Mutagenetix > Incidental Mutation

Incidental Mutation 'R3801:Lrtm2'

272979

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

040760-MU

Accession Numbers

Essential gene?

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

Stock #

R3801 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

119292094-119307727 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 119294444 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 229 (T229I)

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: T229I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: T229I

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: T229I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: T229I

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: T229I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: T229I

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: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.0%

Validation Efficiency

Allele List at MGI

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

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700011L22Rik	C	T	8: 79,974,922 (GRCm39)	E54K	probably benign	Het
Als2	A	C	1: 59,206,358 (GRCm39)	M1634R	probably damaging	Het
Ankfy1	T	C	11: 72,640,246 (GRCm39)	S531P	probably benign	Het
Atp6v1e1	A	G	6: 120,778,020 (GRCm39)	Y172H	probably benign	Het
Brd1	C	T	15: 88,601,243 (GRCm39)	V464M	probably damaging	Het
Btaf1	A	T	19: 36,963,948 (GRCm39)	T840S	probably benign	Het
Btaf1	A	T	19: 36,966,373 (GRCm39)	H1047L	probably benign	Het
Cacnb2	A	G	2: 14,829,074 (GRCm39)	D3G	possibly damaging	Het
Capn13	G	A	17: 73,646,396 (GRCm39)	P339L	probably benign	Het
Cgrrf1	G	T	14: 47,069,820 (GRCm39)	G30C	probably damaging	Het
Crnkl1	T	C	2: 145,761,715 (GRCm39)	D614G	probably benign	Het
Cyp2c23	C	T	19: 43,995,478 (GRCm39)	V430I	probably benign	Het
Dazl	G	A	17: 50,588,309 (GRCm39)	R289W	probably benign	Het
Dsg1b	C	T	18: 20,523,260 (GRCm39)	P96S	probably damaging	Het
Dusp14	A	G	11: 83,939,535 (GRCm39)	S169P	possibly damaging	Het
Egfem1	A	G	3: 29,206,075 (GRCm39)	D91G	probably benign	Het
Eif1	A	G	11: 100,211,650 (GRCm39)	K95E	probably damaging	Het
Fap	C	T	2: 62,376,994 (GRCm39)	V191I	probably benign	Het
Flnc	T	C	6: 29,447,403 (GRCm39)	Y1069H	probably damaging	Het
Fndc7	T	C	3: 108,776,464 (GRCm39)	T526A	possibly damaging	Het
Fras1	A	T	5: 96,881,791 (GRCm39)	T2508S	probably benign	Het
Gast	T	C	11: 100,227,636 (GRCm39)	S73P	probably damaging	Het
Grap2	A	G	15: 80,507,947 (GRCm39)	T4A	possibly damaging	Het
Grm8	T	G	6: 28,125,635 (GRCm39)	N164H	possibly damaging	Het
Hyal5	A	T	6: 24,876,523 (GRCm39)	H132L	probably benign	Het
Iqcm	C	A	8: 76,396,021 (GRCm39)	T188K	possibly damaging	Het
Kank4	A	G	4: 98,668,370 (GRCm39)	S26P	probably damaging	Het
Lipo3	C	T	19: 33,762,257 (GRCm39)	C80Y	probably damaging	Het
Lrrk2	A	G	15: 91,621,314 (GRCm39)	R963G	probably benign	Het
Mb21d2	A	T	16: 28,646,755 (GRCm39)	D406E	possibly damaging	Het
Meikin	T	A	11: 54,290,697 (GRCm39)		probably null	Het
Mybl1	A	T	1: 9,743,439 (GRCm39)	F538I	probably damaging	Het
Nectin2	T	C	7: 19,451,561 (GRCm39)	D491G	probably benign	Het
Nf1	A	G	11: 79,450,347 (GRCm39)	D511G	probably null	Het
Nid2	T	C	14: 19,860,065 (GRCm39)	C1328R	probably damaging	Het
Nlrp1a	T	A	11: 71,013,529 (GRCm39)	M574L	probably benign	Het
Nrap	C	T	19: 56,310,211 (GRCm39)	D1595N	probably damaging	Het
Nrg3	G	A	14: 38,098,391 (GRCm39)	P496S	probably damaging	Het
Or4k41	A	T	2: 111,279,910 (GRCm39)	I142F	probably benign	Het
Pak3	G	A	X: 142,492,727 (GRCm39)	V87I	probably damaging	Het
Phf8	T	C	X: 150,355,572 (GRCm39)	S512P	possibly damaging	Het
Phkb	G	T	8: 86,648,858 (GRCm39)	E225*	probably null	Het
Plaa	T	C	4: 94,458,125 (GRCm39)	D615G	probably damaging	Het
Prdm12	A	G	2: 31,541,959 (GRCm39)	K223E	probably damaging	Het
Prkd1	C	A	12: 50,430,205 (GRCm39)	R634L	possibly damaging	Het
Rassf3	T	A	10: 121,250,271 (GRCm39)	I181F	possibly damaging	Het
Samd8	G	A	14: 21,825,133 (GRCm39)	V30M	probably damaging	Het
Sema4f	A	T	6: 82,895,608 (GRCm39)	H308Q	possibly damaging	Het
Skint4	G	T	4: 111,975,378 (GRCm39)	V113L	probably damaging	Het
Slc16a10	G	C	10: 39,932,620 (GRCm39)	H314D	possibly damaging	Het
Slpi	A	G	2: 164,198,158 (GRCm39)	L12P	probably damaging	Het
Smco1	A	G	16: 32,092,716 (GRCm39)	Y129C	probably benign	Het
Spag17	A	G	3: 99,961,169 (GRCm39)	K985R	possibly damaging	Het
Stc1	T	C	14: 69,275,924 (GRCm39)	I239T	probably benign	Het
Suclg2	A	T	6: 95,474,649 (GRCm39)	I372N	probably damaging	Het
Tmed4	C	A	11: 6,224,233 (GRCm39)	V80F	probably damaging	Het
Tnpo2	T	A	8: 85,781,800 (GRCm39)		probably null	Het
Top1	A	G	2: 160,544,688 (GRCm39)	H268R	probably damaging	Het
Triobp	A	T	15: 78,857,900 (GRCm39)	Q1167L	probably benign	Het
Txndc16	G	A	14: 45,388,809 (GRCm39)	P536L	possibly damaging	Het
Usp13	C	T	3: 32,935,657 (GRCm39)	A360V	possibly damaging	Het
Vhl	G	A	6: 113,606,423 (GRCm39)	V147I	probably benign	Het
Vldlr	A	T	19: 27,195,021 (GRCm39)	T3S	probably damaging	Het
Vps54	T	A	11: 21,218,832 (GRCm39)	D130E	probably benign	Het
Zfp808	T	A	13: 62,319,897 (GRCm39)	H375Q	probably damaging	Het
Zfp87	A	T	13: 67,669,334 (GRCm39)	N37K	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
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
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'- CGATGATCACTGTGCCAATG -3'
(R):5'- TAGGTGCTAGTTCCTGCCTG -3'

Sequencing Primer
(F):5'- ACCTCTGCTTCTGTGGGCAG -3'
(R):5'- GCTCTTACTCTCCCGTAATCAGG -3'

Posted On

2015-03-25