Mutagenetix > Incidental Mutation

Incidental Mutation 'R5739:Lrrtm1'

444683

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm1

Ensembl Gene

ENSMUSG00000060780

Gene Name

leucine rich repeat transmembrane neuronal 1

Synonyms

4632401D06Rik

MMRRC Submission

043351-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5739 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

77219672-77234774 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 77221872 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 443 (V443A)

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: V443A

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: V443A

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: V443A

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: V443A

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: V443A

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: V443A

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

Meta Mutation Damage Score

0.2343

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.1%
20x: 95.0%

Validation Efficiency

100% (82/82)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931429L15Rik	A	T	9: 46,220,717 (GRCm39)	S50T	probably benign	Het
A930011G23Rik	A	G	5: 99,369,289 (GRCm39)	L529P	probably damaging	Het
Acer2	A	T	4: 86,818,792 (GRCm39)	N147Y	probably damaging	Het
Adamtsl1	A	G	4: 86,150,901 (GRCm39)	E353G	probably damaging	Het
Alg6	T	C	4: 99,632,737 (GRCm39)	F60L	probably benign	Het
Ano6	A	T	15: 95,811,260 (GRCm39)	D120V	probably damaging	Het
Armc3	A	G	2: 19,258,728 (GRCm39)	D265G	possibly damaging	Het
Aurkc	A	T	7: 7,005,859 (GRCm39)	Y249F	probably benign	Het
Bmal1	G	A	7: 112,884,238 (GRCm39)	R92Q	probably damaging	Het
Cacna2d2	A	G	9: 107,389,528 (GRCm39)	I274V	probably benign	Het
Camk2n2	C	A	16: 20,439,830 (GRCm39)	G39C	probably damaging	Het
Ccdc39	A	G	3: 33,880,710 (GRCm39)	L419P	possibly damaging	Het
Cdh23	T	C	10: 60,141,388 (GRCm39)	M3117V	probably damaging	Het
Celsr3	A	G	9: 108,704,357 (GRCm39)	E280G	probably benign	Het
Cherp	TGCTGGTGGTGGGG	TG	8: 73,221,659 (GRCm39)		probably benign	Het
Clcn6	A	G	4: 148,098,646 (GRCm39)	V494A	probably damaging	Het
Col19a1	C	T	1: 24,376,996 (GRCm39)	G450S	probably damaging	Het
Crb2	T	G	2: 37,683,666 (GRCm39)	V1056G	probably damaging	Het
Crtac1	A	G	19: 42,290,612 (GRCm39)	F363S	probably damaging	Het
Dipk2a	A	T	9: 94,402,594 (GRCm39)	V356E	possibly damaging	Het
Dnaaf2	T	C	12: 69,243,715 (GRCm39)	S449G	probably benign	Het
Dnah7b	A	T	1: 46,273,152 (GRCm39)	I2427F	probably damaging	Het
Dnah8	T	A	17: 30,937,981 (GRCm39)	D1619E	probably benign	Het
Dock3	A	T	9: 106,850,995 (GRCm39)	S836T	possibly damaging	Het
Donson	A	T	16: 91,478,117 (GRCm39)		probably null	Het
Drc3	G	A	11: 60,265,956 (GRCm39)	R215H	possibly damaging	Het
Entpd2	T	C	2: 25,289,504 (GRCm39)	S329P	possibly damaging	Het
Eya2	T	C	2: 165,603,857 (GRCm39)	S332P	probably damaging	Het
Fam83f	T	A	15: 80,576,206 (GRCm39)	Y286N	probably damaging	Het
Fat4	T	C	3: 39,037,283 (GRCm39)	V3645A	probably benign	Het
G2e3	T	C	12: 51,419,287 (GRCm39)	F668L	possibly damaging	Het
Gm14403	T	A	2: 177,201,040 (GRCm39)	C329S	probably damaging	Het
Hmcn1	G	A	1: 150,684,448 (GRCm39)	T374I	probably benign	Het
Hmcn1	A	T	1: 150,634,225 (GRCm39)		probably null	Het
Hrnr	T	C	3: 93,230,436 (GRCm39)	S225P	unknown	Het
Ifi202b	C	T	1: 173,798,918 (GRCm39)		probably null	Het
Il10ra	A	T	9: 45,167,368 (GRCm39)	D394E	possibly damaging	Het
Itga2b	A	T	11: 102,356,735 (GRCm39)	D275E	probably benign	Het
Jaml	A	T	9: 45,000,026 (GRCm39)	D108V	probably damaging	Het
Kir3dl1	G	A	X: 135,427,231 (GRCm39)	D56N	probably damaging	Het
Mkln1	T	A	6: 31,473,637 (GRCm39)	S126R	probably benign	Het
Myo19	T	C	11: 84,788,450 (GRCm39)	I354T	probably damaging	Het
Nucb1	A	T	7: 45,151,084 (GRCm39)	L99Q	probably damaging	Het
Or4f59	A	G	2: 111,873,128 (GRCm39)	F83S	probably damaging	Het
Pask	A	G	1: 93,249,778 (GRCm39)	S541P	probably benign	Het
Pdpr	A	T	8: 111,861,252 (GRCm39)	I749F	possibly damaging	Het
Pgap6	T	A	17: 26,339,425 (GRCm39)	F580I	probably damaging	Het
Phyhipl	T	C	10: 70,395,399 (GRCm39)	D269G	possibly damaging	Het
Pkdcc	A	G	17: 83,523,223 (GRCm39)	D110G	probably benign	Het
Ppox	A	G	1: 171,107,570 (GRCm39)	L115P	probably damaging	Het
Ppp1r12c	A	G	7: 4,500,281 (GRCm39)	L94P	probably damaging	Het
Ppp6r2	T	A	15: 89,143,276 (GRCm39)	M141K	probably benign	Het
Prl3d1	A	T	13: 27,283,995 (GRCm39)	H188L	probably benign	Het
Psmb3	T	A	11: 97,604,296 (GRCm39)		probably benign	Het
Pxdn	T	A	12: 30,032,333 (GRCm39)	S150T	probably benign	Het
Ripor3	T	C	2: 167,823,203 (GRCm39)	T903A	probably damaging	Het
Rnase4	T	C	14: 51,342,306 (GRCm39)	L10S	probably benign	Het
Rnf224	T	C	2: 25,126,012 (GRCm39)	T114A	probably benign	Het
Rp1l1	A	T	14: 64,269,619 (GRCm39)	E1735V	probably benign	Het
Rrp1b	T	A	17: 32,264,950 (GRCm39)	Y60N	probably damaging	Het
Rsbn1l	A	T	5: 21,110,814 (GRCm39)	V508E	probably damaging	Het
Rubcnl	T	C	14: 75,278,381 (GRCm39)		probably null	Het
Rxfp4	A	G	3: 88,559,209 (GRCm39)		probably benign	Het
Sdccag8	A	G	1: 176,653,797 (GRCm39)	T85A	probably benign	Het
Slc46a1	A	T	11: 78,357,975 (GRCm39)	I343F	possibly damaging	Het
Ssh2	A	G	11: 77,340,639 (GRCm39)	D597G	probably damaging	Het
Syne2	T	A	12: 76,044,239 (GRCm39)	V3942E	possibly damaging	Het
Timd4	T	C	11: 46,708,573 (GRCm39)	S200P	probably benign	Het
Tmc5	G	A	7: 118,265,834 (GRCm39)		probably null	Het
Trbv16	A	G	6: 41,129,013 (GRCm39)	T66A	probably benign	Het
Ttc3	A	T	16: 94,240,183 (GRCm39)	K1103*	probably null	Het
Ttc7b	A	G	12: 100,350,492 (GRCm39)	V458A	probably damaging	Het
Ubxn10	A	G	4: 138,448,134 (GRCm39)	S181P	probably benign	Het
Vmn2r11	A	G	5: 109,207,114 (GRCm39)		probably null	Het
Vmn2r26	A	T	6: 124,002,925 (GRCm39)	N112Y	probably benign	Het
Vmn2r5	T	C	3: 64,411,497 (GRCm39)	D357G	probably damaging	Het
Zc3h10	T	C	10: 128,380,670 (GRCm39)	N229S	probably benign	Het
Zfp407	T	C	18: 84,226,867 (GRCm39)	*2247W	probably null	Het
Zfyve1	C	A	12: 83,621,910 (GRCm39)	V162L	possibly damaging	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
R0540:Lrrtm1	UTSW	6	77,221,611 (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
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'- TTTCCACCTGTGTGAGGATG -3'
(R):5'- CGTTGATGATAACCAGGGCC -3'

Sequencing Primer
(F):5'- CCGTCACTAACCGCAGTG -3'
(R):5'- GATGATAACCAGGGCCCCCTC -3'

Posted On

2016-11-21