Mutagenetix > Incidental Mutation

Incidental Mutation 'R8239:Lrtm2'

637499

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

067646-MU

Accession Numbers

Essential gene?

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

Stock #

R8239 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

119292094-119307727 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 119297778 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Valine at position 88 (F88V)

Ref Sequence

ENSEMBL: ENSMUSP00000108376 (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: F88V

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: F88V

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: F88V

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: F88V

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: F88V

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: F88V

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: 99.9%
3x: 99.8%
10x: 99.5%
20x: 98.9%

Validation Efficiency

Allele List at MGI

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

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam39	T	C	8: 41,278,106 (GRCm39)	S166P	probably damaging	Het
Appl1	T	A	14: 26,686,914 (GRCm39)	T19S	probably damaging	Het
Arid4b	T	A	13: 14,344,594 (GRCm39)	D557E	probably benign	Het
Aven	C	T	2: 112,390,120 (GRCm39)	R8W	probably benign	Het
C2cd2l	T	C	9: 44,227,502 (GRCm39)	E307G	possibly damaging	Het
Cdh20	A	C	1: 110,027,832 (GRCm39)	T526P	probably benign	Het
Dchs1	C	T	7: 105,414,718 (GRCm39)	V775M	probably benign	Het
Dennd1b	A	G	1: 138,969,673 (GRCm39)	N63S	probably benign	Het
Dtnb	A	T	12: 3,694,056 (GRCm39)	Y248F	unknown	Het
Ehbp1l1	T	A	19: 5,770,089 (GRCm39)	T405S	possibly damaging	Het
Fam149a	A	G	8: 45,803,490 (GRCm39)	Y415H	possibly damaging	Het
Fam186a	A	G	15: 99,839,191 (GRCm39)	L2351P	unknown	Het
Fsip2	T	G	2: 82,819,687 (GRCm39)	I5140S	possibly damaging	Het
Gm8674	T	C	13: 50,054,262 (GRCm39)	T749A	noncoding transcript	Het
Kalrn	A	G	16: 33,870,153 (GRCm39)	V1894A	noncoding transcript	Het
Kpna3	A	T	14: 61,624,919 (GRCm39)	N141K	probably damaging	Het
Lrba	G	A	3: 86,449,882 (GRCm39)	G2067D	probably damaging	Het
Lrp2	G	T	2: 69,311,611 (GRCm39)	Y2622*	probably null	Het
Mboat1	T	C	13: 30,429,333 (GRCm39)	S454P	probably damaging	Het
Nkpd1	C	T	7: 19,253,753 (GRCm39)	P40S	probably benign	Het
Or2b7	T	C	13: 21,739,788 (GRCm39)	I135V	probably benign	Het
Or4a76	T	A	2: 89,460,907 (GRCm39)	I112F	probably damaging	Het
Or8b54	G	A	9: 38,686,577 (GRCm39)	V9M	noncoding transcript	Het
Or8k27	C	A	2: 86,275,473 (GRCm39)	M284I	noncoding transcript	Het
Patj	A	G	4: 98,570,308 (GRCm39)	E1711G	possibly damaging	Het
Pcdha4	A	T	18: 37,086,128 (GRCm39)	I104F	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Plekhg4	C	T	8: 106,107,546 (GRCm39)	R990*	probably null	Het
Pphln1	T	C	15: 93,386,930 (GRCm39)	S343P	probably benign	Het
Pram1	A	T	17: 33,860,241 (GRCm39)	K269N	probably damaging	Het
Psmd13	T	A	7: 140,466,450 (GRCm39)	I79K	probably damaging	Het
Ptprf	T	C	4: 118,069,309 (GRCm39)	D1586G	possibly damaging	Het
Ptprh	T	A	7: 4,584,090 (GRCm39)	Q167H	probably damaging	Het
Rbm46	C	T	3: 82,772,775 (GRCm39)	R119Q	probably benign	Het
Rreb1	T	C	13: 38,077,848 (GRCm39)	M20T	probably damaging	Het
Scrn2	T	G	11: 96,923,046 (GRCm39)	L163R	probably damaging	Het
Slc36a3	C	T	11: 55,022,433 (GRCm39)	V254I	probably benign	Het
Slc6a6	T	C	6: 91,701,951 (GRCm39)	F120L	probably benign	Het
Slc8a2	A	T	7: 15,879,230 (GRCm39)	H572L	probably benign	Het
Spats2	T	A	15: 99,106,776 (GRCm39)	D357E	probably damaging	Het
Speg	A	T	1: 75,395,677 (GRCm39)	N1816I	probably damaging	Het
Sult2b1	A	G	7: 45,433,361 (GRCm39)	V2A	unknown	Het
Susd3	T	C	13: 49,384,731 (GRCm39)	T231A	probably benign	Het
Tamalin	C	T	15: 101,128,902 (GRCm39)	L217F	probably damaging	Het
Tcp1	A	G	17: 13,139,738 (GRCm39)	D261G	probably benign	Het
Trpm2	C	G	10: 77,771,836 (GRCm39)	S601T	probably benign	Het
Ugt2b38	A	T	5: 87,571,659 (GRCm39)	F124L	probably benign	Het
Unc80	G	T	1: 66,693,178 (GRCm39)	E2522D	probably benign	Het
Usp34	A	G	11: 23,396,750 (GRCm39)	T2365A		Het
Vmn2r92	G	T	17: 18,405,278 (GRCm39)	M807I	probably benign	Het
Vps13b	C	A	15: 35,597,550 (GRCm39)	P1030Q	probably damaging	Het
Wrn	T	G	8: 33,819,213 (GRCm39)	K246N	probably damaging	Het
Zer1	T	A	2: 29,991,147 (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
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
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'- ATCCAGATGTCTAAGTAGTGGGG -3'
(R):5'- GGGAGTCCAATAGCCTGTTATTC -3'

Sequencing Primer
(F):5'- CAGATGTCTAAGTAGTGGGGAGTGC -3'
(R):5'- TGACTGCTCCCTAGGGATCAC -3'

Posted On

2020-07-13