Incidental Mutation 'R4725:Lcmt2'
| ID |
358383 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lcmt2
|
| Ensembl Gene |
ENSMUSG00000074890 |
| Gene Name |
leucine carboxyl methyltransferase 2 |
| Synonyms |
Tyw4 |
| MMRRC Submission |
041960-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.095)
|
| Stock # |
R4725 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
120967773-120971179 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to G
at 120969911 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Leucine
at position 171
(V171L)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000097085
(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
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:A_deaminase
|
1 |
276 |
1.8e-37 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000066155
|
| SMART Domains |
Protein: ENSMUSP00000067133
Gene: ENSMUSG00000027259
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:A_deaminase
|
16 |
343 |
1.6e-36 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000099486
AA Change: V171L
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: V171L
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:A_deaminase
|
2 |
200 |
1.1e-28 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110665
|
| SMART Domains |
Protein: ENSMUSP00000106293
Gene: ENSMUSG00000027259
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:A_deaminase
|
2 |
236 |
4.3e-24 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000110674
AA Change: V391L
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: V391L
| Domain | Start | End | E-Value | Type |
|---|
|
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
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:A_deaminase
|
16 |
343 |
3e-44 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156132
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000158384
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130221
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147271
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000146750
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
| Validation Efficiency |
96% (64/67) |
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 5830454E08Rik |
T |
C |
9: 120,406,769 (GRCm39) |
|
probably benign |
Het |
| Adamts20 |
T |
C |
15: 94,249,643 (GRCm39) |
E458G |
probably damaging |
Het |
| Adgrl3 |
T |
C |
5: 81,914,052 (GRCm39) |
I1220T |
possibly damaging |
Het |
| Aldh1a1 |
T |
A |
19: 20,617,445 (GRCm39) |
M459K |
probably benign |
Het |
| Bmal1 |
C |
A |
7: 112,903,566 (GRCm39) |
P454Q |
possibly damaging |
Het |
| Camta1 |
A |
G |
4: 151,232,953 (GRCm39) |
V240A |
probably benign |
Het |
| Ccdc88b |
C |
T |
19: 6,834,481 (GRCm39) |
G149R |
probably damaging |
Het |
| Ceacam5 |
T |
C |
7: 17,494,602 (GRCm39) |
V870A |
probably benign |
Het |
| Cep192 |
A |
C |
18: 67,949,837 (GRCm39) |
Q307P |
probably benign |
Het |
| Cep63 |
T |
C |
9: 102,467,755 (GRCm39) |
|
probably benign |
Het |
| Cldn12 |
A |
G |
5: 5,558,385 (GRCm39) |
F14S |
probably damaging |
Het |
| Ctdsp1 |
G |
A |
1: 74,433,823 (GRCm39) |
V135I |
possibly damaging |
Het |
| Dcaf10 |
G |
A |
4: 45,372,769 (GRCm39) |
R394Q |
possibly damaging |
Het |
| Dchs1 |
T |
C |
7: 105,404,460 (GRCm39) |
D2694G |
probably damaging |
Het |
| Dchs1 |
C |
G |
7: 105,414,759 (GRCm39) |
G761A |
probably damaging |
Het |
| Dennd5b |
A |
G |
6: 148,946,277 (GRCm39) |
Y445H |
probably damaging |
Het |
| Dock1 |
T |
A |
7: 134,346,743 (GRCm39) |
L225* |
probably null |
Het |
| Drd3 |
G |
T |
16: 43,643,164 (GRCm39) |
E467* |
probably null |
Het |
| Dysf |
A |
T |
6: 84,074,738 (GRCm39) |
N527I |
probably damaging |
Het |
| Erbb2 |
A |
G |
11: 98,315,970 (GRCm39) |
T358A |
possibly damaging |
Het |
| Fhad1 |
A |
T |
4: 141,655,689 (GRCm39) |
|
probably null |
Het |
| Ganc |
T |
C |
2: 120,265,754 (GRCm39) |
I434T |
probably damaging |
Het |
| Gm5830 |
T |
A |
1: 78,945,549 (GRCm39) |
|
noncoding transcript |
Het |
| Gm6096 |
G |
T |
7: 33,950,484 (GRCm39) |
E8* |
probably null |
Het |
| Gne |
A |
G |
4: 44,066,806 (GRCm39) |
F63S |
probably benign |
Het |
| Gpat2 |
T |
C |
2: 127,273,902 (GRCm39) |
V315A |
possibly damaging |
Het |
| Gpr33 |
A |
G |
12: 52,070,892 (GRCm39) |
L49P |
probably damaging |
Het |
| Heatr1 |
C |
T |
13: 12,439,543 (GRCm39) |
Q1374* |
probably null |
Het |
| Hivep1 |
A |
G |
13: 42,316,887 (GRCm39) |
I2032V |
probably benign |
Het |
| Igkv2-112 |
A |
C |
6: 68,197,450 (GRCm39) |
I40L |
probably benign |
Het |
| Kcnab3 |
A |
G |
11: 69,221,294 (GRCm39) |
N204D |
probably benign |
Het |
| Kcnj10 |
T |
A |
1: 172,196,726 (GRCm39) |
F80Y |
probably damaging |
Het |
| Loxhd1 |
T |
A |
18: 77,483,153 (GRCm39) |
Y1245N |
probably damaging |
Het |
| Lrrc7 |
GAAGTTGTTTGGAGATTCTTATCTTA |
GA |
3: 158,024,045 (GRCm39) |
|
probably benign |
Het |
| Mast1 |
A |
G |
8: 85,655,635 (GRCm39) |
S170P |
possibly damaging |
Het |
| Mroh4 |
A |
G |
15: 74,487,956 (GRCm39) |
L322P |
probably damaging |
Het |
| Npdc1 |
G |
A |
2: 25,298,957 (GRCm39) |
D284N |
probably damaging |
Het |
| Nudcd3 |
A |
T |
11: 6,143,475 (GRCm39) |
V1D |
probably damaging |
Het |
| Pah |
T |
A |
10: 87,390,238 (GRCm39) |
L25Q |
probably damaging |
Het |
| Pik3cg |
A |
T |
12: 32,243,596 (GRCm39) |
|
probably null |
Het |
| Pira13 |
A |
C |
7: 3,824,547 (GRCm39) |
S611A |
probably benign |
Het |
| Plekha6 |
C |
A |
1: 133,211,058 (GRCm39) |
S625Y |
probably damaging |
Het |
| Rtn4 |
T |
A |
11: 29,658,362 (GRCm39) |
S839T |
probably damaging |
Het |
| Rusc1 |
A |
G |
3: 88,998,736 (GRCm39) |
S349P |
possibly damaging |
Het |
| Samsn1 |
A |
T |
16: 75,742,217 (GRCm39) |
|
noncoding transcript |
Het |
| Scimp |
A |
G |
11: 70,691,539 (GRCm39) |
V30A |
probably damaging |
Het |
| Serpinb13 |
C |
T |
1: 106,910,574 (GRCm39) |
S66L |
probably damaging |
Het |
| Sgip1 |
A |
G |
4: 102,823,419 (GRCm39) |
D680G |
probably damaging |
Het |
| Slc44a2 |
G |
A |
9: 21,259,691 (GRCm39) |
V613M |
probably damaging |
Het |
| Smpdl3b |
T |
C |
4: 132,472,489 (GRCm39) |
T95A |
probably damaging |
Het |
| Spag6l |
A |
T |
16: 16,610,395 (GRCm39) |
L85H |
probably damaging |
Het |
| Sucla2 |
T |
A |
14: 73,806,429 (GRCm39) |
Y167N |
possibly damaging |
Het |
| Svop |
G |
T |
5: 114,203,546 (GRCm39) |
|
probably benign |
Het |
| Tnxb |
A |
T |
17: 34,918,041 (GRCm39) |
D2318V |
probably damaging |
Het |
| Trbv14 |
A |
G |
6: 41,112,332 (GRCm39) |
D43G |
probably benign |
Het |
| Ubn2 |
A |
G |
6: 38,499,240 (GRCm39) |
|
probably benign |
Het |
| Ufsp1 |
T |
C |
5: 137,293,569 (GRCm39) |
I173T |
probably damaging |
Het |
| Zbtb40 |
A |
G |
4: 136,746,072 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Lcmt2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |
|
R3812:Lcmt2
|
UTSW |
2 |
120,969,187 (GRCm39) |
missense |
probably benign |
0.01 |
|
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'- TAAATCAAGTTGGAGAGCCCC -3'
(R):5'- AGAAACTCCAGTGTTTGAGCC -3'
Sequencing Primer
(F):5'- CAGAGGCTGGACTTACTGGG -3'
(R):5'- TCCAGTGTTTGAGCCCTCAGAG -3'
|
| Posted On |
2015-11-11 |
Incidental Mutation