Incidental Mutation 'IGL02142:Lcmt2'
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Lcmt2
Ensembl Gene ENSMUSG00000074890
Gene Nameleucine carboxyl methyltransferase 2
Accession Numbers
Is this an essential gene? Probably non essential (E-score: 0.080) question?
Stock #IGL02142
Quality Score
Chromosomal Location121128307-121140653 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 121138913 bp
Amino Acid Change Leucine to Proline at position 343 (L343P)
Ref Sequence ENSEMBL: ENSMUSP00000097085 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028702] [ENSMUST00000066155] [ENSMUST00000099486] [ENSMUST00000110662] [ENSMUST00000110665] [ENSMUST00000110674] [ENSMUST00000119031]
Predicted Effect probably benign
Transcript: ENSMUST00000028702
SMART Domains Protein: ENSMUSP00000028702
Gene: ENSMUSG00000027259

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

Pfam:A_deaminase 16 343 1.6e-36 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000099486
AA Change: L343P

PolyPhen 2 Score 0.945 (Sensitivity: 0.80; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: L343P

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

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

Pfam:A_deaminase 2 236 4.3e-24 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000110674
AA Change: L563P

PolyPhen 2 Score 0.909 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: L563P

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 probably benign
Transcript: ENSMUST00000119031
SMART Domains Protein: ENSMUSP00000113052
Gene: ENSMUSG00000027259

Pfam:A_deaminase 16 343 3e-44 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130221
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146750
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147271
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156132
Predicted Effect noncoding transcript
Transcript: ENSMUST00000158384
Coding Region Coverage
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 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: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017D01Rik G A 19: 11,110,331 Q79* probably null Het
Abca4 T C 3: 122,169,926 S2060P probably benign Het
Abcg4 A G 9: 44,277,717 F426S probably benign Het
Actn1 C T 12: 80,176,155 probably null Het
Adgrd1 T A 5: 129,131,584 H251Q probably benign Het
Adgrg3 C T 8: 95,039,855 P385S probably damaging Het
Ampd2 G T 3: 108,080,344 probably benign Het
Arhgap42 A G 9: 9,155,359 S86P probably damaging Het
Armc4 C A 18: 7,214,601 W733C probably damaging Het
Art5 C T 7: 102,097,916 E121K probably null Het
Atad5 G A 11: 80,094,197 E37K probably benign Het
Atp13a5 A G 16: 29,234,563 V1084A probably benign Het
Cfap44 T C 16: 44,421,144 I626T probably benign Het
Col16a1 T A 4: 130,051,647 probably null Het
Defa22 T G 8: 21,163,114 C81G possibly damaging Het
Dnm2 A G 9: 21,500,353 Y622C probably damaging Het
Efna5 T A 17: 62,607,345 L201F unknown Het
Elac1 T C 18: 73,738,920 R335G probably benign Het
Enpp5 T C 17: 44,085,577 V460A probably benign Het
Esr2 A G 12: 76,123,195 V453A probably benign Het
Fam210b T A 2: 172,352,577 probably benign Het
Fcgr1 T C 3: 96,284,577 Y305C probably benign Het
Fcrlb A G 1: 170,908,679 V176A probably damaging Het
Gabrq T A X: 72,836,177 V256E possibly damaging Het
Gba T C 3: 89,205,841 L193P probably damaging Het
Gm10717 C T 9: 3,025,616 S67L probably benign Het
Helq A G 5: 100,783,094 F597L probably benign Het
Hrh1 A T 6: 114,480,243 I162L probably damaging Het
Jph1 A T 1: 17,091,660 F259L probably damaging Het
Kdm2b C T 5: 122,947,835 E238K probably damaging Het
Kdm4c T A 4: 74,307,016 probably null Het
Kif13a T C 13: 46,771,535 T308A probably benign Het
Lars C T 18: 42,227,280 V704M probably benign Het
Lhfpl1 A G X: 145,340,737 F125L probably benign Het
Lmbrd2 C A 15: 9,186,685 D582E probably damaging Het
Lrrn2 T A 1: 132,939,245 S683T possibly damaging Het
Macf1 T C 4: 123,472,049 D1408G probably benign Het
Magi3 T C 3: 104,015,903 K1166R probably benign Het
March5 T C 19: 37,220,493 probably benign Het
Naa25 A G 5: 121,426,762 Q555R possibly damaging Het
Npat A G 9: 53,569,907 T1005A probably benign Het
Nt5c3 G A 6: 56,886,685 A108V probably damaging Het
Ocrl T A X: 47,936,118 M322K probably damaging Het
Olfr229 A G 9: 39,910,639 T279A possibly damaging Het
Psg23 A T 7: 18,610,420 V370E probably benign Het
Rassf2 A T 2: 131,996,433 M311K possibly damaging Het
Rhobtb3 A G 13: 75,877,495 Y501H probably damaging Het
Rpl4 A G 9: 64,176,206 D179G possibly damaging Het
Scn2a T A 2: 65,715,838 I915N probably damaging Het
Scn3a T A 2: 65,526,621 T160S possibly damaging Het
Slx4ip T G 2: 137,068,022 N242K possibly damaging Het
Spidr T A 16: 16,048,081 Q288L probably benign Het
Sun1 A T 5: 139,231,163 H255L possibly damaging Het
Tacc1 C T 8: 25,175,217 G51S probably damaging Het
Tet2 T A 3: 133,480,139 N1179I possibly damaging Het
Tgfbrap1 T C 1: 43,062,592 Y349C probably damaging Het
Tnrc6a T C 7: 123,152,191 probably benign Het
Trim32 T C 4: 65,614,499 L431P probably damaging Het
Vmn1r35 A G 6: 66,679,350 L112S probably damaging Het
Vmn2r100 A C 17: 19,522,321 H319P probably damaging Het
Wdr20rt A G 12: 65,227,265 T328A probably benign Het
Zbtb17 T C 4: 141,464,982 Y413H probably benign Het
Other mutations in Lcmt2
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0352:Lcmt2 UTSW 2 121138896 missense probably benign 0.06
R0519:Lcmt2 UTSW 2 121139344 unclassified probably null
R0685:Lcmt2 UTSW 2 121139240 missense probably benign 0.14
R1437:Lcmt2 UTSW 2 121138896 missense probably benign 0.06
R1500:Lcmt2 UTSW 2 121140007 missense probably benign 0.00
R1569:Lcmt2 UTSW 2 121139828 missense probably damaging 1.00
R1612:Lcmt2 UTSW 2 121139120 missense probably damaging 1.00
R1618:Lcmt2 UTSW 2 121138652 missense probably damaging 0.98
R1990:Lcmt2 UTSW 2 121140281 missense probably benign 0.07
R2091:Lcmt2 UTSW 2 121138616 missense probably damaging 1.00
R2159:Lcmt2 UTSW 2 121139285 missense probably damaging 1.00
R3812:Lcmt2 UTSW 2 121138706 missense probably benign 0.01
R4725:Lcmt2 UTSW 2 121139430 missense probably benign 0.00
R4727:Lcmt2 UTSW 2 121139430 missense probably benign 0.00
R4968:Lcmt2 UTSW 2 121139736 missense probably benign 0.00
R5626:Lcmt2 UTSW 2 121139462 missense probably benign
R6246:Lcmt2 UTSW 2 121140389 missense probably damaging 1.00
R6326:Lcmt2 UTSW 2 121139457 nonsense probably null
R6524:Lcmt2 UTSW 2 121138931 missense possibly damaging 0.75
R6924:Lcmt2 UTSW 2 121140003 missense probably benign
R7282:Lcmt2 UTSW 2 121138790 missense probably damaging 1.00
R7405:Lcmt2 UTSW 2 121139387 missense probably benign 0.07
R7408:Lcmt2 UTSW 2 121138704 missense probably benign 0.08
Posted On2015-04-16