Mutagenetix > Incidental Mutation

Incidental Mutation 'R9569:Lcmt2'

721817

Institutional Source

Beutler Lab

Gene Symbol

Lcmt2

Ensembl Gene

ENSMUSG00000074890

Gene Name

leucine carboxyl methyltransferase 2

Synonyms

Tyw4

MMRRC Submission

068966-MU

Accession Numbers

Essential gene?

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

Stock #

R9569 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

120967773-120971179 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 120970522 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 187 (A187V)

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 damaging
Transcript: ENSMUST00000110674
AA Change: A187V

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

SMART Domains

Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: A187V

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi2	T	A	1: 60,503,763 (GRCm39)	V356D	probably damaging	Het
Adgrd1	T	C	5: 129,256,701 (GRCm39)	V690A	possibly damaging	Het
Apba2	T	C	7: 64,393,138 (GRCm39)	M553T	possibly damaging	Het
Apeh	C	T	9: 107,971,609 (GRCm39)	V13M	unknown	Het
Apol11b	C	T	15: 77,524,771 (GRCm39)	E5K	possibly damaging	Het
Apol7e	C	T	15: 77,601,933 (GRCm39)	T177I	probably damaging	Het
Bltp1	T	C	3: 37,066,770 (GRCm39)	M211T		Het
Bub1b	T	C	2: 118,468,884 (GRCm39)	I883T	probably damaging	Het
C9	T	C	15: 6,489,062 (GRCm39)	S140P	probably damaging	Het
Cbfa2t2	T	A	2: 154,346,485 (GRCm39)	I64N	probably benign	Het
Cd180	A	T	13: 102,842,486 (GRCm39)	I511F	possibly damaging	Het
Cic	T	C	7: 24,972,120 (GRCm39)	V617A	possibly damaging	Het
Clca3a2	A	C	3: 144,513,075 (GRCm39)		probably null	Het
D5Ertd579e	T	C	5: 36,759,979 (GRCm39)	T1394A	probably damaging	Het
Dclk1	A	T	3: 55,387,852 (GRCm39)	E422D	probably benign	Het
Depdc5	A	T	5: 33,025,321 (GRCm39)	D21V	probably damaging	Het
Dis3l	A	G	9: 64,236,829 (GRCm39)	F40S	unknown	Het
Duox1	T	C	2: 122,148,971 (GRCm39)	V82A	probably benign	Het
Dus2	T	C	8: 106,771,507 (GRCm39)	V211A	probably damaging	Het
Eif2ak4	G	A	2: 118,251,316 (GRCm39)	S326N	probably benign	Het
Fat3	A	C	9: 15,830,495 (GRCm39)	L153R		Het
Gpx8	C	T	13: 113,182,125 (GRCm39)	V103I	probably damaging	Het
Gtf2a1l	A	G	17: 89,001,948 (GRCm39)	D268G	probably benign	Het
Hc	T	C	2: 34,926,359 (GRCm39)	I342V	probably benign	Het
Hsp90ab1	T	A	17: 45,879,878 (GRCm39)	D546V	possibly damaging	Het
Ifi206	T	G	1: 173,314,209 (GRCm39)	D77A		Het
Igfbp1	A	G	11: 7,147,881 (GRCm39)		probably benign	Het
Kdm3a	T	C	6: 71,584,434 (GRCm39)	D559G	probably benign	Het
Kif2a	A	G	13: 107,105,246 (GRCm39)	I565T	probably benign	Het
Krt1c	T	C	15: 101,724,924 (GRCm39)	T229A	probably damaging	Het
Mapk8ip1	A	G	2: 92,217,599 (GRCm39)	M241T	probably benign	Het
Mup15	T	C	4: 61,357,875 (GRCm39)		probably benign	Het
Myo9b	T	C	8: 71,811,629 (GRCm39)	V1912A	probably benign	Het
Naip5	T	A	13: 100,356,338 (GRCm39)	E1092D	probably benign	Het
Naip5	T	C	13: 100,359,821 (GRCm39)	T472A	probably benign	Het
Net1	A	G	13: 3,938,518 (GRCm39)	F123S	probably benign	Het
Or1j8	T	C	2: 36,191,946 (GRCm39)	Y132H	probably damaging	Het
Or52n2	C	T	7: 104,542,525 (GRCm39)	M103I	possibly damaging	Het
Or5h17	A	G	16: 58,820,228 (GRCm39)	Y60C	probably damaging	Het
Pcdhb13	T	C	18: 37,576,153 (GRCm39)	F177S	probably damaging	Het
Pclo	T	C	5: 14,907,065 (GRCm39)		probably null	Het
Perm1	A	G	4: 156,303,039 (GRCm39)	T528A	probably benign	Het
Pik3c2a	C	T	7: 115,957,939 (GRCm39)	A1116T	possibly damaging	Het
Prox2	G	A	12: 85,141,766 (GRCm39)	Q146*	probably null	Het
Psd	A	T	19: 46,308,717 (GRCm39)	C639S	possibly damaging	Het
Rffl	T	A	11: 82,703,264 (GRCm39)	T220S	probably benign	Het
Scn2a	A	G	2: 65,560,622 (GRCm39)	D1284G	probably damaging	Het
Scube1	T	C	15: 83,513,605 (GRCm39)	Y385C	probably damaging	Het
Sec14l3	A	T	11: 4,026,324 (GRCm39)	D388V	probably damaging	Het
Slc26a1	G	T	5: 108,819,460 (GRCm39)	Q596K	probably benign	Het
Slc6a19	T	C	13: 73,834,030 (GRCm39)	T343A	probably benign	Het
Slc7a4	A	G	16: 17,393,262 (GRCm39)	V179A		Het
Sox14	T	G	9: 99,757,562 (GRCm39)	D49A		Het
Spata31g1	G	C	4: 42,971,740 (GRCm39)	V358L	probably benign	Het
Timm22	A	G	11: 76,298,196 (GRCm39)	S56G	probably benign	Het
Tmub2	G	A	11: 102,179,153 (GRCm39)	W322*	probably null	Het
Tsc22d4	A	G	5: 137,756,428 (GRCm39)	T8A	probably benign	Het
Ttn	T	C	2: 76,539,652 (GRCm39)	I34445V	probably benign	Het
Tyms	A	T	5: 30,268,360 (GRCm39)	Y196*	probably null	Het
Ube2o	G	A	11: 116,434,823 (GRCm39)	T546M	probably damaging	Het
Umodl1	A	G	17: 31,217,143 (GRCm39)	Y1125C	probably damaging	Het
Unc13b	CGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGC	CGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGCCAGAGC	4: 43,177,312 (GRCm39)		probably benign	Het
Unk	A	T	11: 115,950,035 (GRCm39)	Q747L	probably damaging	Het
Vmn1r170	A	G	7: 23,306,294 (GRCm39)	E232G	probably benign	Het
Vps41	A	G	13: 19,013,396 (GRCm39)	Y338C	possibly damaging	Het
Washc5	T	C	15: 59,215,980 (GRCm39)	M800V	probably benign	Het
Wt1	T	A	2: 104,993,711 (GRCm39)	I348N	possibly damaging	Het
Xirp2	A	G	2: 67,341,242 (GRCm39)	Y1161C	probably damaging	Het
Xpo7	A	G	14: 70,906,140 (GRCm39)	M1001T	possibly damaging	Het
Yeats2	A	T	16: 19,972,902 (GRCm39)	R19W	probably damaging	Het
Zfp142	T	C	1: 74,615,386 (GRCm39)	T476A	probably damaging	Het
Zfp229	T	C	17: 21,964,573 (GRCm39)	W268R	possibly damaging	Het
Zfp473	A	G	7: 44,388,971 (GRCm39)	F50S	probably damaging	Het
Zfp975	A	T	7: 42,311,413 (GRCm39)	M400K	probably benign	Het
Zkscan5	A	G	5: 145,144,419 (GRCm39)	M150V	probably benign	Het
Znfx1	T	A	2: 166,897,875 (GRCm39)	I350F		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
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

Predicted Primers

PCR Primer
(F):5'- TTCACGACGGGAAACAGCTC -3'
(R):5'- TATTTTCGTCTGAAAGCGGCGG -3'

Sequencing Primer
(F):5'- GGAAACAGCTCCAGGCCATG -3'
(R):5'- ACGTGTCTCGGCTCAAGG -3'

Posted On

2022-08-09