Mutagenetix > Incidental Mutation

Incidental Mutation 'R5931:Lcmt1'

461845

Institutional Source

Beutler Lab

Gene Symbol

Lcmt1

Ensembl Gene

ENSMUSG00000030763

Gene Name

leucine carboxyl methyltransferase 1

Synonyms

Lcmt, LCMT-1

MMRRC Submission

044126-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5931 (G1)

Quality Score

178

Status

Not validated

Chromosome

Chromosomal Location

122977026-123029581 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123020839 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 255 (T255A)

Ref Sequence

ENSEMBL: ENSMUSP00000145539 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000033025] [ENSMUST00000206574]

AlphaFold

A0A0U1RNF2

Predicted Effect

probably benign
Transcript: ENSMUST00000033025
AA Change: T255A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000033025
Gene: ENSMUSG00000030763
AA Change: T255A

Domain	Start	End	E-Value	Type
low complexity region	3	16	N/A	INTRINSIC
Pfam:LCM	23	215	3.6e-41	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205880

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206488

Predicted Effect

probably benign
Transcript: ENSMUST00000206574
AA Change: T255A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.4%

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	A	T	6: 91,896,096 (GRCm39)	R315W	probably damaging	Het
Atrn	A	T	2: 130,775,356 (GRCm39)	Y153F	possibly damaging	Het
C4b	A	G	17: 34,948,167 (GRCm39)	V1644A	probably damaging	Het
Carmil3	A	C	14: 55,736,397 (GRCm39)	K654T	probably damaging	Het
Cdh1	T	C	8: 107,392,964 (GRCm39)		probably null	Het
Chrna1	C	T	2: 73,398,444 (GRCm39)	V332M	probably benign	Het
Clca3a2	A	C	3: 144,797,886 (GRCm39)	V193G	possibly damaging	Het
Cyld	A	G	8: 89,456,470 (GRCm39)		probably null	Het
Dbt	A	T	3: 116,317,074 (GRCm39)	E83D	possibly damaging	Het
Deup1	T	C	9: 15,472,618 (GRCm39)	R471G	possibly damaging	Het
Dgcr2	T	A	16: 17,675,173 (GRCm39)	I188F	possibly damaging	Het
Dgkg	G	A	16: 22,376,788 (GRCm39)	R524*	probably null	Het
Dnaaf9	G	A	2: 130,656,109 (GRCm39)	T2M	probably damaging	Het
Dnah5	A	T	15: 28,453,425 (GRCm39)	R4399W	probably damaging	Het
Egflam	G	A	15: 7,273,338 (GRCm39)	T579I	possibly damaging	Het
Eif2b2	C	T	12: 85,269,561 (GRCm39)	T211I	probably damaging	Het
Ep400	A	G	5: 110,883,386 (GRCm39)		probably benign	Het
Ermp1	C	G	19: 29,593,129 (GRCm39)	A788P	probably benign	Het
Ern1	A	G	11: 106,317,699 (GRCm39)	S142P	possibly damaging	Het
Fbxo15	T	A	18: 84,999,250 (GRCm39)	C351S	probably damaging	Het
Fndc3a	A	T	14: 72,806,307 (GRCm39)	S444T	probably benign	Het
Gabra6	G	A	11: 42,198,268 (GRCm39)	T384M	probably benign	Het
Gpbp1l1	T	C	4: 116,447,457 (GRCm39)	V379A	probably benign	Het
Hook2	G	T	8: 85,722,375 (GRCm39)	E305*	probably null	Het
Hoxa3	G	A	6: 52,149,568 (GRCm39)	A21V	probably damaging	Het
Hs1bp3	C	A	12: 8,391,915 (GRCm39)	P339Q	probably benign	Het
Igha	T	A	12: 113,223,710 (GRCm39)	T49S	probably benign	Het
Klra4	C	T	6: 130,030,016 (GRCm39)	V190M	possibly damaging	Het
Lats2	A	G	14: 57,933,588 (GRCm39)	L843P	probably damaging	Het
Lpar6	A	G	14: 73,476,368 (GRCm39)	I110V	probably damaging	Het
Lrrtm4	A	G	6: 79,998,722 (GRCm39)	I44V	probably damaging	Het
Mcm3ap	T	C	10: 76,307,000 (GRCm39)	V371A	probably benign	Het
Muc20	A	T	16: 32,614,944 (GRCm39)	D144E	possibly damaging	Het
Nphp3	T	A	9: 103,897,945 (GRCm39)	D417E	probably damaging	Het
Or7g33	A	T	9: 19,448,629 (GRCm39)	I199K	probably benign	Het
Or8b40	A	G	9: 38,027,670 (GRCm39)	I193V	probably benign	Het
Paqr7	A	C	4: 134,235,031 (GRCm39)	Y296S	probably damaging	Het
Pcdha4	A	T	18: 37,087,808 (GRCm39)	T664S	probably damaging	Het
Pelo	T	A	13: 115,225,379 (GRCm39)	Y282F	probably benign	Het
Plxna2	A	T	1: 194,493,178 (GRCm39)	I1818F	probably damaging	Het
Pnkd	A	G	1: 74,389,833 (GRCm39)	D319G	probably benign	Het
Pnma8a	C	A	7: 16,694,809 (GRCm39)	N221K	probably benign	Het
Ppp1cb	T	A	5: 32,640,810 (GRCm39)		probably null	Het
Prkca	T	G	11: 107,905,136 (GRCm39)	I201L	probably benign	Het
Prp2rt	A	G	13: 97,235,705 (GRCm39)	L14S	probably benign	Het
Rfx2	G	A	17: 57,087,778 (GRCm39)	R538C	probably damaging	Het
Rph3a	T	C	5: 121,101,936 (GRCm39)	Q100R	probably damaging	Het
Rtel1	C	T	2: 180,972,608 (GRCm39)	R29*	probably null	Het
Scel	T	A	14: 103,843,060 (GRCm39)	Y547*	probably null	Het
Sp100	C	T	1: 85,606,804 (GRCm39)	P303L	probably damaging	Het
Stk31	A	G	6: 49,446,236 (GRCm39)	S958G	probably benign	Het
Syne2	T	A	12: 76,055,639 (GRCm39)	V4168E	probably benign	Het
Tenm3	A	T	8: 49,099,533 (GRCm39)	S91T	probably benign	Het
Tmcc2	TTGCTGCTGCTGCTGCTGC	TTGCTGCTGCTGCTGC	1: 132,285,493 (GRCm39)		probably benign	Het
Tmem248	T	A	5: 130,258,349 (GRCm39)	I14N	probably damaging	Het
Tor3a	T	C	1: 156,484,057 (GRCm39)	I298V	probably benign	Het
Trim69	A	T	2: 122,009,075 (GRCm39)	K378N	probably damaging	Het
Ttc28	C	T	5: 111,232,975 (GRCm39)	P151S	possibly damaging	Het
Uaca	T	C	9: 60,779,294 (GRCm39)	V1225A	probably damaging	Het
Vps4b	T	C	1: 106,705,065 (GRCm39)	I343V	probably benign	Het
Wnk4	A	G	11: 101,152,047 (GRCm39)	T184A	probably damaging	Het
Ythdc2	T	A	18: 45,006,023 (GRCm39)	I1172K	possibly damaging	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
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
RF046:Lcmt1	UTSW	7	122,969,057 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TTGTGTCACGTGTCCCACAAC -3'
(R):5'- GCGCACTGTAGGAAATGTTAAC -3'

Sequencing Primer
(F):5'- GCTCCTGTGTGCATTACCAGATG -3'
(R):5'- CGCACTGTAGGAAATGTTAACTTGTG -3'

Posted On

2017-02-28