Mutagenetix > Incidental Mutation

Incidental Mutation 'RF013:Lcmt1'

603339

Institutional Source

Beutler Lab

Gene Symbol

Lcmt1

Ensembl Gene

ENSMUSG00000030763

Gene Name

leucine carboxyl methyltransferase 1

Synonyms

LCMT-1, Lcmt

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

RF013 (G1)

Quality Score

210.475

Status

Not validated

Chromosome

Chromosomal Location

123369784-123430358 bp(+) (GRCm38)

Type of Mutation

frame shift

DNA Base Change (assembly)

C to CCGCGGGGCTT at 123369836 bp (GRCm38)

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: 99.4%
20x: 98.9%

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700019N19Rik	A	G	19: 58,789,294	F28S	probably damaging	Het
4930435E12Rik	T	C	16: 38,828,001	T249A	probably benign	Het
4932438A13Rik	TTAT	TTATTATTATTATTAGTAT	3: 37,050,757		probably benign	Het
Acap3	CCTGGGCTGCTG	CCTGGGCTGCTGCATACTGGGCTGCTG	4: 155,905,096		probably benign	Het
Adamts9	A	G	6: 92,943,145	V4A	possibly damaging	Het
AI837181	GGC	GGCTGC	19: 5,425,232		probably benign	Het
Alk	A	G	17: 71,895,936	Y1135H	probably damaging	Het
Ankhd1	CGGCGG	CGGCGGAGGCGG	18: 36,560,926		probably benign	Het
Ano3	A	C	2: 110,697,036	L609R	probably benign	Het
Bicc1	A	G	10: 70,935,830		probably null	Het
Card6	T	C	15: 5,100,142	I591V	probably benign	Het
Ccdc18	A	G	5: 108,220,716	N1235D	probably benign	Het
Cd109	TTAT	TTATTTATTTATCTAT	9: 78,712,531		probably benign	Het
Cnpy3	CCT	CCTGCT	17: 46,736,744		probably benign	Het
Col6a5	GCAGTC	GCAGTCTCCAGTC	9: 105,878,597		probably null	Het
Cyb5r4	GACACACTGCCCAGGGA	GACACACTGCCCAGGGATGTGACACACACACTGCCCAGGGA	9: 87,040,432		probably benign	Het
Cyp8b1	A	T	9: 121,915,495	M257K	possibly damaging	Het
Dbf4	A	T	5: 8,397,985	H408Q	possibly damaging	Het
Defb22	TTGCGGCA	TTGCGGCAGAGCTGGCCTGTGCGGCA	2: 152,485,831		probably benign	Het
Ercc6l2	A	T	13: 63,853,017	T417S	probably benign	Het
Exd2	AGCCACAG	A	12: 80,475,932		probably null	Het
Fam171b	GC	GCAGCATC	2: 83,812,895		probably benign	Het
Fam71e1	CCTGGGTCTGAGGGAGGA	CCTGGGTCTGAGGGAGGACGGCTGGATCCTGGATCACTGGGTCTGAGGGAGGA	7: 44,500,520		probably null	Het
Flvcr2	T	A	12: 85,747,186	L112Q	probably damaging	Het
Flywch1	GTG	GTGGGGGGAGGCTACGTACTCACCCACTCCTTTTG	17: 23,762,175		probably null	Het
Gabre	TCAGGCTCAGGCT	TCAGGCTCAGGCTCAGGCT	X: 72,270,416		probably benign	Het
Gm4884	C	A	7: 41,040,809	P43Q	probably damaging	Het
Gm6588	T	A	5: 112,450,071	N161K	probably benign	Het
Grm8	A	G	6: 27,363,780	W579R	probably damaging	Het
Hsdl2	AG	AGCAGCAGCCACAGCTGCCG	4: 59,610,657		probably benign	Het
Ivl	CTGCTGCTGCTGCTGT	C	3: 92,572,343		probably benign	Het
Kif18b	T	C	11: 102,912,366	D506G	probably benign	Het
Krtap28-10	AGCCAC	AGCCACGGCCAC	1: 83,042,135		probably benign	Het
Krtap28-10	GCCACAGCCACCACA	GCCACAGCCACCACATCCACAGCCACCACA	1: 83,042,274		probably benign	Het
Lama1	C	A	17: 67,781,062	S1558R		Het
Lmna	A	G	3: 88,484,054	V494A	probably benign	Het
Mapk6	CCAC	CCACCTCAC	9: 75,388,260		probably null	Het
Mboat7	T	A	7: 3,691,857	H52L	probably damaging	Het
Med12l	CAG	CAGAAG	3: 59,275,966		probably benign	Het
Morc2a	T	A	11: 3,676,191	M225K	probably benign	Het
Mpdz	G	A	4: 81,293,592	A1566V	possibly damaging	Het
Mpi	T	C	9: 57,548,641	D186G	probably benign	Het
Mtmr12	C	A	15: 12,261,898	N386K	probably damaging	Het
Myh3	ATTAC	ATTACTTAC	11: 67,086,356		probably null	Het
Myo10	T	A	15: 25,799,479	M1376K	probably damaging	Het
Nbas	C	T	12: 13,279,408	T118I	possibly damaging	Het
Nedd4l	C	T	18: 65,209,680	R755C	probably damaging	Het
Nefh	GACTTGGCCTCACCTGGG	GACTTGGCCTCACCTGGGTACTTGGCCTCACCTGGG	11: 4,941,032		probably benign	Het
Numa1	T	C	7: 101,999,780	L906P	probably damaging	Het
Olfr750	G	A	14: 51,071,012	A127V	probably damaging	Het
Olfr871	T	C	9: 20,212,894	S182P	probably benign	Het
Otop2	G	T	11: 115,323,666	R83L	probably benign	Het
Pmm1	T	A	15: 81,957,813	Q62L	probably damaging	Het
Pramef25	C	G	4: 143,948,908	Q449H	probably damaging	Het
Ptprj	A	T	2: 90,471,170	L206*	probably null	Het
Rassf6	TC	TCTGCCTCACTCATGGTCCTGTAGAGCATTGGGGATCC	5: 90,608,941		probably benign	Het
Rps19	A	AGAAAAT	7: 24,889,180		probably benign	Het
Rsrp1	T	A	4: 134,923,955	V10E	unknown	Het
Sh2d6	C	T	6: 72,516,388		probably null	Het
Six4	TG	T	12: 73,103,582		probably null	Het
Slc6a15	T	A	10: 103,400,216	V264D	probably damaging	Het
Snapc5	ATGGAAGAAGAGG	A	9: 64,182,211		probably benign	Het
Sost	A	T	11: 101,964,132	I117N	probably damaging	Het
Tbc1d22a	AGGTGTGTG	A	15: 86,299,774		probably null	Het
Tcaf1	C	T	6: 42,679,173	V290I	probably benign	Het
Tcof1	GCA	GCACCA	18: 60,835,743		probably benign	Het
Tgfbr1	A	G	4: 47,353,354	I15V	unknown	Het
Tmem241	A	T	18: 11,983,561	L288Q	probably damaging	Het
Tnfrsf13b	T	G	11: 61,141,444	V100G	probably benign	Het
Trim66	A	G	7: 109,460,753	S809P	probably damaging	Het
Tubb4a	C	G	17: 57,087,464	G17A	possibly damaging	Het
Txndc16	A	G	14: 45,169,338	V220A	probably benign	Het
Zan	T	A	5: 137,391,720	Q4830L	unknown	Het

Other mutations in Lcmt1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01472:Lcmt1	APN	7	123428153	missense	probably damaging	1.00
IGL01536:Lcmt1	APN	7	123422743	missense	possibly damaging	0.46
IGL01564:Lcmt1	APN	7	123404440	missense	probably benign	0.00
IGL02598:Lcmt1	APN	7	123421648	splice site	probably benign
rancho	UTSW	7	123401495	missense	probably benign	0.03
relasso	UTSW	7	123401468	missense	probably damaging	1.00
R0665:Lcmt1	UTSW	7	123402871	missense	probably damaging	1.00
R0668:Lcmt1	UTSW	7	123402871	missense	probably damaging	1.00
R0943:Lcmt1	UTSW	7	123401439	splice site	probably null
R1574:Lcmt1	UTSW	7	123402908	missense	probably damaging	1.00
R1574:Lcmt1	UTSW	7	123402908	missense	probably damaging	1.00
R2896:Lcmt1	UTSW	7	123421586	missense	possibly damaging	0.95
R3017:Lcmt1	UTSW	7	123430136	missense	probably damaging	1.00
R3547:Lcmt1	UTSW	7	123400479	missense	probably benign	0.07
R3714:Lcmt1	UTSW	7	123404460	missense	probably damaging	0.98
R4092:Lcmt1	UTSW	7	123418253	missense	probably damaging	1.00
R4628:Lcmt1	UTSW	7	123410812	nonsense	probably null
R5062:Lcmt1	UTSW	7	123410830	splice site	probably null
R5096:Lcmt1	UTSW	7	123401468	missense	probably damaging	1.00
R5549:Lcmt1	UTSW	7	123428107	missense	probably damaging	1.00
R5573:Lcmt1	UTSW	7	123401463	missense	probably benign	0.03
R5931:Lcmt1	UTSW	7	123421616	missense	probably benign
R6331:Lcmt1	UTSW	7	123378182	intron	probably benign
R7752:Lcmt1	UTSW	7	123369807	missense	unknown
R7784:Lcmt1	UTSW	7	123401495	missense	probably benign	0.03
R8447:Lcmt1	UTSW	7	123421602	missense	probably damaging	1.00
R8499:Lcmt1	UTSW	7	123430148	missense	probably benign	0.02
R8743:Lcmt1	UTSW	7	123400468	missense	probably damaging	1.00
R8962:Lcmt1	UTSW	7	123401446	missense	probably damaging	1.00
R9760:Lcmt1	UTSW	7	123430152	nonsense	probably null
RF025:Lcmt1	UTSW	7	123369834	frame shift	probably null
RF046:Lcmt1	UTSW	7	123369834	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TAAAGACCCTCGTGAGTCTCCC -3'
(R):5'- TTAACTCCGCCCATGTTGG -3'

Sequencing Primer
(F):5'- TGAGTCTCCCGAGGACGATG -3'
(R):5'- ATGTTGGGTCCGTCCGCAC -3'

Posted On

2019-12-04