Incidental Mutation 'R0699:Trmt2a'
ID 218766
Institutional Source Beutler Lab
Gene Symbol Trmt2a
Ensembl Gene ENSMUSG00000022721
Gene Name TRM2 tRNA methyltransferase 2A
Synonyms Htf9c
MMRRC Submission 038883-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0699 (G1)
Quality Score 53
Status Validated
Chromosome 16
Chromosomal Location 18066711-18072636 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 18067393 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 22 (V22A)
Ref Sequence ENSEMBL: ENSMUSP00000111304 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000009321] [ENSMUST00000052325] [ENSMUST00000100099] [ENSMUST00000115640] [ENSMUST00000115645] [ENSMUST00000140206] [ENSMUST00000128045] [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 benign
Transcript: ENSMUST00000100099
AA Change: V22A

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000111303
Gene: ENSMUSG00000022721
AA Change: V22A

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 probably benign
Transcript: ENSMUST00000115640
AA Change: V22A

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000111304
Gene: ENSMUSG00000022721
AA Change: V22A

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 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 noncoding transcript
Transcript: ENSMUST00000123073
Predicted Effect probably benign
Transcript: ENSMUST00000140206
AA Change: V22A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000121216
Gene: ENSMUSG00000022721
AA Change: V22A

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: ENSMUST00000131211
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127239
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147273
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153292
Predicted Effect noncoding transcript
Transcript: ENSMUST00000134035
Predicted Effect probably benign
Transcript: ENSMUST00000232293
Predicted Effect probably benign
Transcript: ENSMUST00000232144
Predicted Effect probably benign
Transcript: ENSMUST00000128045
Predicted Effect probably benign
Transcript: ENSMUST00000231509
Predicted Effect probably benign
Transcript: ENSMUST00000145112
SMART Domains Protein: ENSMUSP00000117026
Gene: ENSMUSG00000022721

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: ENSMUST00000232015
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232342
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 94.8%
Validation Efficiency 98% (120/123)
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: 95 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 G A 11: 9,538,508 (GRCm39) probably benign Het
Abcb6 C T 1: 75,148,553 (GRCm39) E89K probably damaging Het
Adam25 C A 8: 41,209,011 (GRCm39) T759K probably benign Het
Adgrf5 G A 17: 43,733,552 (GRCm39) probably null Het
Aimp1 A T 3: 132,380,626 (GRCm39) probably benign Het
Aldh3a2 C T 11: 61,153,148 (GRCm39) V193I probably benign Het
Ank2 C T 3: 126,723,478 (GRCm39) V950I probably benign Het
Aspn A G 13: 49,705,258 (GRCm39) D40G possibly damaging Het
C1rl A G 6: 124,485,595 (GRCm39) D322G probably benign Het
Car5a T C 8: 122,671,555 (GRCm39) probably benign Het
Cfap107 G T 4: 144,146,322 (GRCm39) N110K probably damaging Het
Cfap157 T A 2: 32,669,022 (GRCm39) K360N probably damaging Het
Cilp T A 9: 65,177,608 (GRCm39) F117Y probably damaging Het
Cntnap5c T G 17: 58,349,493 (GRCm39) W269G probably damaging Het
Col6a1 A G 10: 76,552,114 (GRCm39) V459A unknown Het
Commd3 A G 2: 18,679,786 (GRCm39) E165G possibly damaging Het
Cops3 A C 11: 59,717,148 (GRCm39) Y244D probably damaging Het
Cpne5 T A 17: 29,428,667 (GRCm39) K108N probably damaging Het
Cracdl T C 1: 37,651,411 (GRCm39) D1152G possibly damaging Het
Ddx41 A G 13: 55,679,112 (GRCm39) probably benign Het
Dnhd1 T C 7: 105,301,113 (GRCm39) Y157H probably damaging Het
Dpp8 A T 9: 64,962,176 (GRCm39) L405F probably benign Het
Dync2h1 G T 9: 7,103,680 (GRCm39) A365E probably benign Het
Dysf C T 6: 84,167,828 (GRCm39) R1757W probably benign Het
Eif1ad T A 19: 5,418,726 (GRCm39) V93D possibly damaging Het
Eif2ak3 T C 6: 70,869,514 (GRCm39) F734L probably benign Het
F8 T C X: 74,423,230 (GRCm39) probably benign Het
Fbxl14 T C 6: 119,457,715 (GRCm39) Y299H probably benign Het
Fmo1 T C 1: 162,661,341 (GRCm39) N314S probably benign Het
Fnip2 T C 3: 79,388,446 (GRCm39) T762A probably benign Het
Gfra1 A C 19: 58,258,555 (GRCm39) S271A probably benign Het
Gm9932 T C 5: 100,346,931 (GRCm39) V43A probably damaging Het
Herc6 T C 6: 57,558,092 (GRCm39) L24P probably damaging Het
Hmcn1 T C 1: 150,695,161 (GRCm39) T248A probably damaging Het
Hook1 T A 4: 95,884,077 (GRCm39) probably benign Het
Ifne T C 4: 88,798,014 (GRCm39) S135G probably benign Het
Igkv13-84 G A 6: 68,916,635 (GRCm39) probably benign Het
Itm2b T A 14: 73,602,065 (GRCm39) N211I probably damaging Het
Kcnh5 A T 12: 75,023,305 (GRCm39) C588S possibly damaging Het
Kif13a A T 13: 46,952,689 (GRCm39) W699R possibly damaging Het
Kmt2e T C 5: 23,678,581 (GRCm39) V220A probably benign Het
Macrod2 T C 2: 140,260,836 (GRCm39) probably null Het
Map3k6 A G 4: 132,975,437 (GRCm39) E724G probably damaging Het
Mgam T C 6: 40,619,953 (GRCm39) L14P possibly damaging Het
Morc1 T A 16: 48,412,977 (GRCm39) M706K probably benign Het
Muc2 T C 7: 141,306,037 (GRCm39) V242A probably damaging Het
Mx2 T A 16: 97,345,753 (GRCm39) V57E probably damaging Het
Myh14 C A 7: 44,274,395 (GRCm39) A1339S possibly damaging Het
Myom1 G T 17: 71,374,308 (GRCm39) S595I probably damaging Het
Nav1 T A 1: 135,380,687 (GRCm39) M1471L probably benign Het
Ncapd2 A C 6: 125,146,843 (GRCm39) S1248A probably benign Het
Ncbp1 T C 4: 46,147,528 (GRCm39) V125A probably benign Het
Ncor2 A T 5: 125,106,176 (GRCm39) probably benign Het
Nobox T A 6: 43,284,144 (GRCm39) Q134L probably benign Het
Npc1 T C 18: 12,343,632 (GRCm39) T454A probably benign Het
Ntng1 G T 3: 109,779,611 (GRCm39) T322K probably damaging Het
Olfm5 T C 7: 103,803,326 (GRCm39) E379G probably damaging Het
Oma1 T C 4: 103,210,792 (GRCm39) S433P probably damaging Het
Or1ad6 T C 11: 50,860,645 (GRCm39) S267P probably damaging Het
Or1b1 T C 2: 36,995,074 (GRCm39) D196G possibly damaging Het
Or4c105 A T 2: 88,647,568 (GRCm39) N18Y probably damaging Het
Or4c107 C T 2: 88,788,960 (GRCm39) T50I probably benign Het
Or4c113 C T 2: 88,885,636 (GRCm39) V45M possibly damaging Het
Parp14 G A 16: 35,680,955 (GRCm39) T226M probably damaging Het
Parp8 A T 13: 117,059,120 (GRCm39) H168Q probably benign Het
Pik3cg G A 12: 32,247,341 (GRCm39) probably benign Het
Pla2g3 T C 11: 3,442,000 (GRCm39) F388S probably damaging Het
Plaat3 T A 19: 7,535,366 (GRCm39) probably null Het
Pllp T C 8: 95,422,660 (GRCm39) probably null Het
Ppfibp1 T A 6: 146,927,720 (GRCm39) V778E probably damaging Het
Prkci T C 3: 31,104,422 (GRCm39) V595A possibly damaging Het
Prune2 T A 19: 17,101,319 (GRCm39) D2274E probably damaging Het
Rad51ap2 A T 12: 11,507,601 (GRCm39) T508S probably benign Het
Ranbp3l T C 15: 9,058,850 (GRCm39) probably null Het
Rfc1 A C 5: 65,476,742 (GRCm39) probably null Het
Rin3 G A 12: 102,335,834 (GRCm39) V502I probably damaging Het
Rtn4rl1 A T 11: 75,156,048 (GRCm39) H160L possibly damaging Het
Rtn4rl1 A T 11: 75,156,050 (GRCm39) I161F probably benign Het
Serpinb9b A T 13: 33,217,549 (GRCm39) M116L probably benign Het
Sgo2a C T 1: 58,037,308 (GRCm39) R18* probably null Het
Sh3gl2 T A 4: 85,265,408 (GRCm39) D31E probably benign Het
Slc38a9 T C 13: 112,859,823 (GRCm39) L419S probably damaging Het
Sp8 AGCGGCGGCGGCGGCGG AGCGGCGGCGGCGG 12: 118,812,555 (GRCm39) probably benign Het
Spen G T 4: 141,201,702 (GRCm39) N2308K possibly damaging Het
Stac2 A G 11: 97,933,611 (GRCm39) I156T possibly damaging Het
Stambp A G 6: 83,533,303 (GRCm39) F320S probably damaging Het
Tas2r117 A T 6: 132,780,161 (GRCm39) N100Y probably damaging Het
Tigd3 A T 19: 5,941,974 (GRCm39) S385R probably benign Het
Tmem30c T C 16: 57,097,152 (GRCm39) D136G possibly damaging Het
Tnfrsf21 C T 17: 43,349,104 (GRCm39) H239Y probably benign Het
Tnrc6c A G 11: 117,613,447 (GRCm39) Q535R probably benign Het
Tut7 G A 13: 59,929,828 (GRCm39) probably benign Het
Wipf3 A C 6: 54,460,817 (GRCm39) K88N probably damaging Het
Zfp974 T C 7: 27,611,416 (GRCm39) E103G possibly damaging Het
Zscan10 C T 17: 23,827,092 (GRCm39) T135I probably damaging 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
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
R5452:Trmt2a UTSW 16 18,068,814 (GRCm39) missense probably damaging 1.00
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'- AAAGAACGGGTTTCTCCAGGGC -3'
(R):5'- CGGAATGTTACAAAGGCACATGGTG -3'

Sequencing Primer
(F):5'- TTTCTCCAGGGCTTCGTG -3'
(R):5'- TTTGTGGGACTGTAGACCAAAAC -3'
Posted On 2014-08-20