Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01924:Lrrtm1'

180226

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Lrrtm1

Ensembl Gene

ENSMUSG00000060780

Gene Name

leucine rich repeat transmembrane neuronal 1

Synonyms

4632401D06Rik

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

IGL01924

Quality Score

Status

Chromosome

Chromosomal Location

77242689-77257791 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 77244186 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 209 (F209L)

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

possibly damaging
Transcript: ENSMUST00000020400
AA Change: F209L

PolyPhen 2 Score 0.813 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: F209L

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

possibly damaging
Transcript: ENSMUST00000159616
AA Change: F209L

PolyPhen 2 Score 0.813 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: F209L

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

possibly damaging
Transcript: ENSMUST00000161677
AA Change: F209L

PolyPhen 2 Score 0.813 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: F209L

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

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acacb	C	T	5: 114,223,986		probably benign	Het
Adamts13	A	G	2: 26,996,583	E938G	possibly damaging	Het
Aox2	C	T	1: 58,287,743	T167I	possibly damaging	Het
Apba3	G	T	10: 81,273,073	A557S	probably benign	Het
Atad2b	T	C	12: 5,034,093	L1382P	probably damaging	Het
Atrn	C	T	2: 130,935,565	T178I	probably damaging	Het
B4galnt1	A	G	10: 127,166,761	S88G	probably benign	Het
Baz2b	T	C	2: 59,935,271	K887E	probably damaging	Het
Ccdc162	A	C	10: 41,569,887	F430V	probably damaging	Het
Cdc42bpb	T	A	12: 111,317,453		probably benign	Het
Chit1	A	G	1: 134,149,410	D317G	probably benign	Het
Chrnb1	A	T	11: 69,795,019		probably benign	Het
Cobl	G	T	11: 12,254,596	T620K	probably benign	Het
Creld1	T	C	6: 113,483,960	F20L	probably benign	Het
Csmd2	A	T	4: 128,559,947	D3475V	unknown	Het
Cyp3a57	A	G	5: 145,372,629	D259G	probably benign	Het
Dbnl	A	G	11: 5,797,142	Y224C	probably damaging	Het
Det1	A	T	7: 78,843,823	C144*	probably null	Het
Fbxo47	G	T	11: 97,856,160	A360D	probably damaging	Het
Frrs1	G	A	3: 116,885,239	G237R	probably damaging	Het
Gatsl2	T	C	5: 134,135,602	F134S	probably benign	Het
Gm10718	A	T	9: 3,025,118	Y194F	probably benign	Het
Gm21738	G	A	14: 19,416,979	S144L	probably benign	Het
Gm4788	G	A	1: 139,739,206	L444F	probably damaging	Het
Gm5862	A	C	5: 26,022,771	W41G	probably benign	Het
Gria2	T	C	3: 80,710,331	T372A	probably benign	Het
Hmcn2	A	T	2: 31,398,917	Q2246L	probably benign	Het
Ide	T	C	19: 37,272,164	M930V	unknown	Het
Kdm5a	T	C	6: 120,394,255		probably null	Het
Khnyn	A	G	14: 55,894,969	T625A	probably benign	Het
Med13	C	A	11: 86,308,696		probably benign	Het
Myom2	A	G	8: 15,069,685	E147G	probably benign	Het
Myrip	T	A	9: 120,388,264	V88D	probably damaging	Het
Nbeal2	T	C	9: 110,631,414	H1784R	probably benign	Het
Nlrp4e	T	A	7: 23,320,830	C247*	probably null	Het
Nup54	G	A	5: 92,424,435	P252L	probably benign	Het
Olfr610	A	G	7: 103,506,796	I50T	possibly damaging	Het
Otoa	C	A	7: 121,105,968	N244K	probably damaging	Het
Pbrm1	G	A	14: 31,082,604	R960H	probably damaging	Het
Ptcd3	A	T	6: 71,898,427	N190K	probably damaging	Het
Rhobtb1	T	A	10: 69,270,304	L233H	probably damaging	Het
Sec24c	T	A	14: 20,689,689	F545I	probably damaging	Het
Slc6a15	T	C	10: 103,404,825		probably null	Het
Slitrk1	G	A	14: 108,911,239	A680V	probably benign	Het
Smpd1	C	T	7: 105,555,448	S178L	probably benign	Het
Spindoc	A	G	19: 7,382,677	L42P	probably damaging	Het
Tenm4	A	G	7: 96,895,212	E2145G	probably damaging	Het
Tmem144	G	T	3: 79,839,194	A18E	probably damaging	Het
Tmem213	A	T	6: 38,109,438	S10C	possibly damaging	Het
Trav6-3	A	T	14: 53,430,343	I102L	probably benign	Het
Trip11	T	G	12: 101,886,884	N483T	possibly damaging	Het
Unc13b	C	T	4: 43,239,385	R1056*	probably null	Het
Wdr27	T	G	17: 14,917,226	K433N	probably damaging	Het
Wls	C	A	3: 159,901,443	S189*	probably null	Het
Yeats2	A	G	16: 20,206,167	N706D	probably damaging	Het
Zbp1	A	G	2: 173,212,254	V158A	probably benign	Het
Zfp595	G	T	13: 67,317,783	H139N	possibly damaging	Het

Other mutations in Lrrtm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00927:Lrrtm1	APN	6	77244063	missense	probably benign	0.00
IGL01011:Lrrtm1	APN	6	77244235	splice site	probably null
IGL01125:Lrrtm1	APN	6	77244453	missense	probably damaging	1.00
IGL02508:Lrrtm1	APN	6	77244591	missense	probably damaging	1.00
IGL03005:Lrrtm1	APN	6	77244156	missense	probably damaging	1.00
IGL03076:Lrrtm1	APN	6	77244585	missense	probably damaging	1.00
R0077:Lrrtm1	UTSW	6	77243872	missense	probably damaging	1.00
R0540:Lrrtm1	UTSW	6	77244628	missense	probably damaging	1.00
R0607:Lrrtm1	UTSW	6	77244628	missense	probably damaging	1.00
R0927:Lrrtm1	UTSW	6	77244860	missense	probably damaging	1.00
R1742:Lrrtm1	UTSW	6	77244091	missense	probably damaging	1.00
R1762:Lrrtm1	UTSW	6	77244697	missense	probably benign
R1933:Lrrtm1	UTSW	6	77244966	splice site	probably null
R1934:Lrrtm1	UTSW	6	77244966	splice site	probably null
R2180:Lrrtm1	UTSW	6	77244346	missense	probably damaging	1.00
R2267:Lrrtm1	UTSW	6	77244013	missense	probably damaging	0.97
R2914:Lrrtm1	UTSW	6	77244979	missense	probably damaging	0.99
R2937:Lrrtm1	UTSW	6	77243652	missense	probably benign	0.03
R2938:Lrrtm1	UTSW	6	77243652	missense	probably benign	0.03
R4604:Lrrtm1	UTSW	6	77244144	missense	probably damaging	1.00
R4908:Lrrtm1	UTSW	6	77244678	missense	probably benign	0.01
R4910:Lrrtm1	UTSW	6	77244901	missense	probably damaging	1.00
R5739:Lrrtm1	UTSW	6	77244889	missense	probably damaging	0.99
R6604:Lrrtm1	UTSW	6	77244238	missense	possibly damaging	0.70
R6845:Lrrtm1	UTSW	6	77243881	missense	probably benign	0.02
R7048:Lrrtm1	UTSW	6	77244169	missense	probably damaging	1.00
R7203:Lrrtm1	UTSW	6	77243601	missense	probably damaging	1.00
R7783:Lrrtm1	UTSW	6	77244253	missense	probably damaging	1.00
R7826:Lrrtm1	UTSW	6	77244112	splice site	probably null
R8164:Lrrtm1	UTSW	6	77244216	missense	probably damaging	1.00
R8303:Lrrtm1	UTSW	6	77244679	missense	probably benign	0.03
R8856:Lrrtm1	UTSW	6	77244824	missense	possibly damaging	0.85
R9221:Lrrtm1	UTSW	6	77244613	missense	probably damaging	1.00
R9564:Lrrtm1	UTSW	6	77244553	missense	probably benign	0.00
R9749:Lrrtm1	UTSW	6	77243872	missense	probably damaging	1.00
RF018:Lrrtm1	UTSW	6	77244351	missense	possibly damaging	0.63

Posted On

2014-05-07