Incidental Mutation 'R2091:Lcmt2'
ID 323543
Institutional Source Beutler Lab
Gene Symbol Lcmt2
Ensembl Gene ENSMUSG00000074890
Gene Name leucine carboxyl methyltransferase 2
Synonyms Tyw4
MMRRC Submission 040096-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.095) question?
Stock # R2091 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 120967773-120971179 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 120969097 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 662 (N662S)
Ref Sequence ENSEMBL: ENSMUSP00000106302 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028702] [ENSMUST00000066155] [ENSMUST00000099486] [ENSMUST00000110662] [ENSMUST00000110665] [ENSMUST00000110674] [ENSMUST00000119031]
AlphaFold Q8BYR1
Predicted Effect probably benign
Transcript: ENSMUST00000028702
SMART Domains Protein: ENSMUSP00000028702
Gene: ENSMUSG00000027259

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

DomainStartEndE-ValueType
Pfam:A_deaminase 16 343 1.6e-36 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000099486
SMART Domains Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890

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

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

DomainStartEndE-ValueType
Pfam:A_deaminase 2 236 4.3e-24 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000110674
AA Change: N662S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: N662S

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: ENSMUST00000156132
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130221
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146750
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147271
Predicted Effect noncoding transcript
Transcript: ENSMUST00000158384
Predicted Effect probably benign
Transcript: ENSMUST00000119031
SMART Domains Protein: ENSMUSP00000113052
Gene: ENSMUSG00000027259

DomainStartEndE-ValueType
Pfam:A_deaminase 16 343 3e-44 PFAM
Meta Mutation Damage Score 0.3353 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.5%
Validation Efficiency 96% (55/57)
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: 100 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921504E06Rik G C 2: 19,522,357 (GRCm39) N247K probably damaging Het
4930402F06Rik T C 2: 35,266,079 (GRCm39) K197R probably benign Het
AA986860 T C 1: 130,670,906 (GRCm39) L376P probably benign Het
Adamts10 T C 17: 33,770,166 (GRCm39) probably null Het
Adamts7 T C 9: 90,070,493 (GRCm39) probably null Het
Adgrl1 T C 8: 84,661,093 (GRCm39) I862T probably damaging Het
Agbl1 G A 7: 76,239,248 (GRCm39) V583M probably damaging Het
Apba2 T A 7: 64,345,341 (GRCm39) V177D probably benign Het
Arfgap2 A G 2: 91,100,586 (GRCm39) K297R probably benign Het
Armh3 A T 19: 45,941,119 (GRCm39) L300Q probably damaging Het
Atg14 A T 14: 47,780,352 (GRCm39) I474N probably damaging Het
Atp2b4 C A 1: 133,642,968 (GRCm39) V1046F probably benign Het
Best1 A G 19: 9,969,443 (GRCm39) V205A probably benign Het
Bicdl1 A G 5: 115,862,638 (GRCm39) S206P probably damaging Het
Bltp1 T C 3: 37,008,119 (GRCm39) V1725A probably damaging Het
Bltp1 C T 3: 37,042,405 (GRCm39) T2797I probably damaging Het
Cacna1h C T 17: 25,651,850 (GRCm39) C98Y possibly damaging Het
Calhm3 T A 19: 47,140,430 (GRCm39) D221V probably damaging Het
Ccdc93 T A 1: 121,411,071 (GRCm39) probably null Het
Cd248 A T 19: 5,120,074 (GRCm39) I641F possibly damaging Het
Chrnb3 C T 8: 27,884,262 (GRCm39) T333M probably damaging Het
Cyb5rl A G 4: 106,928,203 (GRCm39) H113R probably damaging Het
Dab1 C T 4: 104,588,948 (GRCm39) A524V probably benign Het
Ddx59 T A 1: 136,344,447 (GRCm39) D39E probably benign Het
Defa5 A G 8: 21,787,513 (GRCm39) D20G probably damaging Het
Dido1 A T 2: 180,303,677 (GRCm39) V1409E probably benign Het
Dlc1 A T 8: 37,404,763 (GRCm39) V342E probably benign Het
Dsc2 G A 18: 20,166,351 (GRCm39) T760I possibly damaging Het
Dync1h1 A G 12: 110,616,022 (GRCm39) I3057V probably benign Het
Etnk2 T G 1: 133,304,791 (GRCm39) probably null Het
Fbp2 G T 13: 63,006,021 (GRCm39) L31I probably damaging Het
Gbp7 A T 3: 142,240,383 (GRCm39) I34F probably damaging Het
Gcfc2 A G 6: 81,920,460 (GRCm39) E415G probably damaging Het
Glp1r T C 17: 31,144,523 (GRCm39) L232P probably damaging Het
Gm10822 A G 2: 73,729,619 (GRCm39) noncoding transcript Het
Gm42669 G A 5: 107,655,776 (GRCm39) V1192M probably benign Het
Gpr37 A G 6: 25,689,062 (GRCm39) S12P possibly damaging Het
Gpt A G 15: 76,582,176 (GRCm39) E211G possibly damaging Het
Grxcr1 T C 5: 68,267,755 (GRCm39) I168T probably damaging Het
Hat1 T C 2: 71,264,378 (GRCm39) V272A probably benign Het
Igkv8-30 A C 6: 70,094,070 (GRCm39) C114G probably damaging Het
Kcne4 T C 1: 78,795,624 (GRCm39) S91P probably benign Het
Kif5b G A 18: 6,213,248 (GRCm39) Q715* probably null Het
Lamb1 T A 12: 31,337,428 (GRCm39) N386K probably damaging Het
Lnx1 G T 5: 74,780,727 (GRCm39) H324N probably benign Het
Lrrc4 T G 6: 28,830,586 (GRCm39) D343A probably benign Het
Mars1 A G 10: 127,135,154 (GRCm39) S646P probably damaging Het
Mboat7 T C 7: 3,687,010 (GRCm39) probably benign Het
Mlip C T 9: 77,072,145 (GRCm39) V341I possibly damaging Het
Mterf1b A T 5: 4,247,057 (GRCm39) T233S possibly damaging Het
Myo3a A T 2: 22,338,488 (GRCm39) H442L probably damaging Het
Myrf A T 19: 10,201,964 (GRCm39) V171D possibly damaging Het
Nbas G A 12: 13,411,046 (GRCm39) D897N probably benign Het
Nfx1 T C 4: 40,977,004 (GRCm39) V226A probably benign Het
Nlrp4a T C 7: 26,149,578 (GRCm39) L395P probably damaging Het
Nrros C T 16: 31,962,975 (GRCm39) W311* probably null Het
Nsun6 A G 2: 15,044,542 (GRCm39) probably null Het
Ntrk2 A G 13: 59,007,115 (GRCm39) H239R possibly damaging Het
Or10g9 T C 9: 39,912,500 (GRCm39) T8A probably benign Het
Or4k51 A T 2: 111,584,731 (GRCm39) M46L probably benign Het
Or5aq7 T C 2: 86,938,606 (GRCm39) N42D probably damaging Het
Or5p70 A G 7: 107,995,068 (GRCm39) H247R probably damaging Het
Pate4 C A 9: 35,519,553 (GRCm39) A46S possibly damaging Het
Pcdhb18 T C 18: 37,623,653 (GRCm39) S328P probably damaging Het
Pdk4 A G 6: 5,494,857 (GRCm39) probably benign Het
Pigm T C 1: 172,205,100 (GRCm39) Y279H probably damaging Het
Plaat3 A G 19: 7,556,474 (GRCm39) I92V probably damaging Het
Plxdc2 A G 2: 16,718,494 (GRCm39) I379M probably damaging Het
Ppp1r35 A G 5: 137,778,156 (GRCm39) N217S possibly damaging Het
Prex1 G A 2: 166,411,285 (GRCm39) T1438I possibly damaging Het
Ptger4 T A 15: 5,272,326 (GRCm39) I98F possibly damaging Het
Rasl11a T A 5: 146,783,927 (GRCm39) I124N probably damaging Het
Rest A G 5: 77,429,126 (GRCm39) K515R possibly damaging Het
Ryr1 A G 7: 28,785,474 (GRCm39) L1746P probably damaging Het
Ryr2 G T 13: 11,960,863 (GRCm39) T25K probably benign Het
Sacs A T 14: 61,429,368 (GRCm39) I476L possibly damaging Het
Serpina3g A T 12: 104,205,417 (GRCm39) D52V probably damaging Het
Skint6 T C 4: 112,703,881 (GRCm39) N998S probably benign Het
Skp2 C A 15: 9,113,786 (GRCm39) G376C probably damaging Het
Slc10a4 G A 5: 73,174,482 (GRCm39) probably benign Het
Slc24a2 G T 4: 86,929,883 (GRCm39) P538T probably damaging Het
Sntg1 T A 1: 8,665,763 (GRCm39) T184S probably benign Het
Ssbp1 A G 6: 40,453,433 (GRCm39) Y73C probably null Het
St18 G A 1: 6,898,195 (GRCm39) V666M probably benign Het
Suclg1 A G 6: 73,241,259 (GRCm39) K193R probably benign Het
Tcp11l1 T C 2: 104,514,484 (GRCm39) I428V possibly damaging Het
Th T A 7: 142,449,280 (GRCm39) D275V probably damaging Het
Tnrc18 A C 5: 142,759,396 (GRCm39) S813R unknown Het
Tnrc6a T C 7: 122,771,343 (GRCm39) probably null Het
Trap1 A C 16: 3,863,903 (GRCm39) Y472* probably null Het
Trdv1 C A 14: 54,119,626 (GRCm39) Q96K probably benign Het
Trpm8 T C 1: 88,271,048 (GRCm39) I446T probably damaging Het
Tti2 T C 8: 31,644,294 (GRCm39) L297P probably damaging Het
Ttn C T 2: 76,565,355 (GRCm39) G26545R probably damaging Het
Ttn T C 2: 76,587,488 (GRCm39) D13208G probably damaging Het
Tubb3 A G 8: 124,148,417 (GRCm39) probably null Het
Umodl1 A G 17: 31,190,893 (GRCm39) M247V probably benign Het
Wrn T A 8: 33,757,853 (GRCm39) H812L probably benign Het
Zfp174 A G 16: 3,672,506 (GRCm39) R352G possibly damaging Het
Zfp955a T A 17: 33,461,731 (GRCm39) K134* probably null 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
R0519:Lcmt2 UTSW 2 120,969,825 (GRCm39) splice site probably null
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
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'- CTGCTCAATGGTGTGGTAAGGAAG -3'
(R):5'- AAGGTACTCTCACACGGCTC -3'

Sequencing Primer
(F):5'- TAAGGAAGAAAGGTGTGTGTGTTG -3'
(R):5'- CACGGCTCATGTGTTTAATGGAAAG -3'
Posted On 2015-06-24