Mutagenetix > Incidental Mutation

Incidental Mutation 'R0458:Lrtm2'

41303

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

038658-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.081) question?

Stock #

R0458 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

119292094-119307727 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 119294229 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 301 (P301S)

Ref Sequence

ENSEMBL: ENSMUSP00000126661 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037434] [ENSMUST00000068351] [ENSMUST00000112756] [ENSMUST00000168793] [ENSMUST00000186622]

AlphaFold

Q8BGX3

Predicted Effect

probably benign
Transcript: ENSMUST00000037434

SMART Domains

Protein: ENSMUSP00000044660
Gene: ENSMUSG00000041460

Domain	Start	End	E-Value	Type
Blast:WNT1	79	144	1e-13	BLAST
Pfam:VWA_N	155	271	7.3e-40	PFAM
VWA	296	481	4.37e-14	SMART
Pfam:Cache_1	494	586	1.1e-24	PFAM
low complexity region	837	849	N/A	INTRINSIC
low complexity region	975	984	N/A	INTRINSIC
low complexity region	1000	1011	N/A	INTRINSIC
low complexity region	1120	1143	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000068351
AA Change: P301S

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

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: P301S

Domain	Start	End	E-Value	Type
LRRNT	38	72	5.22e-8	SMART
LRR	71	90	1.58e2	SMART
LRR_TYP	91	114	2.43e-4	SMART
LRR_TYP	115	138	7.78e-3	SMART
LRR	140	162	5.72e-1	SMART
LRR	163	186	3.78e-1	SMART
LRRCT	198	251	3.1e-7	SMART
low complexity region	271	290	N/A	INTRINSIC
transmembrane domain	312	334	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000112756
AA Change: P301S

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

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: P301S

Domain	Start	End	E-Value	Type
LRRNT	38	72	5.22e-8	SMART
LRR	71	90	1.58e2	SMART
LRR_TYP	91	114	2.43e-4	SMART
LRR_TYP	115	138	7.78e-3	SMART
LRR	140	162	5.72e-1	SMART
LRR	163	186	3.78e-1	SMART
LRRCT	198	251	3.1e-7	SMART
low complexity region	271	290	N/A	INTRINSIC
transmembrane domain	312	334	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000168793
AA Change: P301S

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

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: P301S

Domain	Start	End	E-Value	Type
LRRNT	38	72	5.22e-8	SMART
LRR	71	90	1.58e2	SMART
LRR_TYP	91	114	2.43e-4	SMART
LRR_TYP	115	138	7.78e-3	SMART
LRR	140	162	5.72e-1	SMART
LRR	163	186	3.78e-1	SMART
LRRCT	198	251	3.1e-7	SMART
low complexity region	271	290	N/A	INTRINSIC
transmembrane domain	312	334	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186622

SMART Domains

Protein: ENSMUSP00000140197
Gene: ENSMUSG00000041460

Domain	Start	End	E-Value	Type
Blast:WNT1	79	144	1e-13	BLAST
Pfam:VWA_N	155	271	6.4e-44	PFAM
VWA	296	481	2.7e-16	SMART
Pfam:Cache_1	494	559	1.1e-7	PFAM
low complexity region	812	824	N/A	INTRINSIC
low complexity region	950	959	N/A	INTRINSIC
low complexity region	975	986	N/A	INTRINSIC
low complexity region	1095	1118	N/A	INTRINSIC

Meta Mutation Damage Score

0.1697

Coding Region Coverage

1x: 99.7%
3x: 98.9%
10x: 97.0%
20x: 94.3%

Validation Efficiency

100% (79/79)

Allele List at MGI

All alleles(5) : Targeted, other(2) Gene trapped(3)

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933407L21Rik	A	G	1: 85,856,747 (GRCm39)	E8G	unknown	Het
9130008F23Rik	T	C	17: 41,191,127 (GRCm39)	T101A	probably benign	Het
Abcb8	C	T	5: 24,611,231 (GRCm39)	T455I	probably benign	Het
Abcb9	C	A	5: 124,220,209 (GRCm39)		probably null	Het
Akp3	T	G	1: 87,054,259 (GRCm39)	Y265*	probably null	Het
Atp6v1b1	A	T	6: 83,729,390 (GRCm39)	D109V	probably damaging	Het
Aurka	C	A	2: 172,212,366 (GRCm39)	E4*	probably null	Het
Cacna1g	T	A	11: 94,300,266 (GRCm39)	Q2168L	probably damaging	Het
Cdc45	T	A	16: 18,600,722 (GRCm39)		probably benign	Het
Cfap61	T	C	2: 145,850,837 (GRCm39)	V325A	probably benign	Het
Clasp2	T	A	9: 113,735,292 (GRCm39)		probably null	Het
Crim1	T	A	17: 78,620,655 (GRCm39)	I365N	probably damaging	Het
Dcaf8	A	G	1: 172,001,610 (GRCm39)	N269S	probably benign	Het
Dnaaf5	T	C	5: 139,147,633 (GRCm39)	V399A	possibly damaging	Het
Ear2	A	G	14: 44,340,705 (GRCm39)	Y121C	probably damaging	Het
Eef2k	T	C	7: 120,502,513 (GRCm39)	Y692H	probably damaging	Het
Elavl2	A	T	4: 91,197,104 (GRCm39)		probably benign	Het
Epn2	C	A	11: 61,437,281 (GRCm39)	R97L	possibly damaging	Het
Fam243	T	C	16: 92,117,995 (GRCm39)	I98V	probably benign	Het
Fzd6	G	A	15: 38,894,676 (GRCm39)	A281T	probably damaging	Het
Garem2	T	A	5: 30,319,180 (GRCm39)	I214N	probably damaging	Het
Glg1	A	G	8: 111,887,238 (GRCm39)		probably benign	Het
Golm1	T	C	13: 59,812,178 (GRCm39)	E48G	probably damaging	Het
Gpaa1	G	T	15: 76,216,233 (GRCm39)	R12L	probably benign	Het
Gstm1	T	A	3: 107,924,679 (GRCm39)	T34S	probably benign	Het
Gtf3c1	G	A	7: 125,243,306 (GRCm39)	P1766L	possibly damaging	Het
Herc1	A	T	9: 66,383,663 (GRCm39)	Q3709L	probably benign	Het
Hoxa13	CCG	CCGCG	6: 52,237,618 (GRCm39)		probably null	Het
Icam1	A	G	9: 20,939,157 (GRCm39)		probably null	Het
Itga9	T	C	9: 118,510,096 (GRCm39)		probably null	Het
Kif15	T	C	9: 122,838,424 (GRCm39)	F1121L	probably benign	Het
Klhl30	T	A	1: 91,288,718 (GRCm39)		probably benign	Het
Ldlrad1	T	C	4: 107,073,387 (GRCm39)	C141R	probably damaging	Het
Lemd2	T	C	17: 27,409,627 (GRCm39)	D508G	probably damaging	Het
Lilra5	A	C	7: 4,241,218 (GRCm39)	T52P	probably benign	Het
Mcoln2	A	G	3: 145,855,768 (GRCm39)		probably benign	Het
Mkrn2os	A	G	6: 115,563,631 (GRCm39)	S135P	probably damaging	Het
Mlxipl	T	C	5: 135,162,224 (GRCm39)	V607A	probably benign	Het
Mmadhc	T	C	2: 50,171,173 (GRCm39)	Y213C	probably benign	Het
Mpo	C	A	11: 87,687,123 (GRCm39)	A223E	probably benign	Het
Mthfd2l	C	G	5: 91,168,036 (GRCm39)	I310M	probably damaging	Het
Muc5b	C	A	7: 141,418,709 (GRCm39)	A3885D	probably benign	Het
Mvp	A	G	7: 126,597,663 (GRCm39)	W152R	probably damaging	Het
Nmur2	A	T	11: 55,931,394 (GRCm39)	F106I	possibly damaging	Het
Nr3c2	T	A	8: 77,636,167 (GRCm39)	F423I	probably damaging	Het
Or1l8	A	G	2: 36,817,349 (GRCm39)	V259A	probably damaging	Het
Or5m5	A	G	2: 85,814,600 (GRCm39)	S139G	probably benign	Het
Or8c16	G	A	9: 38,130,344 (GRCm39)	C75Y	probably damaging	Het
Or9q1	G	T	19: 13,805,593 (GRCm39)	H56N	probably benign	Het
Pappa	A	G	4: 65,074,119 (GRCm39)	I224M	probably damaging	Het
Prex1	A	C	2: 166,427,743 (GRCm39)	S800A	probably damaging	Het
Prkaca	T	C	8: 84,721,911 (GRCm39)		probably benign	Het
Ptpru	A	T	4: 131,526,986 (GRCm39)	V662E	possibly damaging	Het
Rabep1	T	A	11: 70,777,824 (GRCm39)		probably null	Het
Rbms2	C	T	10: 127,987,058 (GRCm39)	C50Y	probably damaging	Het
Rd3	C	T	1: 191,709,414 (GRCm39)	P25S	probably damaging	Het
Rnf148	T	G	6: 23,654,256 (GRCm39)	I247L	probably benign	Het
Sf3b3	A	G	8: 111,538,768 (GRCm39)		probably benign	Het
Slc35c1	A	T	2: 92,284,858 (GRCm39)	F252Y	probably damaging	Het
Slc38a11	T	C	2: 65,193,813 (GRCm39)		probably null	Het
Snx6	G	T	12: 54,814,921 (GRCm39)	Y17*	probably null	Het
Sox6	C	A	7: 115,089,029 (GRCm39)	R611L	probably damaging	Het
Spata13	G	A	14: 60,929,492 (GRCm39)	R350H	probably damaging	Het
Sppl2a	G	T	2: 126,746,879 (GRCm39)	A483D	probably damaging	Het
Stat1	C	T	1: 52,188,211 (GRCm39)		probably benign	Het
Tab2	A	T	10: 7,795,319 (GRCm39)	Y314N	probably damaging	Het
Tor1aip1	T	C	1: 155,906,153 (GRCm39)	N213S	probably damaging	Het
Trim39	T	C	17: 36,572,404 (GRCm39)	K300E	probably damaging	Het
Tubal3	T	C	13: 3,983,137 (GRCm39)	S306P	probably damaging	Het
Ufm1	A	G	3: 53,768,655 (GRCm39)	L33P	probably damaging	Het
Washc4	G	A	10: 83,382,663 (GRCm39)	V26I	possibly damaging	Het
Wfs1	A	G	5: 37,126,013 (GRCm39)	Y293H	probably damaging	Het
Zbtb41	T	C	1: 139,351,214 (GRCm39)	V109A	probably damaging	Het
Zfp667	T	C	7: 6,307,844 (GRCm39)	S171P	probably benign	Het
Zkscan5	T	A	5: 145,142,281 (GRCm39)	H59Q	probably damaging	Het
Zswim8	C	T	14: 20,768,965 (GRCm39)	R1128W	probably damaging	Het

Other mutations in Lrtm2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01089:Lrtm2	APN	6	119,297,753 (GRCm39)	missense	possibly damaging	0.91
IGL02619:Lrtm2	APN	6	119,294,199 (GRCm39)	missense	probably damaging	1.00
IGL02694:Lrtm2	APN	6	119,297,846 (GRCm39)	missense	possibly damaging	0.80
1mM(1):Lrtm2	UTSW	6	119,294,252 (GRCm39)	missense	probably damaging	0.99
R1183:Lrtm2	UTSW	6	119,297,846 (GRCm39)	missense	probably benign	0.02
R1502:Lrtm2	UTSW	6	119,294,235 (GRCm39)	missense	probably benign	0.02
R3801:Lrtm2	UTSW	6	119,294,444 (GRCm39)	missense	probably damaging	1.00
R4373:Lrtm2	UTSW	6	119,297,489 (GRCm39)	missense	probably damaging	1.00
R5126:Lrtm2	UTSW	6	119,294,400 (GRCm39)	missense	probably benign	0.04
R6366:Lrtm2	UTSW	6	119,294,238 (GRCm39)	missense	probably damaging	0.99
R7177:Lrtm2	UTSW	6	119,294,113 (GRCm39)	missense	probably damaging	0.99
R7442:Lrtm2	UTSW	6	119,294,392 (GRCm39)	missense	probably damaging	0.99
R7448:Lrtm2	UTSW	6	119,297,784 (GRCm39)	missense	probably benign	0.00
R7921:Lrtm2	UTSW	6	119,294,328 (GRCm39)	missense	possibly damaging	0.94
R7936:Lrtm2	UTSW	6	119,297,394 (GRCm39)	missense	probably benign	0.01
R8204:Lrtm2	UTSW	6	119,294,369 (GRCm39)	missense	probably benign	0.03
R8239:Lrtm2	UTSW	6	119,297,778 (GRCm39)	missense	probably damaging	0.99
R8364:Lrtm2	UTSW	6	119,294,259 (GRCm39)	missense	probably benign	0.14
R8415:Lrtm2	UTSW	6	119,294,458 (GRCm39)	missense	probably damaging	1.00
R8823:Lrtm2	UTSW	6	119,294,193 (GRCm39)	missense	probably damaging	1.00
R9014:Lrtm2	UTSW	6	119,294,219 (GRCm39)	missense	probably damaging	1.00
R9183:Lrtm2	UTSW	6	119,294,384 (GRCm39)	missense	probably damaging	1.00
R9290:Lrtm2	UTSW	6	119,297,792 (GRCm39)	missense	probably damaging	1.00
R9329:Lrtm2	UTSW	6	119,297,412 (GRCm39)	nonsense	probably null
R9342:Lrtm2	UTSW	6	119,297,934 (GRCm39)	missense	probably benign
R9390:Lrtm2	UTSW	6	119,297,948 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TCTCATGCCACAGACGAGATCTGC -3'
(R):5'- ATAGGTGCTAGTTCCTGCCTGCTC -3'

Sequencing Primer
(F):5'- AGACGAGATCTGCTTCTGATCTTC -3'
(R):5'- AGGTCACCCCAGTTCTAGC -3'

Posted On

2013-05-23