Incidental Mutation 'R2495:Trnt1'
ID 250959
Institutional Source Beutler Lab
Gene Symbol Trnt1
Ensembl Gene ENSMUSG00000013736
Gene Name tRNA nucleotidyl transferase, CCA-adding, 1
Synonyms CGI-47, 2610044E04Rik, 2410043H24Rik
MMRRC Submission 040409-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.966) question?
Stock # R2495 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 106746099-106759435 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 106750330 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 78 (V78E)
Ref Sequence ENSEMBL: ENSMUSP00000144850 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057578] [ENSMUST00000113247] [ENSMUST00000113248] [ENSMUST00000113249] [ENSMUST00000204782] [ENSMUST00000205163]
AlphaFold Q8K1J6
Predicted Effect possibly damaging
Transcript: ENSMUST00000057578
AA Change: V78E

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000060900
Gene: ENSMUSG00000013736
AA Change: V78E

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 3.8e-36 PFAM
Pfam:PolyA_pol_RNAbd 215 271 1.4e-14 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000113247
AA Change: V78E

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000108873
Gene: ENSMUSG00000013736
AA Change: V78E

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 7.7e-37 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000113248
AA Change: V78E

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000108874
Gene: ENSMUSG00000013736
AA Change: V78E

DomainStartEndE-ValueType
Pfam:PolyA_pol 59 182 2.4e-37 PFAM
Pfam:PolyA_pol_RNAbd 215 272 9.3e-15 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000113249
AA Change: V78E

PolyPhen 2 Score 0.488 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000108875
Gene: ENSMUSG00000013736
AA Change: V78E

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 possibly damaging
Transcript: ENSMUST00000204782
AA Change: V78E

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000144850
Gene: ENSMUSG00000013736
AA Change: V78E

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 0.1795 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 98% (63/64)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810062G17Rik T C 3: 36,536,109 (GRCm39) F125S unknown Het
Abhd17c C T 7: 83,759,884 (GRCm39) W290* probably null Het
Acsl5 A T 19: 55,282,031 (GRCm39) K536* probably null Het
Adamts14 A T 10: 61,034,749 (GRCm39) probably null Het
Agbl3 A G 6: 34,823,699 (GRCm39) H788R probably damaging Het
Agrp T C 8: 106,293,408 (GRCm39) N126D possibly damaging Het
Ambn T C 5: 88,615,663 (GRCm39) I349T probably benign Het
Ank1 T C 8: 23,622,280 (GRCm39) W1610R probably damaging Het
Aox3 T C 1: 58,227,567 (GRCm39) L1224P probably damaging Het
Arhgef28 A T 13: 98,165,881 (GRCm39) probably benign Het
Bcl11b G A 12: 107,881,706 (GRCm39) H798Y possibly damaging Het
Capn11 T A 17: 45,949,689 (GRCm39) M426L probably damaging Het
Cep95 A G 11: 106,700,108 (GRCm39) K290E possibly damaging Het
Cic A G 7: 24,991,201 (GRCm39) probably benign Het
Cnbd1 A T 4: 18,860,579 (GRCm39) M389K probably damaging Het
Cnksr1 A T 4: 133,959,473 (GRCm39) L387Q probably benign Het
Cntrob G T 11: 69,213,749 (GRCm39) P14T probably damaging Het
Crmp1 G A 5: 37,403,441 (GRCm39) probably null Het
Dido1 A G 2: 180,331,181 (GRCm39) V89A probably benign Het
Dnah7a T A 1: 53,645,040 (GRCm39) I999F probably damaging Het
Dsp T A 13: 38,377,453 (GRCm39) L1746Q possibly damaging Het
Dst T C 1: 34,238,454 (GRCm39) S3897P probably damaging Het
Fbxo10 A G 4: 45,040,545 (GRCm39) F887L probably benign Het
Gm21961 T A 15: 64,886,722 (GRCm39) H11L unknown Het
Gm4559 A T 7: 141,827,557 (GRCm39) C182S unknown Het
Golga3 T A 5: 110,355,462 (GRCm39) S939T probably damaging Het
Got2 A G 8: 96,614,918 (GRCm39) S6P possibly damaging Het
Gpatch8 A T 11: 102,369,307 (GRCm39) H1410Q probably damaging Het
Gpx5 T A 13: 21,475,610 (GRCm39) T39S probably benign Het
Grin2b T C 6: 135,710,180 (GRCm39) Y1122C probably damaging Het
Gsn A C 2: 35,193,205 (GRCm39) N538T probably damaging Het
Helz2 A G 2: 180,874,705 (GRCm39) S1930P probably damaging Het
Krt6b A T 15: 101,586,757 (GRCm39) F286Y probably damaging Het
Lrriq1 G A 10: 103,038,242 (GRCm39) R854C probably damaging Het
Mipol1 A T 12: 57,507,776 (GRCm39) probably benign Het
Mmp19 A G 10: 128,626,819 (GRCm39) probably benign Het
Msc T G 1: 14,825,473 (GRCm39) Y167S probably benign Het
Mycbp2 T G 14: 103,437,554 (GRCm39) K2103Q probably damaging Het
Myh11 C A 16: 14,023,421 (GRCm39) D1586Y probably damaging Het
Nol6 A T 4: 41,118,427 (GRCm39) D791E probably damaging Het
Pcm1 A G 8: 41,746,616 (GRCm39) T1272A probably benign Het
Phgdh A G 3: 98,247,105 (GRCm39) L15P probably damaging Het
Ptprk A T 10: 28,351,074 (GRCm39) probably benign Het
Ralgapa2 G T 2: 146,203,320 (GRCm39) D1091E possibly damaging Het
Rbbp8nl C A 2: 179,920,895 (GRCm39) K496N probably null Het
Rbm26 T C 14: 105,388,748 (GRCm39) probably benign Het
Rfx6 A C 10: 51,602,771 (GRCm39) probably benign Het
Rras G A 7: 44,667,488 (GRCm39) G17R probably damaging Het
Shisa6 G A 11: 66,108,459 (GRCm39) P473S probably damaging Het
Slc9a3 A G 13: 74,306,822 (GRCm39) K316E probably damaging Het
Slco1a7 C A 6: 141,711,503 (GRCm39) M69I probably benign Het
Spata31d1a A G 13: 59,849,807 (GRCm39) S774P possibly damaging Het
Spsb4 T C 9: 96,877,840 (GRCm39) Y161C probably damaging Het
Taf3 G T 2: 9,957,644 (GRCm39) N174K probably damaging Het
Tectb C G 19: 55,169,431 (GRCm39) probably benign Het
Ubox5 A T 2: 130,441,441 (GRCm39) C415* probably null Het
Ucn2 C T 9: 108,815,477 (GRCm39) P80S possibly damaging Het
Vmn2r10 G A 5: 109,143,961 (GRCm39) T663I probably damaging Het
Wdfy1 A T 1: 79,685,222 (GRCm39) F337L probably null Het
Zfp287 A T 11: 62,605,459 (GRCm39) C483S probably damaging Het
Zyg11b A G 4: 108,101,921 (GRCm39) probably null Het
Other mutations in Trnt1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00819:Trnt1 APN 6 106,753,183 (GRCm39) nonsense probably null
IGL00915:Trnt1 APN 6 106,756,387 (GRCm39) missense probably benign 0.00
IGL01821:Trnt1 APN 6 106,751,436 (GRCm39) missense probably damaging 1.00
IGL02102:Trnt1 APN 6 106,755,073 (GRCm39) critical splice donor site probably null
IGL02610:Trnt1 APN 6 106,755,779 (GRCm39) missense possibly damaging 0.88
IGL02933:Trnt1 APN 6 106,750,387 (GRCm39) missense probably benign 0.40
R0606:Trnt1 UTSW 6 106,754,869 (GRCm39) unclassified probably benign
R0844:Trnt1 UTSW 6 106,751,464 (GRCm39) missense probably damaging 1.00
R2144:Trnt1 UTSW 6 106,755,000 (GRCm39) missense probably damaging 1.00
R4994:Trnt1 UTSW 6 106,755,853 (GRCm39) nonsense probably null
R5294:Trnt1 UTSW 6 106,750,375 (GRCm39) missense probably damaging 1.00
R5742:Trnt1 UTSW 6 106,755,878 (GRCm39) nonsense probably null
R6855:Trnt1 UTSW 6 106,754,883 (GRCm39) missense probably damaging 1.00
R7491:Trnt1 UTSW 6 106,755,865 (GRCm39) missense probably benign
R7492:Trnt1 UTSW 6 106,751,493 (GRCm39) missense possibly damaging 0.76
R7880:Trnt1 UTSW 6 106,746,517 (GRCm39) critical splice donor site probably null
R8212:Trnt1 UTSW 6 106,746,832 (GRCm39) missense probably benign
R8863:Trnt1 UTSW 6 106,751,443 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CATACAAGATTGCTCAGTTCACTG -3'
(R):5'- GGCGGCATGGACATTTCTATTG -3'

Sequencing Primer
(F):5'- CAGTTCACTGACCTCTACTATCTG -3'
(R):5'- ACGGGACAAAAATGTTACACTTC -3'
Posted On 2014-12-04