Mutagenetix > Incidental Mutation

Incidental Mutation 'R2211:Lrrtm4'

239369

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm4

Ensembl Gene

ENSMUSG00000052581

Gene Name

leucine rich repeat transmembrane neuronal 4

Synonyms

7530419J18Rik

MMRRC Submission

040213-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.138) question?

Stock #

R2211 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

80018877-80810143 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 80022640 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Arginine at position 345 (H345R)

Ref Sequence

ENSEMBL: ENSMUSP00000117263 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000074662] [ENSMUST00000126005] [ENSMUST00000126399] [ENSMUST00000128718] [ENSMUST00000133918] [ENSMUST00000136421] [ENSMUST00000145407] [ENSMUST00000147663]

AlphaFold

Q80XG9

Predicted Effect

probably benign
Transcript: ENSMUST00000074662
AA Change: H344R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: H344R

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
LRRNT	33	65	1.66e0	SMART
LRR_TYP	84	107	6.67e-2	SMART
LRR	108	131	3.52e-1	SMART
LRR_TYP	132	155	2.53e-2	SMART
LRR	156	179	1.16e-1	SMART
LRR	180	203	4.34e-1	SMART
LRR	204	224	2.4e1	SMART
LRR	228	251	4.97e0	SMART
LRR	252	275	1.07e0	SMART
LRR	276	299	1.64e-1	SMART
Blast:LRRCT	311	361	4e-25	BLAST
low complexity region	375	392	N/A	INTRINSIC
transmembrane domain	425	447	N/A	INTRINSIC
low complexity region	464	469	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000126005
AA Change: H344R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: H344R

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
LRRNT	33	65	1.66e0	SMART
LRR_TYP	84	107	6.67e-2	SMART
LRR	108	131	3.52e-1	SMART
LRR_TYP	132	155	2.53e-2	SMART
LRR	156	179	1.16e-1	SMART
LRR	180	203	4.34e-1	SMART
LRR	204	224	2.4e1	SMART
LRR	228	251	4.97e0	SMART
LRR	252	275	1.07e0	SMART
LRR	276	299	1.64e-1	SMART
Blast:LRRCT	311	361	4e-25	BLAST
low complexity region	375	392	N/A	INTRINSIC
transmembrane domain	425	447	N/A	INTRINSIC
low complexity region	464	469	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000126399
AA Change: H344R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: H344R

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
LRRNT	33	65	1.66e0	SMART
LRR_TYP	84	107	6.67e-2	SMART
LRR	108	131	3.52e-1	SMART
LRR_TYP	132	155	2.53e-2	SMART
LRR	156	179	1.16e-1	SMART
LRR	180	203	4.34e-1	SMART
LRR	204	224	2.4e1	SMART
LRR	228	251	4.97e0	SMART
LRR	252	275	1.07e0	SMART
LRR	276	299	1.64e-1	SMART
Blast:LRRCT	311	361	2e-25	BLAST
low complexity region	375	392	N/A	INTRINSIC
transmembrane domain	425	447	N/A	INTRINSIC
low complexity region	464	469	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000128718

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130734

Predicted Effect

probably benign
Transcript: ENSMUST00000133918
AA Change: H344R

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: H344R

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
LRRNT	33	65	1.66e0	SMART
LRR_TYP	84	107	6.67e-2	SMART
LRR	108	131	3.52e-1	SMART
LRR_TYP	132	155	2.53e-2	SMART
LRR	156	179	1.16e-1	SMART
LRR	180	203	4.34e-1	SMART
LRR	204	224	2.4e1	SMART
LRR	228	251	4.97e0	SMART
LRR	252	275	1.07e0	SMART
LRR	276	299	1.64e-1	SMART
Blast:LRRCT	311	361	2e-25	BLAST
low complexity region	375	392	N/A	INTRINSIC
transmembrane domain	425	447	N/A	INTRINSIC
low complexity region	464	469	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000136421
AA Change: H345R

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: H345R

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
LRRNT	34	66	1.66e0	SMART
LRR_TYP	85	108	6.67e-2	SMART
LRR	109	132	3.52e-1	SMART
LRR_TYP	133	156	2.53e-2	SMART
LRR	157	180	1.16e-1	SMART
LRR	181	204	4.34e-1	SMART
LRR	205	225	2.4e1	SMART
LRR	229	252	4.97e0	SMART
LRR	253	276	1.07e0	SMART
LRR	277	300	1.64e-1	SMART
Blast:LRRCT	312	362	4e-25	BLAST
low complexity region	376	393	N/A	INTRINSIC
transmembrane domain	426	448	N/A	INTRINSIC
low complexity region	465	470	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000145407

SMART Domains

Protein: ENSMUSP00000114465
Gene: ENSMUSG00000052581

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
LRRNT	33	65	1.66e0	SMART
Blast:LRR_TYP	84	104	3e-7	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000147663
AA Change: H345R

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: H345R

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
LRRNT	34	66	1.66e0	SMART
LRR_TYP	85	108	6.67e-2	SMART
LRR	109	132	3.52e-1	SMART
LRR_TYP	133	156	2.53e-2	SMART
LRR	157	180	1.16e-1	SMART
LRR	181	204	4.34e-1	SMART
LRR	205	225	2.4e1	SMART
LRR	229	252	4.97e0	SMART
LRR	253	276	1.07e0	SMART
LRR	277	300	1.64e-1	SMART
Blast:LRRCT	312	362	2e-25	BLAST
low complexity region	376	393	N/A	INTRINSIC
transmembrane domain	426	448	N/A	INTRINSIC
low complexity region	465	470	N/A	INTRINSIC

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.1%
20x: 94.5%

Validation Efficiency

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit impaired excitatory synapse development and excitatory transmission in dentate gyrus granule cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430078G23Rik	T	C	8: 3,387,680	S268P	possibly damaging	Het
Adam18	A	G	8: 24,628,155	S34P	probably damaging	Het
Adam23	T	A	1: 63,573,129		probably benign	Het
Adcy10	A	T	1: 165,518,212	I277F	probably damaging	Het
Arfgef3	A	T	10: 18,592,245	S1736T	possibly damaging	Het
Arhgap21	A	T	2: 20,881,640	M242K	possibly damaging	Het
Astn1	A	G	1: 158,657,306	R4G	probably benign	Het
AU041133	G	A	10: 82,150,921	C135Y	probably damaging	Het
Cdc42bpb	A	G	12: 111,301,854	V53A	probably benign	Het
Cdh23	T	C	10: 60,466,004	D428G	possibly damaging	Het
Cebpa	T	C	7: 35,120,466	S350P	probably damaging	Het
Cftr	A	G	6: 18,214,280	M152V	probably null	Het
Cpa4	A	G	6: 30,583,650	N255S	possibly damaging	Het
Ddx51	T	A	5: 110,655,768	D343E	probably damaging	Het
Dnah7a	T	C	1: 53,479,773	I2942V	probably benign	Het
Dnajc1	G	T	2: 18,392,475	A9E	probably damaging	Het
Dpysl5	G	A	5: 30,791,597	D399N	probably damaging	Het
Edem3	A	G	1: 151,804,702	D526G	possibly damaging	Het
Emc10	G	A	7: 44,493,192	R109W	probably damaging	Het
Etaa1	G	A	11: 17,952,686	Q84*	probably null	Het
Fabp3	C	T	4: 130,312,387	T57I	probably benign	Het
Fam149a	G	A	8: 45,341,009	T674I	probably damaging	Het
Fam98a	A	G	17: 75,538,945		probably null	Het
Fat4	A	G	3: 38,891,527	N1523S	possibly damaging	Het
Fbxw10	A	G	11: 62,867,535	T529A	probably damaging	Het
Gzf1	C	T	2: 148,684,950	A447V	probably damaging	Het
Hap1	G	A	11: 100,354,724	T138M	probably benign	Het
Hic1	T	A	11: 75,169,384	R46W	possibly damaging	Het
Id4	T	A	13: 48,261,802	L102Q	probably damaging	Het
Il3ra	T	C	14: 14,355,029	C271R	probably benign	Het
Ints4	T	C	7: 97,509,750	I443T	possibly damaging	Het
Lmln	A	G	16: 33,109,778	E535G	probably benign	Het
Ltbp3	T	C	19: 5,753,962	I834T	possibly damaging	Het
Mnd1	C	A	3: 84,134,109	C62F	probably benign	Het
Mpp5	A	T	12: 78,797,248	K75N	possibly damaging	Het
Ms4a18	C	A	19: 10,997,305	V341L	probably benign	Het
Nbr1	T	C	11: 101,567,264		probably null	Het
Nf1	T	C	11: 79,444,064	M914T	probably benign	Het
Notch3	T	A	17: 32,147,978	H861L	probably benign	Het
Nupl1	A	G	14: 60,232,640	F341L	probably damaging	Het
Ogfod2	C	A	5: 124,112,780		probably null	Het
Oit3	T	C	10: 59,428,070	D414G	probably damaging	Het
Olfr1079	T	C	2: 86,538,513	Y132C	probably damaging	Het
Olfr1497	T	A	19: 13,795,369	M81L	probably benign	Het
Olfr787	A	T	10: 129,462,940	K88M	probably damaging	Het
Olfr804	A	G	10: 129,705,451	H191R	probably benign	Het
Pcbp4	C	A	9: 106,460,734	H74Q	probably benign	Het
Pip5k1b	A	T	19: 24,378,850	D241E	probably damaging	Het
Plcb2	T	C	2: 118,723,534	D102G	probably benign	Het
Plekha5	G	A	6: 140,525,861	E4K	possibly damaging	Het
Ppargc1a	A	C	5: 51,474,259	S343A	possibly damaging	Het
Ppwd1	G	A	13: 104,207,142	S585L	probably benign	Het
Rarg	T	C	15: 102,239,524	N284S	probably benign	Het
Rnpepl1	C	T	1: 92,916,380	L278F	probably damaging	Het
Rp1	A	C	1: 4,348,139	S917A	probably damaging	Het
Rsf1	ATGGCG	ATGGCGAGGGTGGCG	7: 97,579,904		probably benign	Het
Rsph3b	T	C	17: 6,941,740	S189G	probably benign	Het
Sec31b	A	T	19: 44,523,150	L604Q	probably damaging	Het
Sema6b	T	A	17: 56,124,741	I641F	probably benign	Het
Slc35f5	A	T	1: 125,579,264	I309F	possibly damaging	Het
Smarca4	A	G	9: 21,686,029	E1360G	probably damaging	Het
Spata31d1c	T	C	13: 65,035,939	S432P	probably benign	Het
Spsb3	T	C	17: 24,890,937		probably null	Het
Sptbn4	T	C	7: 27,367,609	D1960G	probably damaging	Het
Srgap1	A	G	10: 121,853,740	V345A	possibly damaging	Het
Tiam2	C	A	17: 3,414,918	C307*	probably null	Het
Trim43b	T	A	9: 89,085,249	T444S	possibly damaging	Het
Trmt13	A	G	3: 116,594,754	I11T	probably benign	Het
Ylpm1	A	T	12: 85,044,378	R1073*	probably null	Het
Zfp524	T	C	7: 5,017,919	S149P	probably damaging	Het
Zfp777	T	C	6: 48,043,885	I312V	possibly damaging	Het

Other mutations in Lrrtm4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00498:Lrrtm4	APN	6	80022546	missense	probably damaging	1.00
IGL02043:Lrrtm4	APN	6	80021862	missense	possibly damaging	0.89
IGL02603:Lrrtm4	APN	6	80022984	missense	possibly damaging	0.92
IGL02614:Lrrtm4	APN	6	80021844	missense	probably benign	0.01
IGL02735:Lrrtm4	APN	6	80809050	missense	probably benign
IGL02812:Lrrtm4	APN	6	80021964	missense	probably damaging	1.00
IGL02885:Lrrtm4	APN	6	80021803	missense	probably damaging	1.00
IGL02956:Lrrtm4	APN	6	80021650	missense	probably benign	0.04
IGL03242:Lrrtm4	APN	6	80022088	missense	probably benign	0.22
R0504:Lrrtm4	UTSW	6	80022046	missense	probably damaging	1.00
R0537:Lrrtm4	UTSW	6	80022120	missense	probably benign	0.02
R0656:Lrrtm4	UTSW	6	80021970	missense	possibly damaging	0.87
R0698:Lrrtm4	UTSW	6	80022928	missense	probably damaging	1.00
R1651:Lrrtm4	UTSW	6	80022528	missense	probably benign	0.06
R2126:Lrrtm4	UTSW	6	80021739	missense	probably damaging	1.00
R2363:Lrrtm4	UTSW	6	80021874	missense	probably damaging	1.00
R3732:Lrrtm4	UTSW	6	80019655	intron	probably benign
R3817:Lrrtm4	UTSW	6	80022061	missense	probably benign	0.00
R4814:Lrrtm4	UTSW	6	80023134	missense	possibly damaging	0.69
R5304:Lrrtm4	UTSW	6	80022700	missense	probably benign	0.01
R5318:Lrrtm4	UTSW	6	80022512	missense	probably damaging	1.00
R5327:Lrrtm4	UTSW	6	80022637	missense	probably damaging	1.00
R5931:Lrrtm4	UTSW	6	80021739	missense	probably damaging	0.99
R6195:Lrrtm4	UTSW	6	80021956	missense	probably damaging	1.00
R7597:Lrrtm4	UTSW	6	80022445	nonsense	probably null
R7793:Lrrtm4	UTSW	6	80022858	missense	probably damaging	0.97
R7875:Lrrtm4	UTSW	6	80022360	missense	possibly damaging	0.89
R8058:Lrrtm4	UTSW	6	80022545	missense	probably benign
R8238:Lrrtm4	UTSW	6	80022685	missense	probably damaging	0.97
R8324:Lrrtm4	UTSW	6	80021991	missense	probably damaging	1.00
R8751:Lrrtm4	UTSW	6	80022109	missense	probably damaging	1.00
R8859:Lrrtm4	UTSW	6	80021887	missense	probably damaging	1.00
R9142:Lrrtm4	UTSW	6	80022443	missense	probably damaging	1.00
R9633:Lrrtm4	UTSW	6	80023081	missense	probably damaging	1.00
R9709:Lrrtm4	UTSW	6	80809173	missense	probably damaging	0.96
Z1177:Lrrtm4	UTSW	6	80022717	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ATTTGGATTCCAACAAGCTCACC -3'
(R):5'- CGTACTCATGATCCGTACCTGG -3'

Sequencing Primer
(F):5'- GCTCACCAATGTCTCCCAGGAG -3'
(R):5'- GATCCGTACCTGGAATTTGAAAGCC -3'

Posted On

2014-10-15