Mutagenetix > Incidental Mutations

Incidental Mutation 'R4373:Lrtm2'

326061

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

041675-MU

Accession Numbers

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

Is this an essential gene?

Probably non essential (E-score: 0.063) question?

Stock #

R4373 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

119315133-119330766 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 119320528 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 184 (F184S)

Ref Sequence

ENSEMBL: ENSMUSP00000126661 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037434] [ENSMUST00000068351] [ENSMUST00000112756] [ENSMUST00000124192] [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: F184S

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

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: F184S

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: F184S

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

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: F184S

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: ENSMUST00000124192

Predicted Effect

probably damaging
Transcript: ENSMUST00000168793
AA Change: F184S

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

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: F184S

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

0.7747

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

98% (54/55)

Allele List at MGI

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

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610010F05Rik	A	T	11: 23,615,265		probably null	Het
3632451O06Rik	T	A	14: 49,770,436	T527S	probably damaging	Het
Adck5	A	G	15: 76,594,335		probably benign	Het
Akr1b3	A	C	6: 34,304,267		probably benign	Het
Asns	A	T	6: 7,677,978	S367T	probably damaging	Het
BC034090	T	C	1: 155,226,158	N120S	probably benign	Het
Bub1	A	T	2: 127,805,236		probably benign	Het
Csf1	T	A	3: 107,756,739	T38S	probably damaging	Het
Ctsz	T	C	2: 174,428,585	E268G	possibly damaging	Het
Dach1	G	A	14: 97,827,750	T685I	possibly damaging	Het
Dclre1a	A	G	19: 56,545,442	L240S	probably benign	Het
Ercc1	G	A	7: 19,347,132		probably benign	Het
Esam	C	T	9: 37,534,196	T71I	probably benign	Het
Espl1	A	G	15: 102,312,989	I944V	probably damaging	Het
Gde1	A	G	7: 118,698,558	L35P	possibly damaging	Het
Gm10382	A	G	5: 125,389,583		probably benign	Het
H2-M10.6	T	C	17: 36,813,066	Y141H	probably damaging	Het
Hk1	C	A	10: 62,315,540	K10N	probably damaging	Het
Lamc3	A	G	2: 31,898,232	K135E	probably damaging	Het
March11	A	G	15: 26,309,446	E62G	probably damaging	Het
Mtcl1	T	A	17: 66,380,079	T611S	probably benign	Het
Myc	A	T	15: 61,989,664	H373L	probably damaging	Het
Myh6	T	A	14: 54,962,108	I249F	probably damaging	Het
Naaa	T	C	5: 92,278,143		probably benign	Het
Nfib	A	G	4: 82,323,658	V432A	probably damaging	Het
Nmt1	A	G	11: 103,043,200	K55R	probably damaging	Het
Olfr1228	T	C	2: 89,249,245	R150G	possibly damaging	Het
Opa3	C	T	7: 19,244,774	R55W	probably damaging	Het
Pfn4	T	A	12: 4,770,182	D10E	probably damaging	Het
Pld5	T	A	1: 176,140,017	I91F	probably damaging	Het
Plec	A	C	15: 76,183,117	S1350A	probably damaging	Het
Polq	G	T	16: 37,013,181	V79F	probably damaging	Het
Ppp1r16b	T	C	2: 158,761,765	Y537H	probably damaging	Het
Prdm8	T	C	5: 98,186,508	S645P	probably damaging	Het
Rgs1	T	C	1: 144,247,906	T94A	probably benign	Het
Rpl11	G	A	4: 136,051,143		probably benign	Het
Scamp3	G	A	3: 89,181,927		probably null	Het
Sgsm1	TTTTATATT	TTT	5: 113,258,123		probably benign	Het
Sirpb1b	A	T	3: 15,548,761	I87K	probably damaging	Het
Slc14a2	G	A	18: 78,207,068	R62C	probably damaging	Het
Stat4	T	C	1: 52,071,941		probably null	Het
Tex9	A	T	9: 72,480,595		probably null	Het
Tsku	T	C	7: 98,352,831	T98A	probably benign	Het
Ttc23l	CT	CTTGGATT	15: 10,537,562		probably benign	Het
Ttc23l	G	A	15: 10,537,566	S206L	probably benign	Het
Vmn2r116	A	C	17: 23,401,421	I710L	probably benign	Het
Vmn2r16	A	T	5: 109,363,801	I625F	probably damaging	Het
Xpo4	G	A	14: 57,591,022	Q794*	probably null	Het
Zfp112	T	A	7: 24,125,048	I147N	probably damaging	Het
Zmiz1	T	C	14: 25,636,010	S140P	probably 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
R5126:Lrtm2	UTSW	6	119317439	missense	probably benign	0.04
R6366:Lrtm2	UTSW	6	119317277	missense	probably damaging	0.99
R7177:Lrtm2	UTSW	6	119317152	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
R8823:Lrtm2	UTSW	6	119317232	missense	probably damaging	1.00
R9014:Lrtm2	UTSW	6	119317258	missense	probably damaging	1.00
R9183:Lrtm2	UTSW	6	119317423	missense	probably damaging	1.00
R9290:Lrtm2	UTSW	6	119320831	missense	probably damaging	1.00
R9329:Lrtm2	UTSW	6	119320451	nonsense	probably null
R9342:Lrtm2	UTSW	6	119320973	missense	probably benign
R9390:Lrtm2	UTSW	6	119320987	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TTCCTCTGACTGCAGGAATTG -3'
(R):5'- CAGCTTCGGAATAACAGCATCAG -3'

Sequencing Primer
(F):5'- CTCTGACTGCAGGAATTGGTGATG -3'
(R):5'- TAACAGCATCAGGACCCTGG -3'

Posted On

2015-07-06