Mutagenetix > Incidental Mutation

Incidental Mutation 'R5787:Lrtm1'

448106

Institutional Source

Beutler Lab

Gene Symbol

Lrtm1

Ensembl Gene

ENSMUSG00000045776

Gene Name

leucine-rich repeats and transmembrane domains 1

Synonyms

A930016D02Rik

Accession Numbers

Essential gene?

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

Stock #

R5787 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

28740165-28755599 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 28743947 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 138 (E138D)

Ref Sequence

ENSEMBL: ENSMUSP00000153372 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000022567] [ENSMUST00000055662] [ENSMUST00000224708] [ENSMUST00000224760]

AlphaFold

Q8BXQ3

Predicted Effect

probably benign
Transcript: ENSMUST00000022567

SMART Domains

Protein: ENSMUSP00000022567
Gene: ENSMUSG00000021991

Domain	Start	End	E-Value	Type
low complexity region	14	27	N/A	INTRINSIC
Blast:WNT1	28	103	2e-33	BLAST
Pfam:VWA_N	113	229	6.8e-40	PFAM
VWA	254	439	4.13e-24	SMART
Pfam:Cache_1	452	548	3e-32	PFAM
low complexity region	1070	1088	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000055662
AA Change: E138D

PolyPhen 2 Score 0.792 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000061828
Gene: ENSMUSG00000045776
AA Change: E138D

Domain	Start	End	E-Value	Type
LRRNT	32	66	4.41e-6	SMART
LRR	65	84	2.33e2	SMART
LRR	85	108	2.67e-1	SMART
LRR	109	131	1.15e1	SMART
LRR_TYP	133	156	3.89e-3	SMART
LRRCT	192	245	8.63e-6	SMART
transmembrane domain	297	319	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000224708
AA Change: E165D

PolyPhen 2 Score 0.831 (Sensitivity: 0.84; Specificity: 0.93)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000224760
AA Change: E138D

PolyPhen 2 Score 0.894 (Sensitivity: 0.82; Specificity: 0.94)

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.5%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot11	C	T	4: 106,617,327 (GRCm39)	G240R	probably damaging	Het
Adam24	A	G	8: 41,133,941 (GRCm39)	N470D	possibly damaging	Het
Adcy8	T	C	15: 64,576,067 (GRCm39)	D1027G	probably damaging	Het
Amph	A	T	13: 19,132,624 (GRCm39)	I8F	possibly damaging	Het
Ankrd60	TGGCCACGCGG	TGG	2: 173,419,882 (GRCm39)		probably null	Het
Ano5	G	A	7: 51,216,066 (GRCm39)	D348N	possibly damaging	Het
Atp6v0a1	A	G	11: 100,909,400 (GRCm39)	D43G	probably benign	Het
Bltp1	T	C	3: 37,046,882 (GRCm39)		probably null	Het
Btnl10	T	A	11: 58,811,169 (GRCm39)	I164N	probably damaging	Het
Ccdc174	C	T	6: 91,858,291 (GRCm39)	Q71*	probably null	Het
Ceacam3	G	A	7: 16,888,971 (GRCm39)	E247K	possibly damaging	Het
Chrna2	A	G	14: 66,386,457 (GRCm39)	D201G	probably benign	Het
Clasp2	G	A	9: 113,691,310 (GRCm39)	D448N	probably damaging	Het
Clcn2	C	A	16: 20,522,183 (GRCm39)	R829L	probably damaging	Het
Clock	A	G	5: 76,384,898 (GRCm39)	S440P	probably damaging	Het
Cntn2	T	C	1: 132,450,797 (GRCm39)	D29G	probably damaging	Het
Cpne4	A	G	9: 104,899,600 (GRCm39)	T428A	probably benign	Het
Cul3	T	C	1: 80,260,438 (GRCm39)	I304V	probably benign	Het
Cyp11a1	C	A	9: 57,922,550 (GRCm39)	Q77K	probably benign	Het
Cyp3a25	A	G	5: 145,935,313 (GRCm39)	V101A	probably benign	Het
Cyp4f15	T	C	17: 32,921,782 (GRCm39)	F485L	probably damaging	Het
Des	T	A	1: 75,340,290 (GRCm39)	V399E	probably damaging	Het
Dhx58	T	C	11: 100,592,145 (GRCm39)	D301G	possibly damaging	Het
Ear6	A	G	14: 52,091,855 (GRCm39)	E134G	probably benign	Het
Eif2b3	A	G	4: 116,901,637 (GRCm39)	D100G	probably damaging	Het
Erich1	T	C	8: 14,083,776 (GRCm39)		probably null	Het
Gm4787	G	C	12: 81,424,604 (GRCm39)	T518S	probably benign	Het
Htr4	T	C	18: 62,546,693 (GRCm39)	V82A	probably damaging	Het
Hydin	A	G	8: 111,052,985 (GRCm39)	D219G	probably damaging	Het
Ifit1	T	A	19: 34,624,975 (GRCm39)	V37E	probably benign	Het
Isg20	T	A	7: 78,569,558 (GRCm39)	D176E	probably benign	Het
Islr2	A	G	9: 58,105,637 (GRCm39)	V585A	probably damaging	Het
Kat6a	A	G	8: 23,422,663 (GRCm39)	E991G	probably damaging	Het
Kcnv1	T	C	15: 44,977,726 (GRCm39)	Y104C	probably damaging	Het
Mllt3	A	T	4: 87,759,057 (GRCm39)	D330E	probably damaging	Het
Mpp7	T	C	18: 7,461,682 (GRCm39)	N64D	probably benign	Het
Naip6	G	T	13: 100,436,724 (GRCm39)	Q600K	probably benign	Het
Nop9	T	G	14: 55,983,791 (GRCm39)	C141G	possibly damaging	Het
Nos1ap	T	C	1: 170,146,141 (GRCm39)	E471G	probably benign	Het
Npr2	A	G	4: 43,633,593 (GRCm39)	T246A	possibly damaging	Het
Or2t1	A	C	14: 14,328,725 (GRCm38)	M205L	probably damaging	Het
Or4a76	T	A	2: 89,461,018 (GRCm39)	I75F	probably benign	Het
Or6z1	A	T	7: 6,504,989 (GRCm39)	S79T	probably damaging	Het
Pdlim4	T	A	11: 53,946,042 (GRCm39)	D271V	probably damaging	Het
Pik3r6	T	C	11: 68,430,753 (GRCm39)	V518A	possibly damaging	Het
Rab5a	C	T	17: 53,804,650 (GRCm39)	P87S	probably damaging	Het
Rbsn	C	T	6: 92,176,797 (GRCm39)	V239I	possibly damaging	Het
Rsph14	T	A	10: 74,793,460 (GRCm39)	I314F	possibly damaging	Het
S1pr2	A	T	9: 20,879,232 (GRCm39)	S199T	probably benign	Het
Scrib	A	G	15: 75,931,151 (GRCm39)	L902P	probably damaging	Het
Slc25a23	T	C	17: 57,360,825 (GRCm39)	T200A	probably damaging	Het
Slc8a1	A	T	17: 81,696,166 (GRCm39)	I956N	probably damaging	Het
Spef2	A	G	15: 9,748,812 (GRCm39)	V15A	possibly damaging	Het
Stim1	T	A	7: 102,084,647 (GRCm39)	V533E	possibly damaging	Het
Tbck	A	T	3: 132,443,329 (GRCm39)	D585V	probably damaging	Het
Tpr	T	A	1: 150,271,037 (GRCm39)	L80Q	probably benign	Het
Trim67	C	T	8: 125,521,051 (GRCm39)	R138*	probably null	Het
Ttn	T	C	2: 76,580,627 (GRCm39)	N23422S	probably damaging	Het
Uba6	A	G	5: 86,260,511 (GRCm39)	*1023Q	probably null	Het
Vmn1r208	T	C	13: 22,956,841 (GRCm39)	N219D	possibly damaging	Het
Vmn1r8	T	A	6: 57,013,244 (GRCm39)	S98R	probably damaging	Het

Other mutations in Lrtm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02191:Lrtm1	APN	14	28,743,906 (GRCm39)	missense	probably benign	0.00
R0102:Lrtm1	UTSW	14	28,744,184 (GRCm39)	splice site	probably benign
R0102:Lrtm1	UTSW	14	28,744,184 (GRCm39)	splice site	probably benign
R0602:Lrtm1	UTSW	14	28,744,179 (GRCm39)	splice site	probably benign
R5214:Lrtm1	UTSW	14	28,743,651 (GRCm39)	missense	possibly damaging	0.58
R5253:Lrtm1	UTSW	14	28,743,801 (GRCm39)	missense	probably benign	0.13
R5937:Lrtm1	UTSW	14	28,743,787 (GRCm39)	missense	possibly damaging	0.90
R6238:Lrtm1	UTSW	14	28,749,628 (GRCm39)	missense	probably benign	0.02
R6850:Lrtm1	UTSW	14	28,749,407 (GRCm39)	missense	probably benign	0.00
R7304:Lrtm1	UTSW	14	28,744,075 (GRCm39)	missense	probably damaging	0.97
R7363:Lrtm1	UTSW	14	28,743,850 (GRCm39)	missense	probably damaging	1.00
R7385:Lrtm1	UTSW	14	28,749,673 (GRCm39)	missense	probably benign	0.00
R8181:Lrtm1	UTSW	14	28,743,894 (GRCm39)	missense	probably damaging	1.00
R9299:Lrtm1	UTSW	14	28,743,714 (GRCm39)	missense	probably damaging	1.00
RF036:Lrtm1	UTSW	14	28,743,400 (GRCm39)	frame shift	probably null
RF063:Lrtm1	UTSW	14	28,743,400 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TACACTGCTCTTACAAGATAACCGG -3'
(R):5'- GGCAGTCACAAATCCAAGGG -3'

Sequencing Primer
(F):5'- TCTTACAAGATAACCGGATCCACTG -3'
(R):5'- GGTTGTCCTTAAGAAGTACCAGCC -3'

Posted On

2016-12-15