Mutagenetix > Incidental Mutation

Incidental Mutation 'R0540:Lrrtm1'

49813

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm1

Ensembl Gene

ENSMUSG00000060780

Gene Name

leucine rich repeat transmembrane neuronal 1

Synonyms

4632401D06Rik

MMRRC Submission

038732-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0540 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

77219672-77234774 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 77221611 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Glutamic Acid at position 356 (A356E)

Ref Sequence

ENSEMBL: ENSMUSP00000124373 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020400] [ENSMUST00000075340] [ENSMUST00000159616] [ENSMUST00000159626] [ENSMUST00000160894] [ENSMUST00000161677] [ENSMUST00000161811] [ENSMUST00000161846]

AlphaFold

Q8K377

Predicted Effect

probably damaging
Transcript: ENSMUST00000020400
AA Change: A356E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: A356E

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART
LRR	184	207	6.96e0	SMART
LRR	208	236	1.76e2	SMART
LRR	255	278	4.71e1	SMART
LRR	279	302	1.03e1	SMART
Blast:LRRCT	314	364	4e-13	BLAST
transmembrane domain	428	450	N/A	INTRINSIC
low complexity region	467	475	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000075340

SMART Domains

Protein: ENSMUSP00000074809
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	18	337	2e-104	PFAM
Pfam:Vinculin	331	866	7.7e-222	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000159616
AA Change: A356E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: A356E

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART
LRR	184	207	6.96e0	SMART
LRR	208	236	1.76e2	SMART
LRR	255	278	4.71e1	SMART
LRR	279	302	1.03e1	SMART
Blast:LRRCT	314	364	4e-13	BLAST
transmembrane domain	428	450	N/A	INTRINSIC
low complexity region	467	475	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000159626

SMART Domains

Protein: ENSMUSP00000124376
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	18	337	3.4e-105	PFAM
Pfam:Vinculin	330	914	6.6e-214	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160894

SMART Domains

Protein: ENSMUSP00000124764
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	31	352	2.1e-104	PFAM
Pfam:Vinculin	343	927	4.6e-213	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000161677
AA Change: A356E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: A356E

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART
LRR	184	207	6.96e0	SMART
LRR	208	236	1.76e2	SMART
LRR	255	278	4.71e1	SMART
LRR	279	302	1.03e1	SMART
Blast:LRRCT	314	364	4e-13	BLAST
transmembrane domain	428	450	N/A	INTRINSIC
low complexity region	467	475	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000161811

SMART Domains

Protein: ENSMUSP00000124948
Gene: ENSMUSG00000060780

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161846

SMART Domains

Protein: ENSMUSP00000123714
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	31	350	5.3e-105	PFAM
Pfam:Vinculin	344	879	2.1e-222	PFAM

Coding Region Coverage

1x: 99.6%
3x: 98.8%
10x: 96.8%
20x: 93.7%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a null mutation are viable and fertile with grossly normal brain morphology. Mice homozygous for another knock-out allele exhibit impaired cognitive function and altered hippocampal synapse morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 101 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2	A	G	3: 59,926,627 (GRCm39)	T199A	possibly damaging	Het
Als2cl	C	A	9: 110,724,852 (GRCm39)	Y775*	probably null	Het
Ankhd1	G	T	18: 36,773,333 (GRCm39)	V59F	probably damaging	Het
Ano4	T	A	10: 88,859,806 (GRCm39)	I395F	probably benign	Het
Apcdd1	A	G	18: 63,084,967 (GRCm39)	N388S	possibly damaging	Het
Arl9	A	G	5: 77,155,118 (GRCm39)	Y83C	possibly damaging	Het
Armc2	T	A	10: 41,798,691 (GRCm39)	H706L	probably benign	Het
Arrb1	T	C	7: 99,237,403 (GRCm39)		probably null	Het
Atxn1	G	A	13: 45,711,006 (GRCm39)	S642L	probably damaging	Het
Bmp8a	A	G	4: 123,209,723 (GRCm39)	Y322H	probably damaging	Het
Btbd3	C	T	2: 138,125,736 (GRCm39)	R307W	possibly damaging	Het
C1galt1	T	C	6: 7,871,193 (GRCm39)	I343T	probably benign	Het
Capn2	A	T	1: 182,319,749 (GRCm39)	Y146*	probably null	Het
Ccdc42	C	T	11: 68,488,536 (GRCm39)	Q312*	probably null	Het
Cd209e	T	C	8: 3,901,265 (GRCm39)	K130E	probably benign	Het
Chd3	T	C	11: 69,235,184 (GRCm39)	D2054G	probably damaging	Het
Chrna1	T	C	2: 73,401,815 (GRCm39)	N161S	probably damaging	Het
Clp1	C	T	2: 84,555,935 (GRCm39)	A182T	possibly damaging	Het
Cpsf7	G	T	19: 10,510,682 (GRCm39)	E135*	probably null	Het
Csf2rb2	T	C	15: 78,172,108 (GRCm39)	Y325C	probably benign	Het
Cspg5	T	C	9: 110,076,460 (GRCm39)		probably null	Het
Ctnna2	T	C	6: 76,879,413 (GRCm39)	T824A	probably benign	Het
Cyp2b13	G	A	7: 25,781,136 (GRCm39)	V183I	probably benign	Het
D430041D05Rik	C	T	2: 104,063,790 (GRCm39)	R1354H	probably damaging	Het
Ddx24	A	G	12: 103,385,326 (GRCm39)	Y426H	possibly damaging	Het
Dexi	G	T	16: 10,360,426 (GRCm39)	Y43*	probably null	Het
Dlg1	G	A	16: 31,656,992 (GRCm39)	V596I	possibly damaging	Het
Dnah11	A	C	12: 118,046,246 (GRCm39)	W1731G	probably damaging	Het
Dnhd1	T	A	7: 105,369,995 (GRCm39)	N4473K	probably benign	Het
Dync2h1	A	C	9: 7,051,480 (GRCm39)	S3152A	probably benign	Het
Edn3	C	A	2: 174,602,767 (GRCm39)	P3Q	probably damaging	Het
Eif2a	G	A	3: 58,463,073 (GRCm39)		probably null	Het
Emb	G	A	13: 117,369,286 (GRCm39)	V56I	possibly damaging	Het
Enpp4	A	T	17: 44,410,386 (GRCm39)	C397S	probably damaging	Het
Exo5	A	G	4: 120,779,178 (GRCm39)	V229A	probably damaging	Het
Fga	G	A	3: 82,935,869 (GRCm39)	G32E	probably damaging	Het
Fkbpl	T	C	17: 34,864,333 (GRCm39)	F34L	probably benign	Het
Fsd2	T	A	7: 81,194,765 (GRCm39)	D466V	probably damaging	Het
Gcn1	T	C	5: 115,727,015 (GRCm39)	V624A	probably benign	Het
Git2	A	G	5: 114,886,335 (GRCm39)	F336L	probably damaging	Het
Greb1	T	A	12: 16,732,194 (GRCm39)	Y1589F	probably damaging	Het
H2-K2	G	T	17: 34,218,474 (GRCm39)	D127E	probably damaging	Het
Ints8	A	G	4: 11,252,926 (GRCm39)	V52A	possibly damaging	Het
Kifc1	G	A	17: 34,105,621 (GRCm39)	T62I	probably damaging	Het
Klhl6	C	A	16: 19,775,764 (GRCm39)	D265Y	possibly damaging	Het
Kmt5a	T	A	5: 124,589,373 (GRCm39)	N190K	probably damaging	Het
Lce6a	A	T	3: 92,527,635 (GRCm39)	H57Q	probably benign	Het
Lipo3	A	T	19: 33,536,967 (GRCm39)	I251K	possibly damaging	Het
Lnpep	A	T	17: 17,758,816 (GRCm39)	F843I	probably damaging	Het
Lrrc45	C	T	11: 120,605,988 (GRCm39)	R99*	probably null	Het
Map3k1	A	C	13: 111,900,044 (GRCm39)	H493Q	probably benign	Het
Mcm4	A	T	16: 15,449,979 (GRCm39)		probably null	Het
Mllt3	G	A	4: 87,759,281 (GRCm39)	P256S	possibly damaging	Het
Mrtfb	A	G	16: 13,199,465 (GRCm39)	E106G	probably damaging	Het
Myo7a	T	A	7: 97,721,153 (GRCm39)	T1271S	probably damaging	Het
Ncan	C	A	8: 70,567,809 (GRCm39)	R101L	possibly damaging	Het
Ndufaf7	A	G	17: 79,253,885 (GRCm39)	D361G	probably benign	Het
Neurod6	C	T	6: 55,656,572 (GRCm39)	A22T	probably benign	Het
Nexn	T	A	3: 151,953,879 (GRCm39)	K192*	probably null	Het
Nipsnap2	A	T	5: 129,831,909 (GRCm39)	Y234F	probably damaging	Het
Nlrp10	T	C	7: 108,523,492 (GRCm39)	K663E	probably benign	Het
Nprl2	A	T	9: 107,422,497 (GRCm39)	Y329F	possibly damaging	Het
Nr2f2	C	A	7: 70,004,460 (GRCm39)	R264L	probably damaging	Het
Nsun7	A	T	5: 66,440,977 (GRCm39)	K366I	probably damaging	Het
Nup35	T	A	2: 80,472,984 (GRCm39)	M19K	probably benign	Het
Or10a4	T	A	7: 106,696,933 (GRCm39)	I87K	probably benign	Het
Or11i1	A	T	3: 106,729,829 (GRCm39)	F15L	probably damaging	Het
Or1ad6	C	A	11: 50,860,670 (GRCm39)	A275D	possibly damaging	Het
Or2v1	C	G	11: 49,025,549 (GRCm39)	H177D	probably damaging	Het
Or2w2	T	A	13: 21,757,948 (GRCm39)	Y226F	probably benign	Het
Or5af1	T	A	11: 58,722,798 (GRCm39)	S273T	probably damaging	Het
Or5p51	A	G	7: 107,444,776 (GRCm39)	S55P	probably damaging	Het
Patl2	T	C	2: 121,957,150 (GRCm39)	Y128C	probably benign	Het
Pcdhac2	A	G	18: 37,278,942 (GRCm39)	I641V	probably benign	Het
Peli3	T	C	19: 4,991,939 (GRCm39)	M1V	probably null	Het
Pex16	T	A	2: 92,205,982 (GRCm39)	L25*	probably null	Het
Plekhn1	C	A	4: 156,307,204 (GRCm39)	A449S	possibly damaging	Het
Pot1b	A	T	17: 55,972,765 (GRCm39)	I469N	probably damaging	Het
Prdx6	A	C	1: 161,078,673 (GRCm39)	L5W	probably damaging	Het
Prrc1	G	A	18: 57,507,622 (GRCm39)	V259I	possibly damaging	Het
Prss38	T	C	11: 59,266,369 (GRCm39)	S30G	possibly damaging	Het
Rgs6	C	A	12: 83,106,578 (GRCm39)	Y151*	probably null	Het
Ripk4	A	C	16: 97,545,375 (GRCm39)	L361R	probably damaging	Het
Serpinb3d	C	T	1: 107,006,962 (GRCm39)	D249N	probably benign	Het
Skint10	A	T	4: 112,630,224 (GRCm39)		probably null	Het
Smg7	A	T	1: 152,731,713 (GRCm39)	N349K	probably benign	Het
Sohlh2	C	A	3: 55,115,104 (GRCm39)	S363Y	probably damaging	Het
Srsf10	A	G	4: 135,591,179 (GRCm39)	T210A	possibly damaging	Het
Synpo2l	A	T	14: 20,710,748 (GRCm39)	M624K	probably damaging	Het
Thsd7a	T	A	6: 12,331,541 (GRCm39)		probably null	Het
Tnc	A	T	4: 63,938,692 (GRCm39)	V49E	probably damaging	Het
Tnik	A	C	3: 28,704,308 (GRCm39)	K989T	probably damaging	Het
Tnxb	T	A	17: 34,890,892 (GRCm39)	Y412N	probably damaging	Het
Trmt44	A	G	5: 35,726,103 (GRCm39)		probably null	Het
Tsc2	A	T	17: 24,840,686 (GRCm39)	V391E	probably damaging	Het
Ttll5	T	C	12: 85,980,450 (GRCm39)		probably null	Het
Usp28	A	G	9: 48,935,360 (GRCm39)	I104V	probably benign	Het
Vmn1r64	A	G	7: 5,887,096 (GRCm39)	L149S	probably damaging	Het
Yme1l1	T	A	2: 23,082,527 (GRCm39)	M506K	possibly damaging	Het
Zfp280d	T	A	9: 72,215,247 (GRCm39)	F98I	probably damaging	Het
Zfp62	C	A	11: 49,106,227 (GRCm39)	T106K	probably benign	Het

Other mutations in Lrrtm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00927:Lrrtm1	APN	6	77,221,046 (GRCm39)	missense	probably benign	0.00
IGL01011:Lrrtm1	APN	6	77,221,218 (GRCm39)	splice site	probably null
IGL01125:Lrrtm1	APN	6	77,221,436 (GRCm39)	missense	probably damaging	1.00
IGL01924:Lrrtm1	APN	6	77,221,169 (GRCm39)	missense	possibly damaging	0.81
IGL02508:Lrrtm1	APN	6	77,221,574 (GRCm39)	missense	probably damaging	1.00
IGL03005:Lrrtm1	APN	6	77,221,139 (GRCm39)	missense	probably damaging	1.00
IGL03076:Lrrtm1	APN	6	77,221,568 (GRCm39)	missense	probably damaging	1.00
R0077:Lrrtm1	UTSW	6	77,220,855 (GRCm39)	missense	probably damaging	1.00
R0607:Lrrtm1	UTSW	6	77,221,611 (GRCm39)	missense	probably damaging	1.00
R0927:Lrrtm1	UTSW	6	77,221,843 (GRCm39)	missense	probably damaging	1.00
R1742:Lrrtm1	UTSW	6	77,221,074 (GRCm39)	missense	probably damaging	1.00
R1762:Lrrtm1	UTSW	6	77,221,680 (GRCm39)	missense	probably benign
R1933:Lrrtm1	UTSW	6	77,221,949 (GRCm39)	splice site	probably null
R1934:Lrrtm1	UTSW	6	77,221,949 (GRCm39)	splice site	probably null
R2180:Lrrtm1	UTSW	6	77,221,329 (GRCm39)	missense	probably damaging	1.00
R2267:Lrrtm1	UTSW	6	77,220,996 (GRCm39)	missense	probably damaging	0.97
R2914:Lrrtm1	UTSW	6	77,221,962 (GRCm39)	missense	probably damaging	0.99
R2937:Lrrtm1	UTSW	6	77,220,635 (GRCm39)	missense	probably benign	0.03
R2938:Lrrtm1	UTSW	6	77,220,635 (GRCm39)	missense	probably benign	0.03
R4604:Lrrtm1	UTSW	6	77,221,127 (GRCm39)	missense	probably damaging	1.00
R4908:Lrrtm1	UTSW	6	77,221,661 (GRCm39)	missense	probably benign	0.01
R4910:Lrrtm1	UTSW	6	77,221,884 (GRCm39)	missense	probably damaging	1.00
R5739:Lrrtm1	UTSW	6	77,221,872 (GRCm39)	missense	probably damaging	0.99
R6604:Lrrtm1	UTSW	6	77,221,221 (GRCm39)	missense	possibly damaging	0.70
R6845:Lrrtm1	UTSW	6	77,220,864 (GRCm39)	missense	probably benign	0.02
R7048:Lrrtm1	UTSW	6	77,221,152 (GRCm39)	missense	probably damaging	1.00
R7203:Lrrtm1	UTSW	6	77,220,584 (GRCm39)	missense	probably damaging	1.00
R7783:Lrrtm1	UTSW	6	77,221,236 (GRCm39)	missense	probably damaging	1.00
R7826:Lrrtm1	UTSW	6	77,221,095 (GRCm39)	splice site	probably null
R8164:Lrrtm1	UTSW	6	77,221,199 (GRCm39)	missense	probably damaging	1.00
R8303:Lrrtm1	UTSW	6	77,221,662 (GRCm39)	missense	probably benign	0.03
R8856:Lrrtm1	UTSW	6	77,221,807 (GRCm39)	missense	possibly damaging	0.85
R9221:Lrrtm1	UTSW	6	77,221,596 (GRCm39)	missense	probably damaging	1.00
R9564:Lrrtm1	UTSW	6	77,221,536 (GRCm39)	missense	probably benign	0.00
R9749:Lrrtm1	UTSW	6	77,220,855 (GRCm39)	missense	probably damaging	1.00
RF018:Lrrtm1	UTSW	6	77,221,334 (GRCm39)	missense	possibly damaging	0.63

Predicted Primers

PCR Primer
(F):5'- TCCTGGAAGTCCCTTACGAGCATC -3'
(R):5'- AAAGCACTGTCTGAGCTGCCTG -3'

Sequencing Primer
(F):5'- TTACGAGCATCACTCTGGC -3'
(R):5'- TGGGAAACACTTCCAGGATAC -3'

Posted On

2013-06-12