Incidental Mutation 'R3812:Lcmt2'
ID 274095
Institutional Source Beutler Lab
Gene Symbol Lcmt2
Ensembl Gene ENSMUSG00000074890
Gene Name leucine carboxyl methyltransferase 2
Synonyms Tyw4
MMRRC Submission 040768-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.095) question?
Stock # R3812 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 120967773-120971179 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 120969187 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Valine at position 632 (A632V)
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
AA Change: A412V

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: A412V

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 benign
Transcript: ENSMUST00000110674
AA Change: A632V

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: A632V

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: ENSMUST00000158384
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147271
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130221
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146750
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156132
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 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.7%
Validation Efficiency 100% (28/28)
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: 26 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arid2 T C 15: 96,186,967 (GRCm39) V73A probably benign Het
Bpifb2 T A 2: 153,733,871 (GRCm39) D404E probably benign Het
Ccdc150 A G 1: 54,407,469 (GRCm39) M1082V probably benign Het
Cyp4a31 T C 4: 115,423,706 (GRCm39) S137P probably benign Het
Cyp4f15 A G 17: 32,905,151 (GRCm39) I45V probably benign Het
Fbxw28 C A 9: 109,167,598 (GRCm39) C53F possibly damaging Het
Galntl5 T C 5: 25,391,178 (GRCm39) F26L probably benign Het
Gm9637 A T 14: 19,402,398 (GRCm38) noncoding transcript Het
Metap2 A T 10: 93,706,026 (GRCm39) L252* probably null Het
Myo1a A G 10: 127,543,284 (GRCm39) N180S possibly damaging Het
Nlrp4a T C 7: 26,149,118 (GRCm39) W242R probably benign Het
Or4c12b T A 2: 89,647,395 (GRCm39) S242T probably damaging Het
Or5w18 C T 2: 87,633,396 (GRCm39) S221F possibly damaging Het
Or5w19 T A 2: 87,698,745 (GRCm39) S137T probably damaging Het
Otogl A G 10: 107,735,332 (GRCm39) Y151H probably damaging Het
Pkd1 T C 17: 24,784,615 (GRCm39) V387A probably benign Het
Polm A G 11: 5,779,512 (GRCm39) F429L possibly damaging Het
Sco2 T C 15: 89,257,882 (GRCm39) probably benign Het
Secisbp2l C T 2: 125,582,657 (GRCm39) G933D possibly damaging Het
Sorbs2 A G 8: 46,216,067 (GRCm39) T105A probably benign Het
Syt10 A T 15: 89,675,000 (GRCm39) C449S probably benign Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Txndc5 T C 13: 38,707,381 (GRCm39) K99E probably benign Het
Usp34 T A 11: 23,414,517 (GRCm39) F2820Y possibly damaging Het
Vmn1r170 T C 7: 23,305,717 (GRCm39) S40P probably damaging Het
Zfp292 A T 4: 34,810,326 (GRCm39) L906Q 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
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
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
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'- TTGGGAGTGTGGCAATACAAC -3'
(R):5'- GGGAATCAATAGATATCCAGCCC -3'

Sequencing Primer
(F):5'- GAGTGTGGCAATACAACAAATTCAC -3'
(R):5'- TAGATATCCAGCCCTCCATTACC -3'
Posted On 2015-04-02