02
R6459:Tsen54 UTSW 11 115,712,506 (GRCm39) missense probably damaging 1.00
R6555:Tsen54 UTSW 11 115,711,519 (GRCm39) missense probably benign 0.43
R7378:Tsen54 UTSW 11 115,712,531 (GRCm39) missense probably benign 0.19
R7520:Tsen54 UTSW 11 115,711,797 (GRCm39) missense probably damaging 0.99
R8110:Tsen54 UTSW 11 115,705,760 (GRCm39) missense unknown
R8159:Tsen54 UTSW 11 115,711,804 (GRCm39) nonsense probably null
R8497:Tsen54 UTSW 11 115,713,410 (GRCm39) missense probably damaging 1.00
R8529:Tsen54 UTSW 11 115,711,386 (GRCm39) missense possibly damaging 0.95
R8786:Tsen54 UTSW 11 115,711,498 (GRCm39) missense probably damaging 0.98
R9365:Tsen54 UTSW 11 115,713,410 (GRCm39) missense probably damaging 1.00
R9571:Tsen54 UTSW 11 115,707,933 (GRCm39) critical splice donor site probably null
X0028:Tsen54 UTSW 11 115,707,925 (GRCm39) missense possibly damaging 0.50
Z1176:Tsen54 UTSW 11 115,711,404 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- TACCCAGAGGAGAAGTCTCAG -3'
(R):5'- TTATCAGGGTCGAGCAAGGG -3'

Sequencing Primer
(F):5'- TCTGATCTGGCCAGGGAAGAC -3'
(R):5'- TAACGGACTGGCCCCATAG -3'
Posted On 2020-09-15