Mutagenetix > Incidental Mutation

Incidental Mutation 'R1612:Lcmt2'

176844

Institutional Source

Beutler Lab

Gene Symbol

Lcmt2

Ensembl Gene

ENSMUSG00000074890

Gene Name

leucine carboxyl methyltransferase 2

Synonyms

Tyw4

MMRRC Submission

039649-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.095) question?

Stock #

R1612 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120967773-120971179 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120969601 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 274 (Y274C)

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 damaging
Transcript: ENSMUST00000099486
AA Change: Y274C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: Y274C

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 damaging
Transcript: ENSMUST00000110674
AA Change: Y494C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: Y494C

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: ENSMUST00000147271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156132

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146750

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158384

Meta Mutation Damage Score

0.3504

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.6%

Validation Efficiency

97% (69/71)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579G24Rik	A	G	3: 79,538,451 (GRCm39)	T66A	probably benign	Het
Actb	A	G	5: 142,891,350 (GRCm39)	F31S	probably damaging	Het
Adamts7	T	C	9: 90,070,750 (GRCm39)	S624P	possibly damaging	Het
Adh7	T	C	3: 137,934,642 (GRCm39)	I355T	possibly damaging	Het
Arhgef40	A	G	14: 52,241,538 (GRCm39)	E106G	probably damaging	Het
Brd10	A	G	19: 29,695,245 (GRCm39)	V1483A	possibly damaging	Het
Cabp7	T	C	11: 4,689,198 (GRCm39)	D149G	probably damaging	Het
Cass4	A	T	2: 172,268,998 (GRCm39)	Q362L	possibly damaging	Het
Cd14	G	A	18: 36,858,718 (GRCm39)	Q246*	probably null	Het
Cdr2l	A	C	11: 115,284,232 (GRCm39)	E189D	probably benign	Het
Col6a6	A	G	9: 105,654,748 (GRCm39)	V991A	probably damaging	Het
Coq7	A	G	7: 118,109,134 (GRCm39)	W305R	unknown	Het
Cracr2a	G	T	6: 127,580,892 (GRCm39)	G23*	probably null	Het
Dclk2	C	T	3: 86,712,946 (GRCm39)	R503Q	possibly damaging	Het
Epcam	T	C	17: 87,947,366 (GRCm39)	L40P	possibly damaging	Het
Eps8	G	A	6: 137,477,616 (GRCm39)	P531S	probably benign	Het
Faap100	C	A	11: 120,267,914 (GRCm39)	L286F	probably damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Fbn2	A	T	18: 58,194,824 (GRCm39)	C1446S	probably damaging	Het
Fmo3	A	G	1: 162,795,454 (GRCm39)	V127A	probably damaging	Het
Frem3	A	G	8: 81,341,490 (GRCm39)	D1261G	probably damaging	Het
Gabbr1	A	G	17: 37,381,561 (GRCm39)	Y775C	probably damaging	Het
Gbp11	G	T	5: 105,474,462 (GRCm39)	Q405K	possibly damaging	Het
Gdi2	T	A	13: 3,610,051 (GRCm39)	V260E	probably benign	Het
Glp2r	C	T	11: 67,633,033 (GRCm39)	V98M	possibly damaging	Het
Gm13741	T	C	2: 87,486,431 (GRCm39)	Y278C	probably damaging	Het
Gm7732	G	A	17: 21,350,177 (GRCm39)		noncoding transcript	Het
Gnptab	T	A	10: 88,264,344 (GRCm39)		probably null	Het
Hbs1l	T	G	10: 21,234,734 (GRCm39)	F596V	probably damaging	Het
Krt78	A	T	15: 101,860,279 (GRCm39)		probably null	Het
Krt87	A	T	15: 101,386,092 (GRCm39)	L223Q	probably benign	Het
Limd1	A	G	9: 123,347,219 (GRCm39)	Y620C	probably damaging	Het
Lvrn	G	T	18: 47,027,770 (GRCm39)	A862S	probably damaging	Het
Map4k2	A	G	19: 6,393,371 (GRCm39)	E206G	probably damaging	Het
Med16	A	G	10: 79,735,079 (GRCm39)	S461P	probably damaging	Het
Mrfap1	C	A	5: 36,953,706 (GRCm39)	A78S	probably damaging	Het
Nav2	T	A	7: 49,220,959 (GRCm39)	N1715K	probably damaging	Het
Ndc1	A	G	4: 107,252,265 (GRCm39)		probably benign	Het
Ngly1	G	T	14: 16,290,867 (GRCm38)	G450*	probably null	Het
Or13c25	T	A	4: 52,911,501 (GRCm39)	M98L	probably benign	Het
Or5k3	T	C	16: 58,969,987 (GRCm39)	M258T	probably benign	Het
Pde3b	T	A	7: 114,118,791 (GRCm39)	Y643*	probably null	Het
Pdilt	T	G	7: 119,086,198 (GRCm39)	N506H	possibly damaging	Het
Pear1	C	T	3: 87,659,160 (GRCm39)		probably null	Het
Pfkp	A	T	13: 6,638,625 (GRCm39)	M582K	probably damaging	Het
Pigl	T	A	11: 62,403,820 (GRCm39)	F251I	probably benign	Het
Plk3	A	G	4: 116,989,004 (GRCm39)	Y252H	probably damaging	Het
Prdx3	A	G	19: 60,862,872 (GRCm39)	S12P	possibly damaging	Het
Prkag2	T	C	5: 25,082,026 (GRCm39)	I96V	probably benign	Het
Pwwp3a	T	A	10: 80,068,889 (GRCm39)		probably benign	Het
Rgs3	G	A	4: 62,544,172 (GRCm39)	V146M	probably damaging	Het
Serpinh1	T	C	7: 98,998,138 (GRCm39)	D164G	probably damaging	Het
Slc35d2	T	C	13: 64,259,324 (GRCm39)		probably benign	Het
Slc6a6	A	G	6: 91,718,008 (GRCm39)	N316D	probably damaging	Het
Snx14	A	T	9: 88,258,958 (GRCm39)	M973K	possibly damaging	Het
Sptan1	C	G	2: 29,893,348 (GRCm39)	R1126G	probably damaging	Het
Stpg3	T	C	2: 25,103,866 (GRCm39)	T157A	probably benign	Het
Tmem39b	A	T	4: 129,580,715 (GRCm39)	M259K	possibly damaging	Het
Tomm40l	A	T	1: 171,049,471 (GRCm39)		probably null	Het
Tsen34	G	T	7: 3,698,395 (GRCm39)	G180W	probably damaging	Het
Ube2l6	C	T	2: 84,636,717 (GRCm39)	R54W	probably damaging	Het
Vdac1	A	T	11: 52,274,897 (GRCm39)	T182S	probably benign	Het
Wdr3	T	C	3: 100,058,515 (GRCm39)		probably benign	Het
Wsb1	T	A	11: 79,139,411 (GRCm39)	Q95L	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
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
R4725:Lcmt2	UTSW	2	120,969,911 (GRCm39)	missense	probably benign	0.00
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'- CAAGACCTCCAGCGATAAGTGCTC -3'
(R):5'- TGGACGCCTTTATCACACCATGAC -3'

Sequencing Primer
(F):5'- GATAAGTGCTCCCCCTTGC -3'
(R):5'- GTTCTTGGAGGAAGACTCTCCC -3'

Posted On

2014-04-24