Mutagenetix > Incidental Mutation

Incidental Mutation 'R0685:Lcmt2'

61102

Institutional Source

Beutler Lab

Gene Symbol

Lcmt2

Ensembl Gene

ENSMUSG00000074890

Gene Name

leucine carboxyl methyltransferase 2

Synonyms

MMRRC Submission

038870-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.084) question?

Stock #

R0685 (G1)

Quality Score

155

Status

Validated

Chromosome

Chromosomal Location

121128307-121140653 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 121139240 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Isoleucine at position 234 (S234I)

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: S234I

PolyPhen 2 Score 0.136 (Sensitivity: 0.92; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: S234I

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: S454I

PolyPhen 2 Score 0.051 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: S454I

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: ENSMUST00000130221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146750

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156132

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158384

Meta Mutation Damage Score

0.0783

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.6%
20x: 95.6%

Validation Efficiency

98% (89/91)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020N01Rik	A	G	10: 21,593,438 (GRCm38)	D17G	probably damaging	Het
Abi3bp	A	G	16: 56,532,953 (GRCm38)	T82A	possibly damaging	Het
Adgre4	A	C	17: 55,792,035 (GRCm38)	E180D	probably benign	Het
Ankrd28	G	A	14: 31,743,450 (GRCm38)		probably benign	Het
Aoc3	A	G	11: 101,336,447 (GRCm38)	D382G	possibly damaging	Het
Apob	C	A	12: 8,010,742 (GRCm38)	R3075S	probably benign	Het
Aqr	A	G	2: 114,140,977 (GRCm38)	F459S	probably damaging	Het
Bcr	T	C	10: 75,131,643 (GRCm38)	W570R	probably damaging	Het
Bloc1s5	C	T	13: 38,603,919 (GRCm38)	R163K	probably benign	Het
Bod1	A	T	11: 31,669,267 (GRCm38)	N101K	possibly damaging	Het
Bysl	A	T	17: 47,602,471 (GRCm38)	S296T	probably benign	Het
Chl1	G	A	6: 103,708,542 (GRCm38)		probably null	Het
Clstn1	G	A	4: 149,646,855 (GRCm38)	A885T	probably benign	Het
Cyp3a25	G	T	5: 145,998,546 (GRCm38)	P87T	probably damaging	Het
Dync1h1	T	C	12: 110,657,192 (GRCm38)	V3633A	probably damaging	Het
Dynlt5	T	C	4: 103,002,538 (GRCm38)	Y96H	probably damaging	Het
Elp4	C	A	2: 105,792,277 (GRCm38)	C241F	possibly damaging	Het
Fat4	T	A	3: 39,001,178 (GRCm38)	F4182Y	probably benign	Het
Gabbr2	G	A	4: 46,787,521 (GRCm38)	H381Y	possibly damaging	Het
Gm10577	G	T	4: 101,020,318 (GRCm38)		probably benign	Het
Gm9955	G	T	18: 24,709,257 (GRCm38)		probably benign	Het
Gstm5	T	A	3: 107,897,319 (GRCm38)	I73N	probably damaging	Het
Gypa	T	A	8: 80,496,702 (GRCm38)		probably benign	Het
Hectd2	T	A	19: 36,569,431 (GRCm38)	V64D	probably damaging	Het
Igkv10-95	T	A	6: 68,680,559 (GRCm38)	Y20N	probably benign	Het
Il15	T	C	8: 82,337,559 (GRCm38)		probably benign	Het
Iqca1	C	A	1: 90,142,731 (GRCm38)	G133V	probably null	Het
Kiz	C	A	2: 146,856,058 (GRCm38)		probably benign	Het
Lilra5	A	G	7: 4,241,957 (GRCm38)		probably benign	Het
Lin37	T	C	7: 30,555,874 (GRCm38)	E187G	probably damaging	Het
Lrrc37	T	C	11: 103,616,888 (GRCm38)		probably benign	Het
Mcmdc2	T	A	1: 9,911,814 (GRCm38)		probably null	Het
Mctp1	T	C	13: 76,825,799 (GRCm38)		probably null	Het
Mdp1	C	A	14: 55,659,269 (GRCm38)	G112*	probably null	Het
Mmp15	T	C	8: 95,372,134 (GRCm38)	Y530H	possibly damaging	Het
Mtss2	T	C	8: 110,727,397 (GRCm38)		probably null	Het
Muc5ac	T	C	7: 141,807,709 (GRCm38)	S1586P	probably benign	Het
Nap1l5	A	T	6: 58,906,772 (GRCm38)	C66S	possibly damaging	Het
Ninl	G	T	2: 150,939,855 (GRCm38)	Q1237K	possibly damaging	Het
Or5p70	A	T	7: 108,395,263 (GRCm38)	T48S	possibly damaging	Het
Or9m1b	T	C	2: 88,006,418 (GRCm38)	E111G	probably damaging	Het
Orc6	T	G	8: 85,301,154 (GRCm38)	S37R	possibly damaging	Het
Papss1	A	C	3: 131,583,093 (GRCm38)	N119H	possibly damaging	Het
Phf13	A	T	4: 151,991,612 (GRCm38)	F278I	probably damaging	Het
Pole2	C	A	12: 69,211,413 (GRCm38)	A239S	probably damaging	Het
Ppt2	T	C	17: 34,626,572 (GRCm38)	D75G	probably damaging	Het
Psd2	A	G	18: 36,002,991 (GRCm38)	D443G	possibly damaging	Het
Psen1	C	A	12: 83,714,820 (GRCm38)	S132*	probably null	Het
Psme4	A	G	11: 30,878,415 (GRCm38)	T1812A	probably damaging	Het
Rasgrf1	T	C	9: 89,915,482 (GRCm38)		probably benign	Het
Reep3	A	G	10: 67,021,739 (GRCm38)		probably benign	Het
Rexo4	A	T	2: 26,958,574 (GRCm38)		probably benign	Het
Rnf6	A	C	5: 146,211,658 (GRCm38)	S183R	probably damaging	Het
Scai	A	T	2: 39,103,737 (GRCm38)	M297K	probably damaging	Het
Scn9a	A	T	2: 66,483,499 (GRCm38)	S1947R	probably benign	Het
Sema6c	T	C	3: 95,172,710 (GRCm38)	C772R	possibly damaging	Het
Skint7	T	C	4: 111,980,345 (GRCm38)	S107P	possibly damaging	Het
Slc24a3	A	G	2: 145,606,795 (GRCm38)	N420D	probably benign	Het
Smc1b	T	C	15: 85,070,820 (GRCm38)	D1077G	possibly damaging	Het
Smg7	G	A	1: 152,866,648 (GRCm38)	P82L	probably damaging	Het
Sp3	A	C	2: 72,970,998 (GRCm38)	F268V	probably damaging	Het
Srms	T	C	2: 181,212,633 (GRCm38)	D47G	probably benign	Het
Ss18	A	C	18: 14,651,181 (GRCm38)	M150R	probably damaging	Het
Taf5	G	A	19: 47,074,854 (GRCm38)	R281Q	probably benign	Het
Tars1	T	C	15: 11,385,173 (GRCm38)	K644R	probably benign	Het
Tinag	C	A	9: 76,952,003 (GRCm38)	W441L	probably damaging	Het
Tmtc1	T	C	6: 148,411,240 (GRCm38)	S244G	probably benign	Het
Tpr	T	C	1: 150,433,725 (GRCm38)	V1670A	possibly damaging	Het
Trpv3	A	G	11: 73,296,814 (GRCm38)		probably benign	Het
Uhrf1	G	T	17: 56,310,742 (GRCm38)	V155L	probably damaging	Het
Ush2a	G	A	1: 188,400,278 (GRCm38)	C899Y	probably damaging	Het
Vmn2r115	G	A	17: 23,359,275 (GRCm38)	R574H	probably benign	Het
Vmn2r63	T	C	7: 42,928,010 (GRCm38)	D368G	probably benign	Het
Vps13a	A	G	19: 16,780,741 (GRCm38)	V10A	probably damaging	Het
Wbp11	A	G	6: 136,814,638 (GRCm38)		probably benign	Het
Zcwpw1	A	G	5: 137,799,592 (GRCm38)	D145G	probably benign	Het
Zfp607a	G	A	7: 27,878,476 (GRCm38)	V324I	probably damaging	Het
Zfp618	A	G	4: 63,133,774 (GRCm38)	I931V	probably benign	Het
Zfp821	T	C	8: 109,724,542 (GRCm38)	V389A	possibly damaging	Het
Zfp976	T	A	7: 42,613,717 (GRCm38)	H232L	probably damaging	Het

Other mutations in Lcmt2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02142:Lcmt2	APN	2	121,138,913 (GRCm38)	missense	possibly damaging	0.94
R0352:Lcmt2	UTSW	2	121,138,896 (GRCm38)	missense	probably benign	0.06
R0519:Lcmt2	UTSW	2	121,139,344 (GRCm38)	splice site	probably null
R1437:Lcmt2	UTSW	2	121,138,896 (GRCm38)	missense	probably benign	0.06
R1500:Lcmt2	UTSW	2	121,140,007 (GRCm38)	missense	probably benign	0.00
R1569:Lcmt2	UTSW	2	121,139,828 (GRCm38)	missense	probably damaging	1.00
R1612:Lcmt2	UTSW	2	121,139,120 (GRCm38)	missense	probably damaging	1.00
R1618:Lcmt2	UTSW	2	121,138,652 (GRCm38)	missense	probably damaging	0.98
R1990:Lcmt2	UTSW	2	121,140,281 (GRCm38)	missense	probably benign	0.07
R2091:Lcmt2	UTSW	2	121,138,616 (GRCm38)	missense	probably damaging	1.00
R2159:Lcmt2	UTSW	2	121,139,285 (GRCm38)	missense	probably damaging	1.00
R3812:Lcmt2	UTSW	2	121,138,706 (GRCm38)	missense	probably benign	0.01
R4725:Lcmt2	UTSW	2	121,139,430 (GRCm38)	missense	probably benign	0.00
R4727:Lcmt2	UTSW	2	121,139,430 (GRCm38)	missense	probably benign	0.00
R4968:Lcmt2	UTSW	2	121,139,736 (GRCm38)	missense	probably benign	0.00
R5626:Lcmt2	UTSW	2	121,139,462 (GRCm38)	missense	probably benign
R6246:Lcmt2	UTSW	2	121,140,389 (GRCm38)	missense	probably damaging	1.00
R6326:Lcmt2	UTSW	2	121,139,457 (GRCm38)	nonsense	probably null
R6524:Lcmt2	UTSW	2	121,138,931 (GRCm38)	missense	possibly damaging	0.75
R6924:Lcmt2	UTSW	2	121,140,003 (GRCm38)	missense	probably benign
R7282:Lcmt2	UTSW	2	121,138,790 (GRCm38)	missense	probably damaging	1.00
R7405:Lcmt2	UTSW	2	121,139,387 (GRCm38)	missense	probably benign	0.07
R7408:Lcmt2	UTSW	2	121,138,704 (GRCm38)	missense	probably benign	0.08
R8062:Lcmt2	UTSW	2	121,140,272 (GRCm38)	missense	possibly damaging	0.89
R8472:Lcmt2	UTSW	2	121,140,248 (GRCm38)	missense	probably damaging	1.00
R9414:Lcmt2	UTSW	2	121,140,140 (GRCm38)	missense	possibly damaging	0.81
R9569:Lcmt2	UTSW	2	121,140,041 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAAGACCTCCAGCGATAAGTGCTC -3'
(R):5'- TCTCCAGATCCTGTGACTCGGAATG -3'

Sequencing Primer
(F):5'- GGATTCTGACCCAAGCCATTG -3'
(R):5'- CCTGTGACTCGGAATGGGAAG -3'

Posted On

2013-07-30