Incidental Mutation 'R5294:Trnt1'
ID 405294
Institutional Source Beutler Lab
Gene Symbol Trnt1
Ensembl Gene ENSMUSG00000013736
Gene Name tRNA nucleotidyl transferase, CCA-adding, 1
Synonyms CGI-47, 2410043H24Rik, 2610044E04Rik
MMRRC Submission 042877-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.969) question?
Stock # R5294 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 106769120-106782474 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 106773414 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 93 (F93S)
Ref Sequence ENSEMBL: ENSMUSP00000144850 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057578] [ENSMUST00000113247] [ENSMUST00000113248] [ENSMUST00000113249] [ENSMUST00000204782] [ENSMUST00000205163]
AlphaFold Q8K1J6
Predicted Effect probably damaging
Transcript: ENSMUST00000057578
AA Change: F93S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000060900
Gene: ENSMUSG00000013736
AA Change: F93S

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 3.8e-36 PFAM
Pfam:PolyA_pol_RNAbd 215 271 1.4e-14 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000113247
AA Change: F93S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108873
Gene: ENSMUSG00000013736
AA Change: F93S

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 7.7e-37 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000113248
AA Change: F93S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108874
Gene: ENSMUSG00000013736
AA Change: F93S

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 2.4e-37 PFAM
Pfam:PolyA_pol_RNAbd 215 272 9.3e-15 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000113249
AA Change: F93S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108875
Gene: ENSMUSG00000013736
AA Change: F93S

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 3.8e-36 PFAM
Pfam:PolyA_pol_RNAbd 215 271 1.4e-14 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147084
Predicted Effect noncoding transcript
Transcript: ENSMUST00000154026
Predicted Effect probably damaging
Transcript: ENSMUST00000204782
AA Change: F93S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000144850
Gene: ENSMUSG00000013736
AA Change: F93S

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 134 3e-17 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000205163
SMART Domains Protein: ENSMUSP00000144943
Gene: ENSMUSG00000013736

DomainStartEndE-ValueType
PDB:1OU5|B 30 72 2e-22 PDB
Meta Mutation Damage Score 0.9648 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 96.0%
Validation Efficiency 97% (70/72)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3' terminus of tRNA molecules. Mutations in this gene result in sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579C12Rik T C 9: 89,152,003 (GRCm38) noncoding transcript Het
Acaca A G 11: 84,391,519 (GRCm38) E2154G probably benign Het
Acacb T C 5: 114,241,952 (GRCm38) F2056L probably damaging Het
Aff1 A G 5: 103,811,157 (GRCm38) probably benign Het
Amn1 T A 6: 149,185,124 (GRCm38) probably benign Het
Arid1a C A 4: 133,691,055 (GRCm38) probably benign Het
Aste1 T A 9: 105,402,705 (GRCm38) probably null Het
Asxl3 T A 18: 22,516,439 (GRCm38) V495D possibly damaging Het
Atp1a3 T A 7: 24,988,048 (GRCm38) H688L probably damaging Het
B3gnt8 T C 7: 25,628,766 (GRCm38) L207P probably damaging Het
Baz2b T C 2: 59,978,602 (GRCm38) H101R probably benign Het
Bicc1 G A 10: 70,947,900 (GRCm38) T387M possibly damaging Het
Champ1 A C 8: 13,878,981 (GRCm38) K380Q probably damaging Het
Cnst A G 1: 179,610,440 (GRCm38) E523G probably benign Het
Cops6 G C 5: 138,161,116 (GRCm38) probably benign Het
Cp G C 3: 19,966,316 (GRCm38) V158L probably benign Het
Cyfip1 T A 7: 55,873,483 (GRCm38) M52K possibly damaging Het
Dars A T 1: 128,364,302 (GRCm38) F480I probably benign Het
Diaph1 T C 18: 37,897,580 (GRCm38) M274V unknown Het
Diaph1 C A 18: 37,897,550 (GRCm38) E284* probably null Het
Dock8 G A 19: 25,061,153 (GRCm38) V68M probably benign Het
Elavl4 A G 4: 110,211,430 (GRCm38) F247L possibly damaging Het
Emc10 C T 7: 44,496,439 (GRCm38) probably benign Het
Fbxw16 T C 9: 109,436,644 (GRCm38) D369G probably benign Het
Fgr A T 4: 132,997,500 (GRCm38) D304V probably benign Het
Filip1l G A 16: 57,570,036 (GRCm38) S91N possibly damaging Het
Gm884 A G 11: 103,616,231 (GRCm38) probably benign Het
Haus8 A G 8: 71,255,710 (GRCm38) S103P unknown Het
Hscb A G 5: 110,834,792 (GRCm38) L143P probably damaging Het
Hsd11b2 A T 8: 105,523,297 (GRCm38) M347L probably benign Het
Jrk C A 15: 74,707,336 (GRCm38) E33D possibly damaging Het
Kbtbd8 T A 6: 95,121,832 (GRCm38) Y123* probably null Het
Mis18bp1 A C 12: 65,157,043 (GRCm38) M59R probably damaging Het
Mrps27 T C 13: 99,409,873 (GRCm38) V260A probably damaging Het
Ncapg2 G T 12: 116,427,794 (GRCm38) V488L possibly damaging Het
Nepn A T 10: 52,400,800 (GRCm38) N211Y probably benign Het
Ntrk3 A T 7: 78,517,506 (GRCm38) probably null Het
Olfr248 A T 1: 174,391,225 (GRCm38) Y52F probably benign Het
Olfr692 C T 7: 105,368,413 (GRCm38) T20I probably benign Het
Olfr748 A G 14: 50,710,779 (GRCm38) I150V probably benign Het
Olfr748 A G 14: 50,710,443 (GRCm38) T38A possibly damaging Het
Otud4 A T 8: 79,672,892 (GRCm38) Q744L possibly damaging Het
P2ry14 A T 3: 59,115,568 (GRCm38) I166N possibly damaging Het
Pak2 T A 16: 32,021,830 (GRCm38) N478Y probably damaging Het
Papss2 A G 19: 32,639,000 (GRCm38) D202G probably benign Het
Pcdh7 C A 5: 57,728,111 (GRCm38) probably null Het
Peg3 C A 7: 6,717,849 (GRCm38) S19I possibly damaging Het
Prim2 G T 1: 33,668,893 (GRCm38) T40K probably benign Het
Ranbp2 T C 10: 58,478,668 (GRCm38) F1737L probably benign Het
Rex2 A C 4: 147,057,985 (GRCm38) N310T probably benign Het
Rnf123 AT ATT 9: 108,064,003 (GRCm38) probably null Het
Rnf39 C T 17: 36,947,200 (GRCm38) A86V probably damaging Het
Ror1 A T 4: 100,425,938 (GRCm38) N400I probably benign Het
Slc38a8 C T 8: 119,494,289 (GRCm38) G177D probably damaging Het
Slc43a3 T C 2: 84,956,310 (GRCm38) V445A probably benign Het
Sptbn2 A G 19: 4,718,908 (GRCm38) N23S possibly damaging Het
Taf5l A G 8: 124,008,218 (GRCm38) F74L probably benign Het
Trappc11 G C 8: 47,530,731 (GRCm38) A42G possibly damaging Het
Trim30d T C 7: 104,472,488 (GRCm38) K350R probably damaging Het
Ube2c T C 2: 164,777,190 (GRCm38) V161A probably benign Het
Usp24 A G 4: 106,362,357 (GRCm38) E555G possibly damaging Het
Vmn2r55 T G 7: 12,651,864 (GRCm38) S730R probably damaging Het
Vmn2r89 T A 14: 51,455,113 (GRCm38) N124K probably benign Het
Vmn2r98 T A 17: 19,069,754 (GRCm38) C517* probably null Het
Vps13a A T 19: 16,641,667 (GRCm38) I2845N probably damaging Het
Vps51 T G 19: 6,071,033 (GRCm38) E283D probably benign Het
Xpo5 T C 17: 46,236,922 (GRCm38) V896A probably benign Het
Zfp2 T C 11: 50,901,241 (GRCm38) probably benign Het
Zgrf1 G A 3: 127,600,980 (GRCm38) M1328I probably benign Het
Zswim5 A G 4: 116,979,577 (GRCm38) D686G possibly damaging Het
Other mutations in Trnt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00819:Trnt1 APN 6 106,776,222 (GRCm38) nonsense probably null
IGL00915:Trnt1 APN 6 106,779,426 (GRCm38) missense probably benign 0.00
IGL01821:Trnt1 APN 6 106,774,475 (GRCm38) missense probably damaging 1.00
IGL02102:Trnt1 APN 6 106,778,112 (GRCm38) critical splice donor site probably null
IGL02610:Trnt1 APN 6 106,778,818 (GRCm38) missense possibly damaging 0.88
IGL02933:Trnt1 APN 6 106,773,426 (GRCm38) missense probably benign 0.40
R0606:Trnt1 UTSW 6 106,777,908 (GRCm38) unclassified probably benign
R0844:Trnt1 UTSW 6 106,774,503 (GRCm38) missense probably damaging 1.00
R2144:Trnt1 UTSW 6 106,778,039 (GRCm38) missense probably damaging 1.00
R2495:Trnt1 UTSW 6 106,773,369 (GRCm38) missense possibly damaging 0.88
R4994:Trnt1 UTSW 6 106,778,892 (GRCm38) nonsense probably null
R5742:Trnt1 UTSW 6 106,778,917 (GRCm38) nonsense probably null
R6855:Trnt1 UTSW 6 106,777,922 (GRCm38) missense probably damaging 1.00
R7491:Trnt1 UTSW 6 106,778,904 (GRCm38) missense probably benign
R7492:Trnt1 UTSW 6 106,774,532 (GRCm38) missense possibly damaging 0.76
R7880:Trnt1 UTSW 6 106,769,556 (GRCm38) critical splice donor site probably null
R8212:Trnt1 UTSW 6 106,769,871 (GRCm38) missense probably benign
R8863:Trnt1 UTSW 6 106,774,482 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CATACAAGATTGCTCAGTTCACTG -3'
(R):5'- CGGCATGGACATTTCTATTGAGAC -3'

Sequencing Primer
(F):5'- CAGTTCACTGACCTCTACTATCTG -3'
(R):5'- TGAGACTTTTTAAAACACGGGAC -3'
Posted On 2016-07-22