Mutagenetix > Incidental Mutation

Incidental Mutation 'R1990:Lcmt2'

224834

Institutional Source

Beutler Lab

Gene Symbol

Lcmt2

Ensembl Gene

ENSMUSG00000074890

Gene Name

leucine carboxyl methyltransferase 2

Synonyms

Tyw4

Accession Numbers

Essential gene?

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

Stock #

R1990 (G1)

Quality Score

112

Status

Not validated

Chromosome

Chromosomal Location

120967773-120971179 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 120970762 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 107 (R107L)

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 benign
Transcript: ENSMUST00000099486

SMART Domains

Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890

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: R107L

PolyPhen 2 Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: R107L

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: ENSMUST00000146750

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158384

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147271

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156132

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.5%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	C	T	3: 137,771,419 (GRCm39)	R203*	probably null	Het
Acp6	T	C	3: 97,083,054 (GRCm39)	L355P	probably damaging	Het
Aebp2	T	C	6: 140,579,464 (GRCm39)	S234P	probably damaging	Het
Anapc7	A	G	5: 122,577,567 (GRCm39)	D374G	probably benign	Het
Apob	A	T	12: 8,051,039 (GRCm39)	I1088F	probably damaging	Het
Arid4b	T	C	13: 14,307,021 (GRCm39)	V92A	probably damaging	Het
Armc3	T	C	2: 19,297,953 (GRCm39)	Y575H	probably damaging	Het
Asxl2	G	T	12: 3,534,558 (GRCm39)	G252*	probably null	Het
Atl1	A	T	12: 70,010,102 (GRCm39)	K556M	probably damaging	Het
AU018091	A	G	7: 3,212,104 (GRCm39)	V206A	probably benign	Het
Bcas1	A	T	2: 170,212,397 (GRCm39)	D383E	possibly damaging	Het
Bmx	A	G	X: 163,015,192 (GRCm39)	W257R	probably benign	Het
Bpifb6	T	C	2: 153,747,270 (GRCm39)		probably null	Het
Cacna1b	G	A	2: 24,622,318 (GRCm39)	P222L	probably damaging	Het
Cand1	A	G	10: 119,045,972 (GRCm39)	S978P	probably damaging	Het
Cap2	T	A	13: 46,791,357 (GRCm39)	Y175N	possibly damaging	Het
Caps2	G	A	10: 112,036,591 (GRCm39)	A384T	probably benign	Het
Catsperg2	A	T	7: 29,420,470 (GRCm39)	Y223*	probably null	Het
Cd81	G	T	7: 142,620,938 (GRCm39)	G206*	probably null	Het
Cd84	A	G	1: 171,700,317 (GRCm39)	T145A	possibly damaging	Het
Cdkn2aip	G	T	8: 48,165,211 (GRCm39)	N167K	probably benign	Het
Ceacam14	T	A	7: 17,549,290 (GRCm39)	L227*	probably null	Het
Ceacam5	A	T	7: 17,491,805 (GRCm39)	D725V	probably damaging	Het
Cldn34a	A	T	X: 151,346,841 (GRCm39)	H171L	probably benign	Het
Col18a1	T	C	10: 76,916,988 (GRCm39)	I114V	unknown	Het
Cp	A	G	3: 20,033,177 (GRCm39)	D667G	probably damaging	Het
Cr2	G	A	1: 194,836,458 (GRCm39)	P1278S	possibly damaging	Het
Crat	A	G	2: 30,295,060 (GRCm39)	Y452H	possibly damaging	Het
Cyp4f13	T	A	17: 33,144,542 (GRCm39)	H318L	probably damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dmbt1	A	G	7: 130,660,018 (GRCm39)	N527S	probably damaging	Het
Fcgbpl1	A	T	7: 27,853,785 (GRCm39)	D1583V	probably damaging	Het
Fgb	G	T	3: 82,951,560 (GRCm39)	Y256*	probably null	Het
Frmd3	T	A	4: 74,105,676 (GRCm39)	S441T	probably damaging	Het
Glp1r	T	A	17: 31,149,722 (GRCm39)	C329S	possibly damaging	Het
Gm14190	G	T	11: 99,581,431 (GRCm39)	Q46K	unknown	Het
Golt1b	T	A	6: 142,338,080 (GRCm39)	F17Y	probably damaging	Het
Gsdmc	A	G	15: 63,673,748 (GRCm39)	I179T	probably benign	Het
Gsdmc2	T	A	15: 63,700,086 (GRCm39)	M229L	probably benign	Het
Gulp1	A	C	1: 44,805,274 (GRCm39)	N121T	possibly damaging	Het
Ift122	T	A	6: 115,901,328 (GRCm39)	F1037I	probably damaging	Het
Ildr1	A	T	16: 36,536,568 (GRCm39)	Y199F	probably damaging	Het
Ints2	T	A	11: 86,139,760 (GRCm39)	H278L	possibly damaging	Het
Invs	T	C	4: 48,392,599 (GRCm39)	V271A	possibly damaging	Het
Kcnj2	T	C	11: 110,963,709 (GRCm39)	I367T	probably benign	Het
Kif21b	T	C	1: 136,089,508 (GRCm39)	S1115P	probably damaging	Het
Lce1k	A	T	3: 92,714,125 (GRCm39)	C20S	unknown	Het
Letm1	A	AG	5: 33,926,859 (GRCm39)		probably null	Het
Lrrc9	A	C	12: 72,544,635 (GRCm39)	R71S	probably damaging	Het
Mcc	C	A	18: 44,624,382 (GRCm39)	E213*	probably null	Het
Mis18bp1	T	C	12: 65,205,468 (GRCm39)	T235A	probably benign	Het
Mta2	C	T	19: 8,919,696 (GRCm39)		probably benign	Het
Nebl	T	A	2: 17,457,321 (GRCm39)	I80F	probably damaging	Het
Nek10	A	G	14: 14,860,764 (GRCm38)	T467A	probably benign	Het
Nexn	A	T	3: 151,958,576 (GRCm39)	F106I	probably damaging	Het
Nrdc	T	A	4: 108,896,972 (GRCm39)	Y282*	probably null	Het
Nxf3	G	A	X: 134,976,583 (GRCm39)	P380S	possibly damaging	Het
Oma1	C	T	4: 103,178,971 (GRCm39)	T208I	probably damaging	Het
Or1a1	T	C	11: 74,086,989 (GRCm39)	V220A	probably damaging	Het
Or4c31	A	G	2: 88,291,686 (GRCm39)	M1V	probably null	Het
Or4d10c	C	A	19: 12,065,620 (GRCm39)	V179F	probably damaging	Het
Or4p21	A	G	2: 88,277,033 (GRCm39)	L83P	probably damaging	Het
Or51a42	A	T	7: 103,708,335 (GRCm39)	I158N	possibly damaging	Het
Or52l1	A	T	7: 104,830,221 (GRCm39)	C115S	probably damaging	Het
Or5p66	C	A	7: 107,885,566 (GRCm39)	G256*	probably null	Het
Or5p70	A	G	7: 107,995,041 (GRCm39)	Y238C	probably benign	Het
Panx2	A	T	15: 88,953,941 (GRCm39)	Y632F	possibly damaging	Het
Pdia4	T	C	6: 47,773,589 (GRCm39)	T587A	probably benign	Het
Piezo2	A	T	18: 63,207,733 (GRCm39)	L1426Q	probably null	Het
Pigk	T	A	3: 152,450,131 (GRCm39)	Y212N	probably damaging	Het
Pramel22	T	A	4: 143,380,838 (GRCm39)	Y395F	probably damaging	Het
Prl3b1	C	T	13: 27,429,775 (GRCm39)	T71I	possibly damaging	Het
Rab3gap1	A	G	1: 127,870,166 (GRCm39)	E929G	possibly damaging	Het
Rabl3	T	C	16: 37,384,079 (GRCm39)	I162T	probably benign	Het
Rasgrf2	T	A	13: 92,172,473 (GRCm39)	T188S	probably damaging	Het
Slc12a2	A	G	18: 58,043,358 (GRCm39)	I601V	possibly damaging	Het
Slc25a42	A	T	8: 70,644,519 (GRCm39)	I60N	probably benign	Het
Slc2a3	C	T	6: 122,713,694 (GRCm39)	G173S	probably damaging	Het
Slc46a3	G	A	5: 147,823,404 (GRCm39)	T146M	probably damaging	Het
Specc1	C	A	11: 61,920,120 (GRCm39)	P7T	possibly damaging	Het
Sptbn4	T	C	7: 27,123,235 (GRCm39)	D229G	probably benign	Het
Sspo	T	C	6: 48,427,984 (GRCm39)	I154T	probably benign	Het
Stx5a	T	C	19: 8,726,254 (GRCm39)		probably null	Het
Stxbp6	A	T	12: 44,902,640 (GRCm39)	C210*	probably null	Het
Tagap1	C	T	17: 7,224,285 (GRCm39)	R137Q	probably benign	Het
Tbc1d9	A	G	8: 83,997,932 (GRCm39)	Y1163C	probably damaging	Het
Tex14	T	G	11: 87,440,296 (GRCm39)	L1367R	probably damaging	Het
Tnnt3	C	T	7: 142,065,262 (GRCm39)	R131C	possibly damaging	Het
Tpx2	T	A	2: 152,732,544 (GRCm39)	M606K	probably benign	Het
Trim46	A	T	3: 89,145,008 (GRCm39)	Y489N	probably damaging	Het
Ttc28	C	T	5: 111,424,188 (GRCm39)	S1485L	probably benign	Het
Txnl1	T	C	18: 63,812,585 (GRCm39)	T70A	probably benign	Het
Unc80	T	C	1: 66,731,708 (GRCm39)	L3053P	probably damaging	Het
Wars1	G	T	12: 108,854,359 (GRCm39)	N18K	possibly damaging	Het
Wnt8a	A	G	18: 34,677,937 (GRCm39)	D115G	probably damaging	Het
Xndc1	T	A	7: 101,722,398 (GRCm39)	V21E	probably damaging	Het
Zfp493	T	A	13: 67,934,388 (GRCm39)	C114S	probably 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
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'- TAGATCACGAAAAGGGCGTC -3'
(R):5'- TTATCCACCGCGGCTATTAC -3'

Sequencing Primer
(F):5'- GCTCCAAGTAGGTCAGCAC -3'
(R):5'- GCTATTACGTGCGCGCG -3'

Posted On

2014-08-25