Incidental Mutation 'R0519:Lcmt2'
ID 48369
Institutional Source Beutler Lab
Gene Symbol Lcmt2
Ensembl Gene ENSMUSG00000074890
Gene Name leucine carboxyl methyltransferase 2
Synonyms Tyw4
MMRRC Submission 038712-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.095) question?
Stock # R0519 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 120967773-120971179 bp(-) (GRCm39)
Type of Mutation splice site
DNA Base Change (assembly) A to T at 120969825 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000113052 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028702] [ENSMUST00000066155] [ENSMUST00000099486] [ENSMUST00000110662] [ENSMUST00000110665] [ENSMUST00000110674] [ENSMUST00000119031]
AlphaFold Q8BYR1
Predicted Effect probably null
Transcript: ENSMUST00000028702
SMART Domains Protein: ENSMUSP00000028702
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 1 276 1.8e-37 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000066155
SMART Domains Protein: ENSMUSP00000067133
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 16 343 1.6e-36 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000099486
AA Change: Y199*
SMART Domains Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: Y199*

DomainStartEndE-ValueType
PDB:3P71|T 4 94 6e-12 PDB
SCOP:d1k3ia3 137 401 2e-15 SMART
Predicted Effect probably null
Transcript: ENSMUST00000110662
SMART Domains Protein: ENSMUSP00000106290
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 2 200 1.1e-28 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000110665
SMART Domains Protein: ENSMUSP00000106293
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 2 236 4.3e-24 PFAM
Predicted Effect probably null
Transcript: ENSMUST00000110674
AA Change: Y419*
SMART Domains Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: Y419*

DomainStartEndE-ValueType
Pfam:LCM 12 207 5.4e-28 PFAM
Pfam:Kelch_3 492 542 2.2e-6 PFAM
low complexity region 544 563 N/A INTRINSIC
low complexity region 647 661 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146750
Predicted Effect noncoding transcript
Transcript: ENSMUST00000158384
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156132
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147271
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130221
Predicted Effect probably null
Transcript: ENSMUST00000119031
SMART Domains Protein: ENSMUSP00000113052
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 16 343 3e-44 PFAM
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.8%
  • 10x: 96.6%
  • 20x: 93.2%
Validation Efficiency 99% (74/75)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700028K03Rik A G 5: 107,696,067 (GRCm39) R168G probably benign Het
2810004N23Rik C T 8: 125,566,668 (GRCm39) G251R possibly damaging Het
3425401B19Rik A G 14: 32,384,919 (GRCm39) S349P possibly damaging Het
Ackr4 A G 9: 103,976,650 (GRCm39) V99A probably benign Het
Acsbg3 T A 17: 57,192,169 (GRCm39) Y577* probably null Het
Asxl3 A G 18: 22,656,577 (GRCm39) Q1529R possibly damaging Het
Atg12 T C 18: 46,874,477 (GRCm39) E46G probably benign Het
Cdcp2 A G 4: 106,964,389 (GRCm39) probably benign Het
Clasrp A G 7: 19,318,089 (GRCm39) probably benign Het
Clip2 A G 5: 134,545,005 (GRCm39) V383A probably benign Het
Cntln C T 4: 84,923,290 (GRCm39) probably benign Het
Colgalt2 G T 1: 152,384,312 (GRCm39) A551S possibly damaging Het
Csmd2 A C 4: 128,380,798 (GRCm39) Y2118S possibly damaging Het
Dip2c T A 13: 9,613,244 (GRCm39) V415E probably damaging Het
Dpy19l2 C T 9: 24,469,391 (GRCm39) R755Q probably benign Het
Dsn1 A T 2: 156,840,633 (GRCm39) probably benign Het
Dtd2 T C 12: 52,051,742 (GRCm39) probably benign Het
Dync1i1 A G 6: 6,027,399 (GRCm39) T602A probably benign Het
Ercc6 A C 14: 32,248,799 (GRCm39) D450A probably damaging Het
Fgf12 A T 16: 28,008,380 (GRCm39) V104D probably benign Het
Frem1 A T 4: 82,888,870 (GRCm39) probably null Het
Gcgr G T 11: 120,426,982 (GRCm39) W88L probably damaging Het
Glb1 ACCC ACC 9: 114,250,812 (GRCm39) probably null Het
Hapln1 A G 13: 89,732,835 (GRCm39) probably benign Het
Hmgn3 T C 9: 82,994,301 (GRCm39) E40G probably damaging Het
Hsdl1 G A 8: 120,292,450 (GRCm39) A255V probably damaging Het
Hyls1 T C 9: 35,472,499 (GRCm39) K306E probably damaging Het
Jcad C T 18: 4,649,122 (GRCm39) probably benign Het
Kif14 C A 1: 136,396,885 (GRCm39) A397E probably damaging Het
Lifr T C 15: 7,207,061 (GRCm39) L524P probably damaging Het
Ly6g6f T C 17: 35,301,828 (GRCm39) K209E possibly damaging Het
Macf1 G A 4: 123,365,113 (GRCm39) T1651I probably benign Het
Mapk4 T C 18: 74,103,392 (GRCm39) D39G probably damaging Het
Mbl1 A G 14: 40,880,522 (GRCm39) M137V probably damaging Het
Mcm10 G A 2: 5,013,356 (GRCm39) S92L probably benign Het
Mug1 A G 6: 121,828,383 (GRCm39) K265R possibly damaging Het
Mxra7 A G 11: 116,701,612 (GRCm39) probably null Het
Neu3 G A 7: 99,472,524 (GRCm39) probably benign Het
Nsd1 A G 13: 55,460,648 (GRCm39) T2395A probably benign Het
Or1j1 T A 2: 36,702,627 (GRCm39) H159L probably damaging Het
Or5m9 A T 2: 85,877,411 (GRCm39) Y195F probably benign Het
Or6s1 T A 14: 51,308,614 (GRCm39) I79F probably damaging Het
Or7g34 A T 9: 19,478,245 (GRCm39) I145N probably benign Het
Osgepl1 T C 1: 53,360,255 (GRCm39) V327A probably damaging Het
Pcdhb21 T C 18: 37,649,085 (GRCm39) V738A possibly damaging Het
Plekha8 A T 6: 54,599,092 (GRCm39) probably benign Het
Ptprq A C 10: 107,374,781 (GRCm39) probably benign Het
Pus10 T A 11: 23,661,201 (GRCm39) F263Y probably benign Het
Rad54b A T 4: 11,599,809 (GRCm39) I338F probably damaging Het
Rad54l2 A G 9: 106,585,498 (GRCm39) F756L probably damaging Het
Scn11a A G 9: 119,619,185 (GRCm39) L719P probably damaging Het
Slc2a2 G A 3: 28,772,965 (GRCm39) V253I possibly damaging Het
Slc39a4 A T 15: 76,499,338 (GRCm39) N192K probably benign Het
Soat1 T A 1: 156,268,816 (GRCm39) I245F probably damaging Het
Sorcs2 G A 5: 36,188,534 (GRCm39) A858V probably benign Het
Tcim T C 8: 24,928,651 (GRCm39) T88A possibly damaging Het
Tecta G A 9: 42,259,188 (GRCm39) probably benign Het
Tgm5 C A 2: 120,879,376 (GRCm39) L553F probably damaging Het
Tjp1 A G 7: 64,952,669 (GRCm39) V1555A probably benign Het
Tmem214 A C 5: 31,027,012 (GRCm39) M1L probably null Het
Togaram1 T C 12: 65,012,776 (GRCm39) probably benign Het
Topaz1 C A 9: 122,578,544 (GRCm39) L485I possibly damaging Het
Ttn T C 2: 76,548,626 (GRCm39) probably benign Het
Ube2o A G 11: 116,437,285 (GRCm39) probably null Het
Ubr7 T A 12: 102,734,465 (GRCm39) D246E probably benign Het
Vcpkmt T C 12: 69,629,102 (GRCm39) D132G probably benign Het
Vmn2r111 T A 17: 22,792,102 (GRCm39) Q51H probably benign Het
Vmn2r95 C T 17: 18,659,765 (GRCm39) P170S probably damaging Het
Zbtb38 A G 9: 96,567,826 (GRCm39) I1086T probably damaging Het
Zfp444 G A 7: 6,191,172 (GRCm39) A118T probably benign Het
Zp2 A G 7: 119,737,372 (GRCm39) I272T probably damaging Het
Other mutations in Lcmt2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02142:Lcmt2 APN 2 120,969,394 (GRCm39) missense possibly damaging 0.94
R0352:Lcmt2 UTSW 2 120,969,377 (GRCm39) missense probably benign 0.06
R0685:Lcmt2 UTSW 2 120,969,721 (GRCm39) missense probably benign 0.14
R1437:Lcmt2 UTSW 2 120,969,377 (GRCm39) missense probably benign 0.06
R1500:Lcmt2 UTSW 2 120,970,488 (GRCm39) missense probably benign 0.00
R1569:Lcmt2 UTSW 2 120,970,309 (GRCm39) missense probably damaging 1.00
R1612:Lcmt2 UTSW 2 120,969,601 (GRCm39) missense probably damaging 1.00
R1618:Lcmt2 UTSW 2 120,969,133 (GRCm39) missense probably damaging 0.98
R1990:Lcmt2 UTSW 2 120,970,762 (GRCm39) missense probably benign 0.07
R2091:Lcmt2 UTSW 2 120,969,097 (GRCm39) missense probably damaging 1.00
R2159:Lcmt2 UTSW 2 120,969,766 (GRCm39) missense probably damaging 1.00
R3812:Lcmt2 UTSW 2 120,969,187 (GRCm39) missense probably benign 0.01
R4725:Lcmt2 UTSW 2 120,969,911 (GRCm39) missense probably benign 0.00
R4727:Lcmt2 UTSW 2 120,969,911 (GRCm39) missense probably benign 0.00
R4968:Lcmt2 UTSW 2 120,970,217 (GRCm39) missense probably benign 0.00
R5626:Lcmt2 UTSW 2 120,969,943 (GRCm39) missense probably benign
R6246:Lcmt2 UTSW 2 120,970,870 (GRCm39) missense probably damaging 1.00
R6326:Lcmt2 UTSW 2 120,969,938 (GRCm39) nonsense probably null
R6524:Lcmt2 UTSW 2 120,969,412 (GRCm39) missense possibly damaging 0.75
R6924:Lcmt2 UTSW 2 120,970,484 (GRCm39) missense probably benign
R7282:Lcmt2 UTSW 2 120,969,271 (GRCm39) missense probably damaging 1.00
R7405:Lcmt2 UTSW 2 120,969,868 (GRCm39) missense probably benign 0.07
R7408:Lcmt2 UTSW 2 120,969,185 (GRCm39) missense probably benign 0.08
R8062:Lcmt2 UTSW 2 120,970,753 (GRCm39) missense possibly damaging 0.89
R8472:Lcmt2 UTSW 2 120,970,729 (GRCm39) missense probably damaging 1.00
R9414:Lcmt2 UTSW 2 120,970,621 (GRCm39) missense possibly damaging 0.81
R9569:Lcmt2 UTSW 2 120,970,522 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACTTCCGTTGTTGAATGCCGCC -3'
(R):5'- AGCACTCAAGCCTGAAGCGATATG -3'

Sequencing Primer
(F):5'- TTGAATGCCGCCAACATGAC -3'
(R):5'- AGCCCTGGCGTTATTTTCAG -3'
Posted On 2013-06-12