Mutagenetix > Incidental Mutation

Incidental Mutation 'R7936:Lrtm2'

648731

Institutional Source

Beutler Lab

Gene Symbol

Lrtm2

Ensembl Gene

ENSMUSG00000055003

Gene Name

leucine-rich repeats and transmembrane domains 2

Synonyms

MMRRC Submission

045982-MU

Accession Numbers

Essential gene?

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

Stock #

R7936 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

119292094-119307727 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 119297394 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 216 (F216L)

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 benign
Transcript: ENSMUST00000068351
AA Change: F216L

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000063882
Gene: ENSMUSG00000055003
AA Change: F216L

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: ENSMUST00000112756
AA Change: F216L

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000108376
Gene: ENSMUSG00000055003
AA Change: F216L

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 benign
Transcript: ENSMUST00000168793
AA Change: F216L

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000126661
Gene: ENSMUSG00000055003
AA Change: F216L

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

100% (64/64)

Allele List at MGI

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

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	T	A	6: 91,900,445 (GRCm39)	L438*	probably null	Het
Adamts18	T	A	8: 114,493,760 (GRCm39)	I460F	probably damaging	Het
Api5	C	T	2: 94,268,392 (GRCm39)		probably benign	Het
Arap2	A	G	5: 62,888,048 (GRCm39)	S433P	probably damaging	Het
Arhgap26	T	C	18: 39,338,340 (GRCm39)	Y371H	probably damaging	Het
Asf1b	T	C	8: 84,695,848 (GRCm39)	I163T	probably benign	Het
Cacna2d2	A	G	9: 107,401,326 (GRCm39)	N696S	probably damaging	Het
Carns1	A	C	19: 4,216,152 (GRCm39)	S677A	probably benign	Het
Cd276	G	A	9: 58,448,113 (GRCm39)		probably benign	Het
Cdk8	T	A	5: 146,236,644 (GRCm39)	M353K	possibly damaging	Het
Cfap57	C	T	4: 118,472,128 (GRCm39)	V84I	probably benign	Het
Chsy3	A	G	18: 59,542,418 (GRCm39)	I519V	probably damaging	Het
Chtop	T	C	3: 90,414,658 (GRCm39)		probably benign	Het
Clstn3	T	A	6: 124,408,972 (GRCm39)	D892V	possibly damaging	Het
Col16a1	A	T	4: 129,990,664 (GRCm39)		probably null	Het
Dnah5	A	G	15: 28,345,983 (GRCm39)	E2441G	possibly damaging	Het
Dpy19l2	T	G	9: 24,469,454 (GRCm39)	D734A	probably damaging	Het
Dusp2	T	A	2: 127,178,812 (GRCm39)	Y172*	probably null	Het
Efcab3	A	G	11: 104,890,524 (GRCm39)	N4202S	possibly damaging	Het
Efcab3	G	A	11: 104,937,385 (GRCm39)		probably null	Het
Eml4	G	A	17: 83,781,115 (GRCm39)	R771Q	possibly damaging	Het
Fat2	T	A	11: 55,200,993 (GRCm39)	M694L	probably benign	Het
Fat2	C	A	11: 55,201,986 (GRCm39)	E363*	probably null	Het
Gdpgp1	A	G	7: 79,888,826 (GRCm39)	I286V	probably damaging	Het
Gps1	T	A	11: 120,677,199 (GRCm39)	V166E	probably damaging	Het
H60b	T	A	10: 22,162,055 (GRCm39)	N93K	probably benign	Het
Imp4	C	T	1: 34,482,114 (GRCm39)	T79I	probably benign	Het
Kank3	A	G	17: 34,037,841 (GRCm39)	S485G	probably benign	Het
Kcnv2	A	G	19: 27,300,167 (GRCm39)	N6S	probably benign	Het
Krba1	A	T	6: 48,388,603 (GRCm39)	Q534L	probably damaging	Het
Lgr4	A	G	2: 109,836,863 (GRCm39)	N399S	probably damaging	Het
Lgr5	A	G	10: 115,288,952 (GRCm39)	V564A	probably damaging	Het
Lsm8	T	A	6: 18,849,658 (GRCm39)	M22K	probably benign	Het
Mboat2	C	T	12: 25,005,392 (GRCm39)	T389M	probably damaging	Het
Mcoln1	T	G	8: 3,555,924 (GRCm39)	I73S	probably damaging	Het
Myh7	T	A	14: 55,216,920 (GRCm39)	I1146F	possibly damaging	Het
Naa16	G	A	14: 79,578,486 (GRCm39)	T666I	possibly damaging	Het
Ncoa1	A	G	12: 4,385,873 (GRCm39)	S88P	possibly damaging	Het
Obscn	T	C	11: 58,941,334 (GRCm39)	T4496A	possibly damaging	Het
Or13a28	T	C	7: 140,217,652 (GRCm39)	F13L	probably damaging	Het
Or7a35	T	A	10: 78,853,872 (GRCm39)	F239I	probably damaging	Het
Pdxk	G	T	10: 78,277,012 (GRCm39)	A262D	possibly damaging	Het
Pebp4	T	A	14: 70,089,082 (GRCm39)	L68Q	probably damaging	Het
Pfdn5	C	T	15: 102,236,978 (GRCm39)	H77Y	possibly damaging	Het
Pld1	T	C	3: 28,130,651 (GRCm39)	Y484H	probably damaging	Het
Pou3f3	C	A	1: 42,736,560 (GRCm39)	N85K	unknown	Het
Ppm1m	C	A	9: 106,075,144 (GRCm39)	A134S	probably damaging	Het
Prdm11	A	T	2: 92,806,106 (GRCm39)	S281R	possibly damaging	Het
Prdm2	C	A	4: 142,862,434 (GRCm39)	L285F	probably damaging	Het
Ptchd3	C	T	11: 121,721,939 (GRCm39)	R271*	probably null	Het
Ptprq	A	C	10: 107,488,572 (GRCm39)	V955G	probably damaging	Het
Pygb	A	T	2: 150,657,589 (GRCm39)	M351L	probably benign	Het
Rcl1	G	A	19: 29,095,805 (GRCm39)		probably null	Het
Sgip1	A	T	4: 102,786,097 (GRCm39)	T351S	possibly damaging	Het
Slc22a5	T	C	11: 53,760,215 (GRCm39)	N367S	probably damaging	Het
Sox6	A	G	7: 115,143,830 (GRCm39)	V437A	probably benign	Het
Spata16	T	A	3: 26,721,572 (GRCm39)	M31K	possibly damaging	Het
Stab1	C	A	14: 30,879,372 (GRCm39)	V703F	possibly damaging	Het
Tbc1d4	C	T	14: 101,703,190 (GRCm39)	G752R	probably damaging	Het
Tent4b	G	A	8: 88,978,913 (GRCm39)	G505R	probably null	Het
Tes3-ps	C	T	13: 49,647,460 (GRCm39)	A112V	probably benign	Het
Tnfrsf19	T	C	14: 61,208,382 (GRCm39)	T380A	probably benign	Het
Trim75	C	T	8: 65,435,190 (GRCm39)	G420E	probably damaging	Het
Txlnb	A	G	10: 17,703,712 (GRCm39)	D290G	probably benign	Het
Unc5c	T	A	3: 141,534,238 (GRCm39)	F920I	possibly damaging	Het
Vmn1r233	T	A	17: 21,214,237 (GRCm39)	R238*	probably null	Het
Vmn2r113	A	G	17: 23,176,917 (GRCm39)	E567G	probably benign	Het
Vmn2r97	T	A	17: 19,150,662 (GRCm39)	I503K	probably damaging	Het
Wdr62	A	G	7: 29,964,584 (GRCm39)	W387R	probably damaging	Het
Zfp36l2	A	T	17: 84,495,090 (GRCm39)	D11E	probably benign	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
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'- GCATCCGTCGTGTGTCTTTAAG -3'
(R):5'- TTGTCTATCAACGGCTTGGCC -3'

Sequencing Primer
(F):5'- TTCCCATATGAAACCTAAGGAAAGG -3'
(R):5'- CCAATCGTCTGCAGAGC -3'

Posted On

2020-09-15