Incidental Mutation 'R5452:Trmt2a'
ID 432601
Institutional Source Beutler Lab
Gene Symbol Trmt2a
Ensembl Gene ENSMUSG00000022721
Gene Name TRM2 tRNA methyltransferase 2A
Synonyms Htf9c
MMRRC Submission 042848-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5452 (G1)
Quality Score 225
Status Not validated
Chromosome 16
Chromosomal Location 18066711-18072636 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 18068814 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 270 (H270R)
Ref Sequence ENSEMBL: ENSMUSP00000111303 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000009321] [ENSMUST00000052325] [ENSMUST00000100099] [ENSMUST00000115633] [ENSMUST00000115640] [ENSMUST00000140206] [ENSMUST00000128045] [ENSMUST00000115645] [ENSMUST00000231509]
AlphaFold Q8BNV1
Predicted Effect probably benign
Transcript: ENSMUST00000009321
SMART Domains Protein: ENSMUSP00000009321
Gene: ENSMUSG00000022718

DomainStartEndE-ValueType
low complexity region 165 176 N/A INTRINSIC
WW 302 334 7.26e-6 SMART
low complexity region 411 421 N/A INTRINSIC
DSRM 512 577 5.68e-10 SMART
DSRM 620 685 8.26e-1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000052325
SMART Domains Protein: ENSMUSP00000055288
Gene: ENSMUSG00000005732

DomainStartEndE-ValueType
RanBD 1 108 4.92e-46 SMART
coiled coil region 123 153 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000059696
Predicted Effect probably damaging
Transcript: ENSMUST00000100099
AA Change: H270R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: H270R

DomainStartEndE-ValueType
low complexity region 35 44 N/A INTRINSIC
RRM 64 132 1.37e-2 SMART
coiled coil region 171 195 N/A INTRINSIC
Pfam:tRNA_U5-meth_tr 380 579 1.2e-20 PFAM
Pfam:PCMT 386 482 1.1e-8 PFAM
Pfam:MTS 389 489 6.2e-9 PFAM
Pfam:Methyltransf_4 397 497 4.2e-7 PFAM
Pfam:Methyltransf_31 420 546 6.2e-15 PFAM
Pfam:Methyltransf_18 422 523 9.3e-11 PFAM
Pfam:Methyltransf_26 423 538 5.3e-12 PFAM
Pfam:Methyltransf_25 426 511 3.5e-8 PFAM
Pfam:Methyltransf_11 427 487 5.6e-6 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000115633
SMART Domains Protein: ENSMUSP00000111296
Gene: ENSMUSG00000022718

DomainStartEndE-ValueType
low complexity region 165 176 N/A INTRINSIC
WW 302 334 7.26e-6 SMART
low complexity region 411 421 N/A INTRINSIC
DSRM 512 577 5.68e-10 SMART
DSRM 620 685 8.26e-1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000115640
AA Change: H270R

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: H270R

DomainStartEndE-ValueType
low complexity region 35 44 N/A INTRINSIC
RRM 64 132 1.37e-2 SMART
coiled coil region 171 195 N/A INTRINSIC
Pfam:tRNA_U5-meth_tr 380 579 2.6e-20 PFAM
Pfam:PCMT 386 482 3.4e-9 PFAM
Pfam:MTS 392 489 1e-7 PFAM
Pfam:Cons_hypoth95 405 542 2.7e-7 PFAM
Pfam:Methyltransf_31 420 547 2.1e-15 PFAM
Pfam:Methyltransf_18 422 526 2.9e-12 PFAM
Pfam:Methyltransf_4 423 499 2.6e-7 PFAM
Pfam:Methyltransf_25 426 511 1.3e-8 PFAM
Pfam:Methyltransf_11 427 489 3.6e-8 PFAM
Predicted Effect
SMART Domains Protein: ENSMUSP00000117026
Gene: ENSMUSG00000022721
AA Change: H84R

DomainStartEndE-ValueType
Pfam:PCMT 118 220 4.2e-7 PFAM
Pfam:tRNA_U5-meth_tr 118 280 4e-16 PFAM
Pfam:MTS 129 229 5.4e-6 PFAM
Pfam:Cons_hypoth95 143 277 6.5e-5 PFAM
Pfam:PrmA 146 234 2e-4 PFAM
Pfam:Ubie_methyltran 148 223 1e-4 PFAM
Pfam:Methyltransf_31 158 271 6.1e-14 PFAM
Pfam:Methyltransf_18 160 263 8.3e-11 PFAM
Pfam:Methyltransf_4 161 237 7.1e-5 PFAM
Pfam:Methyltransf_26 161 274 2e-6 PFAM
Pfam:Methyltransf_25 164 251 5.2e-7 PFAM
Pfam:Methyltransf_11 165 227 9.4e-7 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127239
Predicted Effect
SMART Domains Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: H270R

DomainStartEndE-ValueType
low complexity region 35 44 N/A INTRINSIC
RRM 64 132 1.37e-2 SMART
coiled coil region 171 195 N/A INTRINSIC
Pfam:tRNA_U5-meth_tr 383 481 3.7e-8 PFAM
Pfam:PCMT 386 481 1.5e-6 PFAM
Pfam:MTS 389 493 2.5e-7 PFAM
Pfam:Methyltransf_31 420 491 1.5e-9 PFAM
Pfam:Methyltransf_18 422 508 4.1e-8 PFAM
Pfam:Methyltransf_26 423 523 3.1e-9 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147273
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153292
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152033
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144536
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131211
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134035
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123073
Predicted Effect probably benign
Transcript: ENSMUST00000128045
Predicted Effect probably benign
Transcript: ENSMUST00000115645
SMART Domains Protein: ENSMUSP00000111309
Gene: ENSMUSG00000005732

DomainStartEndE-ValueType
RanBD 27 158 3.33e-75 SMART
low complexity region 183 202 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000232144
Predicted Effect probably benign
Transcript: ENSMUST00000232293
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232015
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232342
Predicted Effect probably benign
Transcript: ENSMUST00000231509
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.2%
  • 20x: 95.1%
Validation Efficiency
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 of unknown function. However, it is orthologous to the mouse Trmt2a gene and contains an RNA methyltransferase domain. Expression of this gene varies during the cell cycle, with aberrant expression being a possible biomarker in certain breast cancers. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam20 A T 8: 41,248,801 (GRCm39) I304F probably damaging Het
Adamts5 A G 16: 85,666,800 (GRCm39) probably benign Het
Akr1c6 A G 13: 4,504,544 (GRCm39) R132G probably benign Het
Ash1l T A 3: 88,892,183 (GRCm39) M1354K possibly damaging Het
C6 T C 15: 4,844,311 (GRCm39) I911T possibly damaging Het
Calm2 T C 17: 87,743,150 (GRCm39) probably null Het
Ccdc80 G A 16: 44,938,528 (GRCm39) R745Q probably damaging Het
Celsr3 T C 9: 108,721,233 (GRCm39) I2685T possibly damaging Het
Chkb T C 15: 89,313,788 (GRCm39) probably benign Het
Dennd5b T A 6: 148,943,011 (GRCm39) probably null Het
Dnah2 T C 11: 69,415,209 (GRCm39) Y175C probably damaging Het
Dnajc13 A G 9: 104,069,313 (GRCm39) S1154P probably benign Het
Ephb4 T C 5: 137,359,404 (GRCm39) S325P probably damaging Het
Fzd9 C T 5: 135,279,714 (GRCm39) R57H probably damaging Het
Gemin6 T G 17: 80,535,178 (GRCm39) V46G probably damaging Het
Gm9949 A G 18: 62,313,587 (GRCm39) probably benign Het
Gnb4 A T 3: 32,643,994 (GRCm39) M188K probably benign Het
Hr G T 14: 70,794,067 (GRCm39) G109V probably damaging Het
Lrp1b A G 2: 40,812,328 (GRCm39) S2426P probably damaging Het
Map2k4 A G 11: 65,610,413 (GRCm39) W88R probably damaging Het
Map4 C T 9: 109,866,851 (GRCm39) probably benign Het
Moxd2 C T 6: 40,859,048 (GRCm39) probably null Het
Mrgprx1 T C 7: 47,671,556 (GRCm39) I64V probably benign Het
Mtrex T C 13: 113,049,715 (GRCm39) S232G probably null Het
Or5p68 A C 7: 107,945,312 (GRCm39) I292S probably damaging Het
Padi2 T C 4: 140,659,382 (GRCm39) F229S probably benign Het
Pappa2 T C 1: 158,666,172 (GRCm39) N1136S probably benign Het
Pcdhb1 A T 18: 37,398,811 (GRCm39) N254I possibly damaging Het
Plcb2 A G 2: 118,548,727 (GRCm39) Y400H probably damaging Het
Plce1 A C 19: 38,608,926 (GRCm39) T412P probably benign Het
Prg4 T C 1: 150,331,519 (GRCm39) probably benign Het
Prkdc A G 16: 15,586,501 (GRCm39) N2510S possibly damaging Het
Psme4 T A 11: 30,741,168 (GRCm39) S107T probably benign Het
Resf1 C A 6: 149,230,611 (GRCm39) S1219* probably null Het
Rint1 G T 5: 23,999,363 (GRCm39) A51S probably benign Het
Rsad1 T A 11: 94,434,515 (GRCm39) R306S probably damaging Het
Sema3c T G 5: 17,922,068 (GRCm39) probably null Het
Sirt3 G A 7: 140,444,928 (GRCm39) T290I probably damaging Het
Spam1 G A 6: 24,800,731 (GRCm39) G490D probably benign Het
Speer4f2 C T 5: 17,581,498 (GRCm39) R147W possibly damaging Het
Sppl2c A T 11: 104,078,126 (GRCm39) I309L probably benign Het
Srxn1 G A 2: 151,947,799 (GRCm39) V66M probably damaging Het
St3gal4 C T 9: 34,964,752 (GRCm39) R152H probably damaging Het
Sv2c A T 13: 96,114,591 (GRCm39) F532I probably damaging Het
Tacc1 C A 8: 25,654,431 (GRCm39) K705N probably null Het
Tekt3 G T 11: 62,985,619 (GRCm39) S475I probably damaging Het
Tjap1 T C 17: 46,571,101 (GRCm39) T139A probably damaging Het
Tnfrsf8 T A 4: 145,019,214 (GRCm39) K207M possibly damaging Het
Tnn T C 1: 159,937,831 (GRCm39) T965A probably benign Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Ttc21a T C 9: 119,780,037 (GRCm39) L448P probably benign Het
Ttll4 C A 1: 74,718,480 (GRCm39) N110K probably benign Het
Ttn T A 2: 76,585,168 (GRCm39) I22042F probably damaging Het
Tut7 A G 13: 59,948,471 (GRCm39) Y215H probably damaging Het
Ubr1 A G 2: 120,698,783 (GRCm39) Y1595H possibly damaging Het
Unc45a G A 7: 79,978,787 (GRCm39) P621S probably damaging Het
Xrn2 A T 2: 146,866,633 (GRCm39) probably null Het
Other mutations in Trmt2a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00088:Trmt2a APN 16 18,067,351 (GRCm39) missense probably benign
R0050:Trmt2a UTSW 16 18,068,707 (GRCm39) missense probably damaging 1.00
R0050:Trmt2a UTSW 16 18,068,707 (GRCm39) missense probably damaging 1.00
R0377:Trmt2a UTSW 16 18,067,567 (GRCm39) missense possibly damaging 0.68
R0699:Trmt2a UTSW 16 18,067,393 (GRCm39) missense probably benign 0.01
R1034:Trmt2a UTSW 16 18,067,573 (GRCm39) missense probably damaging 1.00
R1114:Trmt2a UTSW 16 18,068,304 (GRCm39) unclassified probably benign
R1882:Trmt2a UTSW 16 18,067,758 (GRCm39) missense possibly damaging 0.88
R1911:Trmt2a UTSW 16 18,069,070 (GRCm39) missense probably benign 0.01
R2184:Trmt2a UTSW 16 18,070,859 (GRCm39) missense probably benign 0.06
R3853:Trmt2a UTSW 16 18,069,055 (GRCm39) missense possibly damaging 0.94
R4427:Trmt2a UTSW 16 18,067,093 (GRCm39) unclassified probably benign
R4737:Trmt2a UTSW 16 18,069,150 (GRCm39) unclassified probably benign
R4896:Trmt2a UTSW 16 18,070,793 (GRCm39) missense probably damaging 0.99
R4903:Trmt2a UTSW 16 18,067,418 (GRCm39) nonsense probably null
R4964:Trmt2a UTSW 16 18,067,418 (GRCm39) nonsense probably null
R4966:Trmt2a UTSW 16 18,067,418 (GRCm39) nonsense probably null
R5216:Trmt2a UTSW 16 18,070,048 (GRCm39) missense probably benign 0.22
R5837:Trmt2a UTSW 16 18,067,326 (GRCm39) unclassified probably benign
R6555:Trmt2a UTSW 16 18,071,067 (GRCm39) missense probably benign 0.03
R6670:Trmt2a UTSW 16 18,068,341 (GRCm39) missense possibly damaging 0.57
R7064:Trmt2a UTSW 16 18,070,868 (GRCm39) missense probably damaging 0.99
R7718:Trmt2a UTSW 16 18,068,487 (GRCm39) missense probably benign 0.16
R8302:Trmt2a UTSW 16 18,067,813 (GRCm39) missense probably damaging 1.00
R8463:Trmt2a UTSW 16 18,069,039 (GRCm39) missense probably damaging 1.00
R9120:Trmt2a UTSW 16 18,067,722 (GRCm39) missense probably damaging 1.00
R9186:Trmt2a UTSW 16 18,069,033 (GRCm39) missense probably benign 0.00
R9487:Trmt2a UTSW 16 18,068,814 (GRCm39) missense probably damaging 1.00
R9710:Trmt2a UTSW 16 18,070,041 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- GTGCTGGGTAATCAAGGTTGAGATC -3'
(R):5'- TGCCGAGTATGGTGTGGAAC -3'

Sequencing Primer
(F):5'- GGTAATCAAGGTTGAGATCTGACTC -3'
(R):5'- CAAATATACTCAGTGTGTGCCC -3'
Posted On 2016-10-06