Mutagenetix > Incidental Mutation

Incidental Mutation 'R6366:Lrtm2'

512687

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

044516-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.069) question?

Stock #

R6366 (G1)

Quality Score

113.008

Status

Not validated

Chromosome

Chromosomal Location

119292094-119307727 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 119294238 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 298 (R298G)

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: R298G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: R298G

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: R298G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: R298G

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: R298G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: R298G

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

0.1826

Coding Region Coverage

1x: 100.0%
3x: 99.7%
10x: 98.0%
20x: 93.4%

Validation Efficiency

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
Agl	A	G	3: 116,584,766 (GRCm39)	F185L	probably damaging	Het
Ank3	A	G	10: 69,835,188 (GRCm39)	D131G	probably damaging	Het
Boc	T	C	16: 44,308,015 (GRCm39)	K947E	probably benign	Het
Ccdc110	A	G	8: 46,396,425 (GRCm39)	E772G	probably damaging	Het
Ccdc7a	A	G	8: 129,582,473 (GRCm39)	V1055A	unknown	Het
Chd1l	A	G	3: 97,501,476 (GRCm39)	V190A	probably benign	Het
Chl1	C	A	6: 103,706,197 (GRCm39)	N396K	possibly damaging	Het
CN725425	T	G	15: 91,131,124 (GRCm39)	Y420D	possibly damaging	Het
Col6a1	A	T	10: 76,546,804 (GRCm39)	I806N	unknown	Het
Csmd2	A	G	4: 128,377,245 (GRCm39)	K2042E	probably benign	Het
Eif4a1	G	T	11: 69,561,781 (GRCm39)	D15E	probably benign	Het
Etfb	T	C	7: 43,102,365 (GRCm39)	L119S	probably damaging	Het
Fbxo42	T	A	4: 140,927,260 (GRCm39)	S513R	probably benign	Het
Gys2	C	A	6: 142,409,120 (GRCm39)	C45F	probably benign	Het
Hspa1a	G	A	17: 35,189,500 (GRCm39)	P468S	probably damaging	Het
Kdm2a	G	T	19: 4,374,960 (GRCm39)	Q724K	probably benign	Het
Lama3	G	T	18: 12,615,194 (GRCm39)	G1373W	probably damaging	Het
Lhx1	A	T	11: 84,413,034 (GRCm39)	F84Y	probably damaging	Het
Lpxn	G	A	19: 12,802,163 (GRCm39)	V163M	probably benign	Het
Lrrc7	T	C	3: 157,841,012 (GRCm39)	Q1389R	probably benign	Het
Ltv1	A	G	10: 13,056,739 (GRCm39)	V268A	probably benign	Het
Mgat4d	T	A	8: 84,095,580 (GRCm39)		probably null	Het
Mknk2	C	A	10: 80,507,767 (GRCm39)	R33L	probably damaging	Het
Ms4a1	A	G	19: 11,236,062 (GRCm39)	S42P	probably damaging	Het
Muc16	T	C	9: 18,557,340 (GRCm39)	I2984M	unknown	Het
Mup12	A	C	4: 60,696,657 (GRCm39)	F74V	probably damaging	Het
Nacad	A	C	11: 6,551,196 (GRCm39)	L665R	probably benign	Het
Pde6a	T	A	18: 61,398,142 (GRCm39)		probably null	Het
Plb1	A	G	5: 32,471,429 (GRCm39)	N579D	possibly damaging	Het
Podn	T	A	4: 107,876,001 (GRCm39)	I552F	possibly damaging	Het
Potefam1	A	G	2: 110,999,937 (GRCm39)		probably null	Het
Pramel32	T	A	4: 88,547,102 (GRCm39)	I106F	probably damaging	Het
Prl3b1	A	T	13: 27,427,875 (GRCm39)	M62L	probably benign	Het
Ptpn13	G	T	5: 103,698,919 (GRCm39)	R1134L	probably damaging	Het
Rpl37	T	A	15: 5,147,990 (GRCm39)		probably null	Het
Samd4	T	A	14: 47,311,607 (GRCm39)		probably null	Het
Sh3rf2	T	C	18: 42,286,130 (GRCm39)	V541A	probably benign	Het
Shcbp1	A	G	8: 4,799,380 (GRCm39)	V335A	probably damaging	Het
Slc7a7	T	C	14: 54,612,057 (GRCm39)	Y282C	probably damaging	Het
Spag7	T	C	11: 70,555,418 (GRCm39)	K125E	possibly damaging	Het
Spata31e4	T	C	13: 50,855,972 (GRCm39)	Y537H	probably benign	Het
Sptan1	T	C	2: 29,910,467 (GRCm39)	S1831P	possibly damaging	Het
Stab1	T	C	14: 30,863,395 (GRCm39)	K2097R	probably benign	Het
Stk38	A	G	17: 29,193,338 (GRCm39)	W364R	probably benign	Het
Tectb	G	A	19: 55,170,350 (GRCm39)	G67D	probably damaging	Het
Ttll9	G	T	2: 152,833,525 (GRCm39)	D208Y	probably damaging	Het
Tyro3	G	A	2: 119,647,156 (GRCm39)	D758N	probably damaging	Het
Tyw1	T	C	5: 130,310,792 (GRCm39)		probably benign	Het
Unc5b	C	T	10: 60,614,091 (GRCm39)	A253T	probably benign	Het
Wtap	A	T	17: 13,186,945 (GRCm39)		probably null	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
R0458:Lrtm2	UTSW	6	119,294,229 (GRCm39)	missense	probably damaging	1.00
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
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'- CAGACAGACAGCTCTCATGC -3'
(R):5'- GGTCCCCATGGAGATGTTTAAC -3'

Sequencing Primer
(F):5'- AGACGAGATCTGCTTCTGATC -3'
(R):5'- ACTACTGTTCCCAGCTAGAGGATG -3'

Posted On

2018-04-27