Mutagenetix > Incidental Mutation

Incidental Mutation 'R4968:Lcmt2'

384172

Institutional Source

Beutler Lab

Gene Symbol

Lcmt2

Ensembl Gene

ENSMUSG00000074890

Gene Name

leucine carboxyl methyltransferase 2

Synonyms

Tyw4

MMRRC Submission

042564-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.083) question?

Stock #

R4968 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120967773-120971179 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120970217 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 69 (T69A)

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: T69A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000097085
Gene: ENSMUSG00000074890
AA Change: T69A

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: T289A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000106302
Gene: ENSMUSG00000074890
AA Change: T289A

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: ENSMUST00000130221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158384

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146750

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156132

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.6%

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810021J22Rik	A	T	11: 58,769,616 (GRCm39)	K53*	probably null	Het
4921513D11Rik	T	C	17: 79,935,651 (GRCm39)	S255P	probably benign	Het
Ace	A	G	11: 105,872,679 (GRCm39)	N367S	possibly damaging	Het
Agl	A	T	3: 116,582,175 (GRCm39)	N282K	probably benign	Het
Ahnak	C	A	19: 8,992,464 (GRCm39)	P4583T	probably damaging	Het
Alpi	T	C	1: 87,029,247 (GRCm39)	D4G	probably benign	Het
Anks6	C	T	4: 47,030,795 (GRCm39)	G601S	probably damaging	Het
Aplnr	T	C	2: 84,967,289 (GRCm39)	Y105H	probably damaging	Het
Arhgap9	G	A	10: 127,162,875 (GRCm39)	R395K	possibly damaging	Het
Asah1	A	G	8: 41,807,067 (GRCm39)	M119T		Het
Atp5f1b	T	C	10: 127,919,856 (GRCm39)	F75L	probably damaging	Het
B4galt6	G	T	18: 20,861,026 (GRCm39)	N75K	possibly damaging	Het
Bco1	A	T	8: 117,857,833 (GRCm39)	H486L	probably benign	Het
Btaf1	T	A	19: 36,947,351 (GRCm39)	L480Q	probably null	Het
Ccdc34	G	T	2: 109,871,078 (GRCm39)		probably null	Het
Cdh19	T	C	1: 110,852,958 (GRCm39)	S326G	probably benign	Het
Cep89	A	G	7: 35,109,055 (GRCm39)	D178G	possibly damaging	Het
Cyp11b2	A	T	15: 74,725,854 (GRCm39)		probably null	Het
Cyp21a1	A	G	17: 35,022,383 (GRCm39)	I157T	possibly damaging	Het
Dcbld2	A	G	16: 58,245,074 (GRCm39)	D116G	probably damaging	Het
Ddx5	T	C	11: 106,674,953 (GRCm39)	Q377R	probably damaging	Het
Deup1	T	C	9: 15,503,724 (GRCm39)	D279G	probably damaging	Het
F11	G	A	8: 45,698,770 (GRCm39)	A458V	probably benign	Het
Fhad1	C	A	4: 141,645,618 (GRCm39)	G326W	probably damaging	Het
Fhit	C	T	14: 10,421,522 (GRCm38)	V26M	probably damaging	Het
Gjb5	A	T	4: 127,250,015 (GRCm39)	V43E	probably damaging	Het
Grtp1	A	T	8: 13,242,184 (GRCm39)	I75N	probably damaging	Het
Hmcn1	A	G	1: 150,533,221 (GRCm39)	I3022T	possibly damaging	Het
Hsp90ab1	T	C	17: 45,881,962 (GRCm39)	T166A	probably benign	Het
Ift70b	T	C	2: 75,768,391 (GRCm39)	I121V	probably benign	Het
Iho1	C	T	9: 108,289,713 (GRCm39)	V170M	probably benign	Het
Ikbke	GCC	G	1: 131,203,004 (GRCm39)		probably null	Het
Kcnk10	T	C	12: 98,401,161 (GRCm39)	I491V	probably benign	Het
Kcp	A	T	6: 29,497,628 (GRCm39)	C519*	probably null	Het
Lmf1	A	G	17: 25,804,592 (GRCm39)	Y90C	probably damaging	Het
Lpp	A	G	16: 24,798,064 (GRCm39)	D612G	probably damaging	Het
Lrfn5	C	A	12: 61,886,461 (GRCm39)	S83Y	probably damaging	Het
Lrp1b	T	C	2: 40,592,719 (GRCm39)		probably null	Het
Lrp1b	C	T	2: 41,679,074 (GRCm39)	C6Y	probably damaging	Het
Lrrc8c	A	G	5: 105,754,993 (GRCm39)	D256G	probably damaging	Het
Mphosph10	A	G	7: 64,032,656 (GRCm39)	Y478H	probably damaging	Het
Mpp2	T	C	11: 101,955,124 (GRCm39)	H167R	probably benign	Het
Mtss1	A	G	15: 58,815,767 (GRCm39)	S598P	probably damaging	Het
Myh10	A	G	11: 68,684,049 (GRCm39)	E1154G	probably damaging	Het
Myo10	T	C	15: 25,808,270 (GRCm39)	V1218A	probably damaging	Het
Myo19	A	G	11: 84,792,328 (GRCm39)	K599R	probably damaging	Het
Neurl4	T	C	11: 69,798,134 (GRCm39)	M771T	probably damaging	Het
Nlrc4	A	G	17: 74,753,936 (GRCm39)	V149A	probably benign	Het
Nup133	A	T	8: 124,641,935 (GRCm39)	S843T	probably benign	Het
Or2y1c	T	C	11: 49,361,358 (GRCm39)	C127R	probably damaging	Het
Or51k1	T	C	7: 103,661,777 (GRCm39)	N44S	probably damaging	Het
P3h2	A	G	16: 25,811,412 (GRCm39)		probably null	Het
Piezo2	A	T	18: 63,278,042 (GRCm39)	Y287*	probably null	Het
Prob1	T	C	18: 35,785,605 (GRCm39)	Y883C	probably damaging	Het
Pxdn	T	A	12: 30,050,011 (GRCm39)	H506Q	probably benign	Het
Ripor3	T	C	2: 167,827,037 (GRCm39)	D658G	probably benign	Het
Rufy1	T	A	11: 50,301,434 (GRCm39)	I333L	probably benign	Het
Selenok	T	A	14: 29,692,064 (GRCm39)	V34E	probably benign	Het
Selplg	T	C	5: 113,957,787 (GRCm39)	E173G	possibly damaging	Het
Septin10	A	G	10: 59,016,943 (GRCm39)	F194L	probably damaging	Het
Sptbn2	A	T	19: 4,779,230 (GRCm39)		probably null	Het
St6galnac6	C	T	2: 32,498,098 (GRCm39)	P6S	probably benign	Het
Syngr2	T	C	11: 117,704,296 (GRCm39)	Y194H	probably damaging	Het
Thbs4	A	G	13: 92,894,576 (GRCm39)	I649T	possibly damaging	Het
Triobp	T	A	15: 78,850,816 (GRCm39)	N323K	probably benign	Het
Tuba8	T	A	6: 121,197,548 (GRCm39)	L70Q	probably damaging	Het
Vmn2r61	A	G	7: 41,949,478 (GRCm39)	T633A	probably benign	Het
Zfp280b	G	T	10: 75,875,188 (GRCm39)	V356L	probably damaging	Het
Zswim4	A	T	8: 84,944,001 (GRCm39)	V746D	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
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
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'- ACTCTGGCAGAAAGAAACCCTG -3'
(R):5'- GACGCCCTTTTCGTGATCTATG -3'

Sequencing Primer
(F):5'- CTGAAGGCGAGGCAGGATCTATC -3'
(R):5'- TCGTGATCTATGAGCAGATGCAGC -3'

Posted On

2016-04-27