Mutagenetix > Incidental Mutation

Incidental Mutation 'R6326:Lcmt2'

510383

Institutional Source

Beutler Lab

Gene Symbol

Lcmt2

Ensembl Gene

ENSMUSG00000074890

Gene Name

leucine carboxyl methyltransferase 2

Synonyms

Tyw4

MMRRC Submission

044480-MU

Accession Numbers

Essential gene?

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

Stock #

R6326 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

120967773-120971179 bp(-) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

G to A at 120969938 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Stop codon at position 382 (R382*)

Ref Sequence

ENSEMBL: ENSMUSP00000106302 (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 null
Transcript: ENSMUST00000099486
AA Change: R162*

SMART Domains

Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: R162*

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 null
Transcript: ENSMUST00000110674
AA Change: R382*

SMART Domains

Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: R382*

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: ENSMUST00000156132

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158384

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146750

Meta Mutation Damage Score

0.9756

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.3%

Validation Efficiency

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts17	A	T	7: 66,770,636 (GRCm39)	Y915F	probably benign	Het
Adap2	T	A	11: 80,045,848 (GRCm39)	F43I	probably damaging	Het
Adprs	A	T	4: 126,210,406 (GRCm39)	L358Q	possibly damaging	Het
Akap9	A	C	5: 4,012,061 (GRCm39)	Q921H	probably damaging	Het
Amigo2	A	G	15: 97,143,256 (GRCm39)	S389P	probably benign	Het
Atg2b	A	T	12: 105,627,351 (GRCm39)	C545*	probably null	Het
C2cd3	A	G	7: 100,065,635 (GRCm39)	E807G	probably benign	Het
Ccdc110	A	G	8: 46,395,078 (GRCm39)	E323G	probably damaging	Het
Cdk5rap2	T	A	4: 70,153,691 (GRCm39)	S1711C	probably damaging	Het
Cebpzos	T	G	17: 79,226,486 (GRCm39)	D39E	probably damaging	Het
Cenpe	A	G	3: 134,945,539 (GRCm39)	N1018D	probably benign	Het
Cfap68	T	G	9: 50,676,057 (GRCm39)	N87T	probably damaging	Het
Clspn	C	A	4: 126,459,532 (GRCm39)	H141Q	probably damaging	Het
Cluh	C	T	11: 74,557,068 (GRCm39)	A1010V	probably benign	Het
Col27a1	G	T	4: 63,242,678 (GRCm39)		probably benign	Het
Cpt2	T	C	4: 107,771,513 (GRCm39)	M61V	probably benign	Het
Ddr2	T	A	1: 169,814,709 (GRCm39)	H578L	probably damaging	Het
Dnah14	T	A	1: 181,611,121 (GRCm39)	I3749N	probably damaging	Het
Dnajc18	T	C	18: 35,813,978 (GRCm39)	T264A	possibly damaging	Het
Ecpas	T	A	4: 58,827,068 (GRCm39)	T1022S	probably benign	Het
Eml6	T	C	11: 29,769,066 (GRCm39)	N693S	probably damaging	Het
Ephx4	A	G	5: 107,553,977 (GRCm39)	E9G	probably damaging	Het
Eps15l1	G	A	8: 73,095,278 (GRCm39)	Q747*	probably null	Het
Flrt1	C	T	19: 7,073,974 (GRCm39)	S191N	probably damaging	Het
Gm5114	C	T	7: 39,057,579 (GRCm39)	R680H	probably benign	Het
Gm5431	T	C	11: 48,780,172 (GRCm39)	H250R	probably damaging	Het
Gm7233	T	C	14: 43,040,342 (GRCm39)	C198R	possibly damaging	Het
Herc2	C	G	7: 55,872,682 (GRCm39)	Q4407E	probably damaging	Het
Hmx3	C	G	7: 131,144,734 (GRCm39)		probably benign	Het
Hoxb7	C	A	11: 96,177,909 (GRCm39)	A119E	probably benign	Het
Ifi207	A	T	1: 173,557,532 (GRCm39)	M402K	probably benign	Het
Ints14	T	C	9: 64,871,719 (GRCm39)	V19A	probably benign	Het
Itgae	T	A	11: 73,022,519 (GRCm39)	N911K	possibly damaging	Het
Kif1a	T	C	1: 93,004,048 (GRCm39)	S145G	probably damaging	Het
Klhdc4	A	G	8: 122,531,793 (GRCm39)	W187R	probably damaging	Het
Krt1	A	T	15: 101,758,684 (GRCm39)	I160N	probably damaging	Het
Krt12	T	C	11: 99,307,745 (GRCm39)	T448A	probably benign	Het
Map3k8	C	T	18: 4,340,651 (GRCm39)	S221N	probably damaging	Het
Med17	T	C	9: 15,190,854 (GRCm39)	D79G	probably benign	Het
Mlf1	A	T	3: 67,307,060 (GRCm39)	I257F	probably damaging	Het
Mov10l1	T	A	15: 88,879,098 (GRCm39)	F153I	probably damaging	Het
Msto1	A	C	3: 88,819,405 (GRCm39)	V149G	probably damaging	Het
Mybl1	T	C	1: 9,748,732 (GRCm39)		probably null	Het
Myoc	A	G	1: 162,476,580 (GRCm39)	Y428C	probably damaging	Het
Nin	A	G	12: 70,091,955 (GRCm39)	S785P	possibly damaging	Het
Oit3	A	T	10: 59,264,061 (GRCm39)	F358I	probably damaging	Het
Or5t15	C	T	2: 86,681,338 (GRCm39)	V235I	probably benign	Het
Or6c88	A	G	10: 129,406,571 (GRCm39)	T16A	possibly damaging	Het
Paip1	A	G	13: 119,566,753 (GRCm39)	N29S	probably benign	Het
Pcdhgb4	T	C	18: 37,855,509 (GRCm39)	S635P	probably benign	Het
Pcsk1	A	G	13: 75,280,298 (GRCm39)	N708D	possibly damaging	Het
Plch1	C	T	3: 63,688,811 (GRCm39)	W131*	probably null	Het
Prag1	A	T	8: 36,569,860 (GRCm39)	M148L	possibly damaging	Het
Ptch1	A	G	13: 63,691,359 (GRCm39)	L176P	probably damaging	Het
Ralgapa1	A	T	12: 55,793,931 (GRCm39)	V568D	probably damaging	Het
Rb1	A	T	14: 73,435,974 (GRCm39)	M897K	probably benign	Het
Resf1	T	A	6: 149,230,493 (GRCm39)	Y1180N	probably damaging	Het
Robo3	T	A	9: 37,338,323 (GRCm39)	Q386L	probably damaging	Het
Rtn4rl1	T	C	11: 75,156,828 (GRCm39)	V420A	possibly damaging	Het
Sall1	A	T	8: 89,756,896 (GRCm39)	N1069K	probably benign	Het
Sipa1l1	A	G	12: 82,419,242 (GRCm39)	E640G	probably damaging	Het
Slc22a2	C	A	17: 12,831,297 (GRCm39)	Y362*	probably null	Het
Slc5a9	T	C	4: 111,737,450 (GRCm39)	E603G	probably benign	Het
Slc6a17	A	T	3: 107,407,722 (GRCm39)	I83N	probably damaging	Het
Snx29	G	T	16: 11,221,430 (GRCm39)	M285I	probably benign	Het
Spata2	T	C	2: 167,326,094 (GRCm39)	T242A	possibly damaging	Het
Stard13	A	G	5: 150,970,384 (GRCm39)	L733P	possibly damaging	Het
Svep1	A	G	4: 58,073,045 (GRCm39)	V2088A	possibly damaging	Het
Tdp2	A	G	13: 25,024,540 (GRCm39)	E279G	probably damaging	Het
Tnfrsf8	T	G	4: 144,995,794 (GRCm39)	I422L	probably damaging	Het
Tpk1	T	A	6: 43,323,736 (GRCm39)	T189S	possibly damaging	Het
Trhde	A	T	10: 114,403,129 (GRCm39)	M498K	probably damaging	Het
Trim35	T	A	14: 66,540,653 (GRCm39)	H168Q	possibly damaging	Het
Tubb5	T	C	17: 36,147,347 (GRCm39)		probably benign	Het
Tut4	C	T	4: 108,336,177 (GRCm39)	T6I	probably benign	Het
Vmn1r181	G	A	7: 23,684,183 (GRCm39)	R216Q	probably benign	Het
Vmn2r77	G	A	7: 86,451,031 (GRCm39)	G306R	probably benign	Het
Xkr4	C	T	1: 3,741,261 (GRCm39)	R104H	possibly damaging	Het
Zfp398	T	C	6: 47,843,355 (GRCm39)	I337T	possibly damaging	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
R1612:Lcmt2	UTSW	2	120,969,601 (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
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'- ATAAATCAAGTTGGAGAGCCCCAG -3'
(R):5'- GAAACTCCAGTGTTTGAGCCC -3'

Sequencing Primer
(F):5'- CAGAGGCTGGACTTACTGGG -3'
(R):5'- TCCAGTGTTTGAGCCCTCAGAG -3'

Posted On

2018-04-02