Incidental Mutation 'IGL01327:Tsen54'
ID74306
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Tsen54
Ensembl Gene ENSMUSG00000020781
Gene NametRNA splicing endonuclease subunit 54
Synonyms
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.962) question?
Stock #IGL01327
Quality Score
Status
Chromosome11
Chromosomal Location115814724-115823094 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 115821712 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Histidine at position 119 (Y119H)
Ref Sequence ENSEMBL: ENSMUSP00000116955 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021134] [ENSMUST00000103032] [ENSMUST00000106481] [ENSMUST00000133250] [ENSMUST00000136343] [ENSMUST00000154304] [ENSMUST00000177736]
Predicted Effect probably benign
Transcript: ENSMUST00000021134
AA Change: Y436H

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000021134
Gene: ENSMUSG00000020781
AA Change: Y436H

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 benign
Transcript: ENSMUST00000106481
AA Change: Y436H

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000102090
Gene: ENSMUSG00000020781
AA Change: Y436H

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 noncoding transcript
Transcript: ENSMUST00000128266
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 benign
Transcript: ENSMUST00000136343
SMART Domains Protein: ENSMUSP00000120506
Gene: ENSMUSG00000020781

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 noncoding transcript
Transcript: ENSMUST00000141748
Predicted Effect possibly damaging
Transcript: ENSMUST00000154304
AA Change: Y119H

PolyPhen 2 Score 0.903 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000116955
Gene: ENSMUSG00000020781
AA Change: Y119H

DomainStartEndE-ValueType
coiled coil region 21 43 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000157061
AA Change: Y73H
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
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2510039O18Rik T A 4: 147,945,064 V497E probably damaging Het
4930563D23Rik T C 16: 92,320,773 Y209C probably benign Het
Adcy7 T G 8: 88,318,790 probably benign Het
Aldh1a2 T A 9: 71,285,966 F486I possibly damaging Het
Alox12 T A 11: 70,254,549 H66L probably benign Het
Apoh T G 11: 108,397,361 Y102D probably damaging Het
Arl9 T C 5: 77,006,554 V43A possibly damaging Het
Atf6 A G 1: 170,788,606 probably null Het
Atp4a T A 7: 30,713,250 I127N possibly damaging Het
AY358078 T A 14: 51,805,709 probably benign Het
Baat T G 4: 49,490,338 K249Q probably damaging Het
Brat1 C T 5: 140,718,208 Q739* probably null Het
C8g A G 2: 25,499,077 F165L probably damaging Het
Cel T G 2: 28,557,955 D353A possibly damaging Het
Col6a1 G T 10: 76,710,979 T803K unknown Het
Cpxm1 A G 2: 130,396,357 L95P probably benign Het
Ctsr A G 13: 61,162,675 probably benign Het
Cyth1 A G 11: 118,193,613 probably null Het
Dync1h1 A T 12: 110,616,692 probably benign Het
Ezh1 C T 11: 101,203,436 C407Y probably damaging Het
Gm3696 A T 14: 7,090,701 W38R probably benign Het
Gm9611 T C 14: 42,294,665 T39A possibly damaging Het
Gnpat T A 8: 124,878,633 L287H probably damaging Het
Golm1 G T 13: 59,645,144 N182K possibly damaging Het
Hdac6 T C X: 7,931,774 M899V probably benign Het
Hsf3 T A X: 96,314,972 M272L probably benign Het
Kif19a C T 11: 114,781,799 probably benign Het
Lcn2 T G 2: 32,386,018 Y100S possibly damaging Het
Lrrc8d T A 5: 105,812,265 S180R probably damaging Het
Ly6h A G 15: 75,565,099 probably benign Het
Macf1 T C 4: 123,509,912 N705D probably benign Het
Mst1r C T 9: 107,907,844 P234S probably benign Het
Msto1 T A 3: 88,910,632 probably null Het
Myo5a T A 9: 75,187,538 probably benign Het
Nipa1 T C 7: 55,979,661 I235V probably benign Het
Nlgn3 T C X: 101,318,622 V399A probably benign Het
Olfr1367 A G 13: 21,347,207 N93S probably benign Het
Olfr412 T A 11: 74,364,912 M81K possibly damaging Het
Pih1d1 T C 7: 45,159,975 S289P probably benign Het
Ppl T C 16: 5,087,644 N1596D probably benign Het
Psmb6 T A 11: 70,526,586 S114R possibly damaging Het
Pum1 C A 4: 130,730,543 Q289K probably damaging Het
Shkbp1 T C 7: 27,355,251 I75V probably benign Het
Slc24a3 T A 2: 145,602,558 I284N probably benign Het
Slc44a3 C T 3: 121,527,193 G53D probably damaging Het
Slc9a4 A C 1: 40,629,405 D736A probably benign Het
Stra6 A G 9: 58,152,571 D605G probably benign Het
Tas2r126 T A 6: 42,434,750 H72Q probably benign Het
Tbrg1 C T 9: 37,653,112 R166Q probably benign Het
Thumpd1 C T 7: 119,720,702 G14R probably benign Het
Ticrr C T 7: 79,694,461 T1358I probably benign Het
Tmtc2 A T 10: 105,348,479 N518K probably benign Het
Trpm4 C A 7: 45,315,073 W533C probably damaging Het
Tulp3 G A 6: 128,327,634 T219M probably damaging Het
Usp19 T C 9: 108,498,961 L1000S possibly damaging Het
Vps16 A T 2: 130,437,696 Y43F probably benign Het
Vsig1 T A X: 140,937,680 V283E possibly damaging Het
Other mutations in Tsen54
AlleleSourceChrCoordTypePredicted EffectPPH Score
PIT4486001:Tsen54 UTSW 11 115822596 missense probably damaging 1.00
R0179:Tsen54 UTSW 11 115822030 missense probably damaging 1.00
R0255:Tsen54 UTSW 11 115815408 missense probably damaging 1.00
R0380:Tsen54 UTSW 11 115822597 missense probably damaging 1.00
R0619:Tsen54 UTSW 11 115815064 missense probably damaging 1.00
R0653:Tsen54 UTSW 11 115815061 missense probably damaging 1.00
R1120:Tsen54 UTSW 11 115815013 missense probably damaging 0.98
R2109:Tsen54 UTSW 11 115815723 missense probably damaging 1.00
R2248:Tsen54 UTSW 11 115815406 missense probably damaging 1.00
R2300:Tsen54 UTSW 11 115822078 missense probably damaging 1.00
R3081:Tsen54 UTSW 11 115820164 missense probably benign 0.08
R3763:Tsen54 UTSW 11 115820411 missense probably benign 0.22
R4179:Tsen54 UTSW 11 115820852 missense probably damaging 0.99
R4521:Tsen54 UTSW 11 115817106 critical splice donor site probably null
R4618:Tsen54 UTSW 11 115815421 unclassified probably benign
R5485:Tsen54 UTSW 11 115815222 missense probably benign 0.15
R6111:Tsen54 UTSW 11 115820130 missense possibly damaging 0.82
R6238:Tsen54 UTSW 11 115820687 missense probably benign 0.02
R6459:Tsen54 UTSW 11 115821680 missense probably damaging 1.00
R6555:Tsen54 UTSW 11 115820693 missense probably benign 0.43
R7378:Tsen54 UTSW 11 115821705 missense probably benign 0.19
R7520:Tsen54 UTSW 11 115820971 missense probably damaging 0.99
R7922:Tsen54 UTSW 11 115820782 nonsense probably null
R8110:Tsen54 UTSW 11 115814934 missense unknown
R8159:Tsen54 UTSW 11 115820978 nonsense probably null
X0028:Tsen54 UTSW 11 115817099 missense possibly damaging 0.50
Z1176:Tsen54 UTSW 11 115820578 missense probably benign 0.03
Posted On2013-10-07