Mutagenetix > Incidental Mutations

Incidental Mutation 'R7177:Lrtm2'

558676

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

Accession Numbers

Genbank: NM_172492.3, NM_001172207.1; Ensembl: ENSMUST00000068351

Is this an essential gene?

Probably non essential (E-score: 0.064) question?

Stock #

R7177 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

119315133-119330766 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 119317152 bp

Zygosity

Heterozygous

Amino Acid Change

Methionine to Isoleucine at position 339 (M339I)

Ref Sequence

ENSEMBL: ENSMUSP00000108376 (fasta)

Gene Model

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

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: M339I

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: M339I

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: M339I

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: M339I

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: M339I

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: M339I

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

Coding Region Coverage

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

Validation Efficiency

Allele List at MGI

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

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029J07Rik	T	A	8: 45,970,407	E89D	possibly damaging	Het
4930550C14Rik	T	C	9: 53,414,385	L74S	probably damaging	Het
4933406M09Rik	T	C	1: 134,390,425	S312P	probably benign	Het
5730409E04Rik	A	G	4: 126,611,732	S18G	probably benign	Het
Adam29	A	G	8: 55,872,624	I265T	probably benign	Het
Aff4	C	T	11: 53,406,639	S896L	probably benign	Het
Ankrd27	T	C	7: 35,619,397	I571T	probably damaging	Het
Bdp1	C	A	13: 100,049,970	R1658I	probably damaging	Het
Carm1	C	T	9: 21,547,027	T7M	unknown	Het
Ccdc105	T	C	10: 78,752,490	D162G	probably damaging	Het
Ccdc183	A	G	2: 25,616,284	V100A	probably damaging	Het
Cd86	CA	CAA	16: 36,606,555		probably null	Het
Ceacam2	T	G	7: 25,520,916	D239A	probably benign	Het
Cmya5	T	C	13: 93,095,328	D1084G	probably benign	Het
Cog5	T	A	12: 31,760,889	I194K	probably damaging	Het
Col20a1	C	T	2: 180,994,214	Q211*	probably null	Het
Col9a1	T	A	1: 24,195,417	L13Q	unknown	Het
Cracr2a	A	T	6: 127,608,706	M156L	probably benign	Het
Cts8	C	T	13: 61,251,691	M151I	possibly damaging	Het
Cyp2ab1	A	T	16: 20,316,719	L11Q	probably null	Het
Dhrs13	T	A	11: 78,034,382	C160S	probably benign	Het
Enthd1	T	A	15: 80,474,214	E368D	probably damaging	Het
Fbxo18	A	G	2: 11,755,711	I676T	probably damaging	Het
Fcgrt	T	C	7: 45,101,997	R176G	probably benign	Het
Gatd1	A	G	7: 141,411,034	F67L	possibly damaging	Het
Gm4353	G	A	7: 116,084,492	P23S	probably damaging	Het
Gm6882	T	A	7: 21,427,752	I64F	possibly damaging	Het
Grwd1	A	T	7: 45,830,780	M1K	probably null	Het
Hook2	T	A	8: 84,991,417	S58T	probably benign	Het
Iqch	T	G	9: 63,421,835	*1072C	probably null	Het
Kmt2d	G	A	15: 98,850,386	T3019I	unknown	Het
Lmx1a	T	C	1: 167,846,678	S356P	probably benign	Het
Lrig3	A	G	10: 126,006,843	M546V	probably benign	Het
Lrrc1	C	A	9: 77,472,222	E96*	probably null	Het
Map10	T	C	8: 125,671,845	V659A	probably benign	Het
Map7d1	A	G	4: 126,236,985	C384R	probably damaging	Het
Mcur1	T	C	13: 43,544,536	D296G	probably damaging	Het
Mettl24	A	T	10: 40,810,512	H295L	probably damaging	Het
Mpl	A	G	4: 118,448,544		probably null	Het
Mrps5	T	C	2: 127,595,697	V148A	probably benign	Het
N4bp2	T	C	5: 65,807,548	V980A	probably damaging	Het
Ncaph	A	T	2: 127,116,586	D504E	probably damaging	Het
Nxph1	A	G	6: 9,247,497	N156S	probably damaging	Het
Odf3l1	T	A	9: 56,849,978	M139L	possibly damaging	Het
Olfr1307	T	A	2: 111,945,156	Q100L	probably damaging	Het
Olfr1395	T	A	11: 49,149,185	C309*	probably null	Het
Pafah1b3	T	A	7: 25,295,232	I186L	probably benign	Het
Papola	C	A	12: 105,809,531	N235K	possibly damaging	Het
Pcnx3	A	T	19: 5,687,499	M98K	probably benign	Het
Pkhd1l1	A	G	15: 44,467,404	N125S	probably damaging	Het
Pls1	T	A	9: 95,773,559	H380L	probably benign	Het
Plxna1	T	C	6: 89,323,329	T1591A	possibly damaging	Het
Pparg	T	G	6: 115,441,620	S147A	probably benign	Het
Prdm10	T	C	9: 31,367,707	S1025P	probably benign	Het
Prkcd	T	A	14: 30,599,707	H510L	probably damaging	Het
Ptprh	T	A	7: 4,569,481	E499D	possibly damaging	Het
Rad51ap1	A	G	6: 126,925,020	S256P	probably benign	Het
Rad54b	A	G	4: 11,599,755	T320A	probably damaging	Het
Rnf207	A	G	4: 152,312,177	I459T	probably benign	Het
Runx2	G	A	17: 44,814,192	P80L	probably damaging	Het
Ryr3	A	T	2: 112,900,843	D727E	probably damaging	Het
Sdk2	C	T	11: 113,829,969	R1378H	possibly damaging	Het
Slc7a11	A	G	3: 50,443,231	S11P	probably benign	Het
Sox4	A	G	13: 28,953,017	V2A	probably damaging	Het
Srf	A	G	17: 46,555,392	F146S	probably damaging	Het
Srrm2	T	C	17: 23,816,773	V797A	unknown	Het
Stk32c	T	C	7: 139,104,302	D463G	possibly damaging	Het
Syne2	C	A	12: 75,971,880	Y3384*	probably null	Het
Tmem55b	A	C	14: 50,930,177	M104R	possibly damaging	Het
Traip	T	A	9: 107,960,985	M139K	possibly damaging	Het
Trappc2l	T	A	8: 122,614,312	F100Y	probably damaging	Het
Ush1c	T	C	7: 46,229,219	D124G	probably damaging	Het
Uty	A	G	Y: 1,099,691	V1168A	probably benign	Het
Vmn2r25	T	C	6: 123,839,923	D233G	possibly damaging	Het
Zdbf2	C	T	1: 63,294,961	R31C	possibly damaging	Het

Other mutations in Lrtm2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01089:Lrtm2	APN	6	119320792	missense	possibly damaging	0.91
IGL02619:Lrtm2	APN	6	119317238	missense	probably damaging	1.00
IGL02694:Lrtm2	APN	6	119320885	missense	possibly damaging	0.80
1mM(1):Lrtm2	UTSW	6	119317291	missense	probably damaging	0.99
R0458:Lrtm2	UTSW	6	119317268	missense	probably damaging	1.00
R1183:Lrtm2	UTSW	6	119320885	missense	probably benign	0.02
R1502:Lrtm2	UTSW	6	119317274	missense	probably benign	0.02
R3801:Lrtm2	UTSW	6	119317483	missense	probably damaging	1.00
R4373:Lrtm2	UTSW	6	119320528	missense	probably damaging	1.00
R5126:Lrtm2	UTSW	6	119317439	missense	probably benign	0.04
R6366:Lrtm2	UTSW	6	119317277	missense	probably damaging	0.99
R7442:Lrtm2	UTSW	6	119317431	missense	probably damaging	0.99
R7448:Lrtm2	UTSW	6	119320823	missense	probably benign	0.00
R7921:Lrtm2	UTSW	6	119317367	missense	possibly damaging	0.94
R7936:Lrtm2	UTSW	6	119320433	missense	probably benign	0.01
R8204:Lrtm2	UTSW	6	119317408	missense	probably benign	0.03
R8239:Lrtm2	UTSW	6	119320817	missense	probably damaging	0.99
R8364:Lrtm2	UTSW	6	119317298	missense	probably benign	0.14
R8415:Lrtm2	UTSW	6	119317497	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTCTGGGAAACTTGGAAAGAGATTG -3'
(R):5'- AACTCTGCTGGGCTAGATGC -3'

Sequencing Primer
(F):5'- TCCCAGTGTCAGGCTGAGAC -3'
(R):5'- TCCTAAACCTAAGCCTGGGG -3'

Posted On

2019-06-26