Incidental Mutation 'RF046:Lcmt1'
| ID |
605023 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Lcmt1
|
| Ensembl Gene |
ENSMUSG00000030763 |
| Gene Name |
leucine carboxyl methyltransferase 1 |
| Synonyms |
Lcmt, LCMT-1 |
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
RF046 (G1)
|
| Quality Score |
203.593 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
122977026-123029581 bp(+) (GRCm39) |
| Type of Mutation |
frame shift |
| DNA Base Change (assembly) |
GGC to GGCCGCGGGGCGC
at 122969057 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000146184
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000098060]
[ENSMUST00000106442]
[ENSMUST00000167309]
[ENSMUST00000205262]
[ENSMUST00000205936]
[ENSMUST00000206117]
[ENSMUST00000206721]
[ENSMUST00000207010]
|
| AlphaFold |
A0A0U1RNF2 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000098060
|
| SMART Domains |
Protein: ENSMUSP00000095668
Gene: ENSMUSG00000030766
| Domain | Start | End | E-Value | Type |
|---|
|
BAR
|
1 |
239 |
4.45e-65 |
SMART |
|
RhoGAP
|
263 |
439 |
1.2e-60 |
SMART |
|
low complexity region
|
554 |
595 |
N/A |
INTRINSIC |
|
low complexity region
|
624 |
640 |
N/A |
INTRINSIC |
|
low complexity region
|
644 |
664 |
N/A |
INTRINSIC |
|
low complexity region
|
683 |
704 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000106442
|
| SMART Domains |
Protein: ENSMUSP00000102050
Gene: ENSMUSG00000030766
| Domain | Start | End | E-Value | Type |
|---|
|
BAR
|
1 |
239 |
4.45e-65 |
SMART |
|
RhoGAP
|
263 |
439 |
1.2e-60 |
SMART |
|
low complexity region
|
542 |
557 |
N/A |
INTRINSIC |
|
low complexity region
|
570 |
582 |
N/A |
INTRINSIC |
|
low complexity region
|
632 |
673 |
N/A |
INTRINSIC |
|
low complexity region
|
702 |
718 |
N/A |
INTRINSIC |
|
low complexity region
|
722 |
742 |
N/A |
INTRINSIC |
|
low complexity region
|
761 |
782 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000167309
|
| SMART Domains |
Protein: ENSMUSP00000128447
Gene: ENSMUSG00000030766
| Domain | Start | End | E-Value | Type |
|---|
|
BAR
|
1 |
239 |
4.45e-65 |
SMART |
|
RhoGAP
|
263 |
439 |
1.2e-60 |
SMART |
|
low complexity region
|
542 |
557 |
N/A |
INTRINSIC |
|
low complexity region
|
570 |
582 |
N/A |
INTRINSIC |
|
low complexity region
|
632 |
673 |
N/A |
INTRINSIC |
|
low complexity region
|
702 |
718 |
N/A |
INTRINSIC |
|
low complexity region
|
722 |
742 |
N/A |
INTRINSIC |
|
low complexity region
|
761 |
782 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000205262
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000205936
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000206117
|
| Predicted Effect |
probably null
Transcript: ENSMUST00000206721
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000207010
|
| Coding Region Coverage |
- 1x: 99.8%
- 3x: 99.7%
- 10x: 99.3%
- 20x: 98.7%
|
| Validation Efficiency |
|
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] LCMT1 catalyzes the methylation of the carboxyl group of the C-terminal leucine residue (leu309) of the catalytic subunit of protein phosphatase-2A (PPP2CA; MIM 176915) (De Baere et al., 1999 [PubMed 10600115]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Mice homozygous for a gene trap allele are embryonic lethal. Mice homozygous for a hypomorphic gene trap allele exhibit partial embryonic lethality, insulin resistance and impaired glucose tolerance. Mice homozygous for a transgenic gene disruption exhibit kidney agenesis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 27 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930505A04Rik |
TTTT |
TTTTT |
11: 30,376,249 (GRCm39) |
|
probably null |
Het |
| Ankhd1 |
CGGCGG |
CGGCGGGGGCGG |
18: 36,693,979 (GRCm39) |
|
probably benign |
Het |
| Apc |
A |
AATAAAGCGC |
18: 34,415,062 (GRCm39) |
|
probably benign |
Het |
| Arid1b |
GGC |
GGCCGC |
17: 5,045,865 (GRCm39) |
|
probably benign |
Het |
| Chd4 |
G |
GTTCCCT |
6: 125,099,094 (GRCm39) |
|
probably benign |
Het |
| Dclre1a |
CTTTGCT |
C |
19: 56,532,564 (GRCm39) |
|
probably benign |
Het |
| Dnaaf9 |
CATC |
CATCATC |
2: 130,612,654 (GRCm39) |
|
probably null |
Het |
| Eps8 |
TCGCTC |
TCGCTCGCTC |
6: 137,494,061 (GRCm39) |
|
probably benign |
Het |
| Fkbp1a |
CGCCGCCGCCA |
C |
2: 151,384,618 (GRCm39) |
|
probably null |
Het |
| Flywch1 |
CTCCTGGTGT |
CTCCTGGTGTGGGGAGGCTACGTACTCACCCAATCCTGGTGT |
17: 23,981,143 (GRCm39) |
|
probably null |
Het |
| Flywch1 |
GGTGT |
GGTGTGGGGAGGCTACGTACTCACCCACTCCTTGTGT |
17: 23,981,148 (GRCm39) |
|
probably null |
Het |
| Gm7247 |
AGACCAGACC |
A |
14: 51,601,781 (GRCm39) |
|
probably benign |
Het |
| H2-T10 |
TTTCCCACTGTA |
T |
17: 36,431,186 (GRCm39) |
|
probably null |
Het |
| Iqcf4 |
TTCCTTTTCCTTTT |
TTCCTTTTCCTTTTCCTTTTCCTTTTCCTTTTCCTTGTCCTTTTCCTTTT |
9: 106,447,809 (GRCm39) |
|
probably benign |
Het |
| Kdm2a |
TTCCTCCTCCTCCTCCTCTTCCTCCTCCTC |
TTCCTCCTCCTCCTCTTCCTCCTCCTC |
19: 4,374,535 (GRCm39) |
|
probably benign |
Het |
| Lce1m |
GCT |
GCTCCCACCCCTTCT |
3: 92,925,600 (GRCm39) |
|
probably benign |
Het |
| Nusap1 |
GAGGAGCAAGCTGAGA |
GAGGAGCAAGCTGAGATACACGTTAGCAGTTAGGAGCAAGCTGAGA |
2: 119,458,076 (GRCm39) |
|
probably null |
Het |
| Pkhd1l1 |
TTTTTTTTTTTTTT |
TTTTTTTTTTTTTTTTTTTTTTT |
15: 44,421,891 (GRCm39) |
|
probably benign |
Het |
| Plxnc1 |
C |
T |
10: 94,700,869 (GRCm39) |
C605Y |
probably damaging |
Het |
| Pnma8a |
TA |
TAACTCATGATGCTCCTGCTTCAACA |
7: 16,695,348 (GRCm39) |
|
probably benign |
Het |
| Polr1has |
CACCACCACCACCAC |
CACCACCACCACCACCACCACAACCACCACCACCAC |
17: 37,275,949 (GRCm39) |
|
probably benign |
Het |
| Rfx4 |
CTCTCTCTCTCTCT |
CTCTCTCTCTCTCTCTATCTCTCTCTCTCT |
10: 84,694,345 (GRCm39) |
|
probably benign |
Het |
| Rtbdn |
C |
CAGCGGG |
8: 85,682,808 (GRCm39) |
|
probably benign |
Het |
| Spmap2l |
CGATCCTCCCCAGTCCCGCAAGGCCAG |
CGATCCTCCCCAGTCCCGCAAGGCCAGGGATCCTCCCCAGTCCCGCAAGGCCAG |
5: 77,164,250 (GRCm39) |
|
probably benign |
Het |
| Trp53bp1 |
TCCTGTGAGGCCCTCTGCTGC |
TC |
2: 121,046,482 (GRCm39) |
|
probably null |
Het |
| Tusc1 |
CCGCCA |
CCGCCAACGCCA |
4: 93,223,539 (GRCm39) |
|
probably benign |
Het |
| Usp2 |
TGACCTGTTCTTCACTTAC |
TGACCTGTTCTTCACTTACTCATGCGACCTGTTCTTCACTTAC |
9: 44,000,408 (GRCm39) |
|
probably benign |
Het |
|
| Other mutations in Lcmt1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL01472:Lcmt1
|
APN |
7 |
123,027,376 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01536:Lcmt1
|
APN |
7 |
123,021,966 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
IGL01564:Lcmt1
|
APN |
7 |
123,003,663 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL02598:Lcmt1
|
APN |
7 |
123,020,871 (GRCm39) |
splice site |
probably benign |
|
|
rancho
|
UTSW |
7 |
123,000,718 (GRCm39) |
missense |
probably benign |
0.03 |
|
relasso
|
UTSW |
7 |
123,000,691 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0665:Lcmt1
|
UTSW |
7 |
123,002,094 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0668:Lcmt1
|
UTSW |
7 |
123,002,094 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0943:Lcmt1
|
UTSW |
7 |
123,000,662 (GRCm39) |
splice site |
probably null |
|
|
R1574:Lcmt1
|
UTSW |
7 |
123,002,131 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1574:Lcmt1
|
UTSW |
7 |
123,002,131 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2896:Lcmt1
|
UTSW |
7 |
123,020,809 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R3017:Lcmt1
|
UTSW |
7 |
123,029,359 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3547:Lcmt1
|
UTSW |
7 |
122,999,702 (GRCm39) |
missense |
probably benign |
0.07 |
|
R3714:Lcmt1
|
UTSW |
7 |
123,003,683 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R4092:Lcmt1
|
UTSW |
7 |
123,017,476 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4628:Lcmt1
|
UTSW |
7 |
123,010,035 (GRCm39) |
nonsense |
probably null |
|
|
R5062:Lcmt1
|
UTSW |
7 |
123,010,053 (GRCm39) |
splice site |
probably null |
|
|
R5096:Lcmt1
|
UTSW |
7 |
123,000,691 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5549:Lcmt1
|
UTSW |
7 |
123,027,330 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5573:Lcmt1
|
UTSW |
7 |
123,000,686 (GRCm39) |
missense |
probably benign |
0.03 |
|
R5931:Lcmt1
|
UTSW |
7 |
123,020,839 (GRCm39) |
missense |
probably benign |
|
|
R6331:Lcmt1
|
UTSW |
7 |
122,977,405 (GRCm39) |
intron |
probably benign |
|
|
R7752:Lcmt1
|
UTSW |
7 |
122,969,030 (GRCm39) |
missense |
unknown |
|
|
R7784:Lcmt1
|
UTSW |
7 |
123,000,718 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8447:Lcmt1
|
UTSW |
7 |
123,020,825 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8499:Lcmt1
|
UTSW |
7 |
123,029,371 (GRCm39) |
missense |
probably benign |
0.02 |
|
R8743:Lcmt1
|
UTSW |
7 |
122,999,691 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8962:Lcmt1
|
UTSW |
7 |
123,000,669 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9760:Lcmt1
|
UTSW |
7 |
123,029,375 (GRCm39) |
nonsense |
probably null |
|
|
RF013:Lcmt1
|
UTSW |
7 |
122,969,059 (GRCm39) |
frame shift |
probably null |
|
|
RF025:Lcmt1
|
UTSW |
7 |
122,969,057 (GRCm39) |
frame shift |
probably null |
|
|
| Predicted Primers |
PCR Primer
(F):5'- TAAAGACCCTCGTGAGTCTCCC -3'
(R):5'- ACTTAACTCCGCCCATGTTG -3'
Sequencing Primer
(F):5'- TGAGTCTCCCGAGGACGATG -3'
(R):5'- ATGTTGGGTCCGTCCGCAC -3'
|
| Posted On |
2019-12-04 |
Incidental Mutation