Mutagenetix > Incidental Mutation

Incidental Mutation 'R6195:Lrrtm4'

502850

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm4

Ensembl Gene

ENSMUSG00000052581

Gene Name

leucine rich repeat transmembrane neuronal 4

Synonyms

7530419J18Rik

MMRRC Submission

044335-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.100) question?

Stock #

R6195 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

79995860-80787124 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 79998939 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 117 (L117P)

Ref Sequence

ENSEMBL: ENSMUSP00000117263 (fasta)

Gene Model

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

AlphaFold

Q80XG9

Predicted Effect

probably damaging
Transcript: ENSMUST00000074662
AA Change: L116P

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

SMART Domains

Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: L116P

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 damaging
Transcript: ENSMUST00000126005
AA Change: L116P

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

SMART Domains

Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: L116P

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 damaging
Transcript: ENSMUST00000126399
AA Change: L116P

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

SMART Domains

Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: L116P

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 damaging
Transcript: ENSMUST00000133918
AA Change: L116P

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

SMART Domains

Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: L116P

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 damaging
Transcript: ENSMUST00000136421
AA Change: L117P

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

SMART Domains

Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: L117P

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 damaging
Transcript: ENSMUST00000147663
AA Change: L117P

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

SMART Domains

Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: L117P

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

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

97% (76/78)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A130010J15Rik	A	G	1: 192,857,142 (GRCm39)		probably null	Het
Aadacl2fm2	G	A	3: 59,659,623 (GRCm39)	V359I	probably damaging	Het
Abtb1	T	C	6: 88,817,718 (GRCm39)	E50G	probably benign	Het
Agbl2	T	A	2: 90,643,657 (GRCm39)	D792E	probably benign	Het
Aoc1	C	A	6: 48,885,611 (GRCm39)	N705K	probably damaging	Het
Araf	G	T	X: 20,726,339 (GRCm39)	R601L	probably damaging	Homo
Arhgef7	C	T	8: 11,872,017 (GRCm39)	T701I	probably damaging	Het
Atg10	G	T	13: 91,356,555 (GRCm39)		probably null	Het
Atp5f1c	T	C	2: 10,068,926 (GRCm39)	I116M	possibly damaging	Het
Baz2b	T	A	2: 59,737,855 (GRCm39)	Q1818L	possibly damaging	Het
Bod1	A	G	11: 31,616,740 (GRCm39)	*174Q	probably null	Het
Cacna1a	A	G	8: 85,315,382 (GRCm39)	Y1539C	probably damaging	Het
Creb3	A	G	4: 43,566,346 (GRCm39)	D260G	probably benign	Het
Cyp1b1	G	T	17: 80,021,695 (GRCm39)	L16M	probably damaging	Het
Dhx29	T	A	13: 113,101,071 (GRCm39)	S1205T	probably benign	Het
Dlec1	A	G	9: 118,966,321 (GRCm39)	K1097E	probably benign	Het
Dnah7b	G	A	1: 46,243,429 (GRCm39)	D1578N	probably damaging	Het
Dok3	T	C	13: 55,671,389 (GRCm39)	N394S	probably benign	Het
Dpcd	A	G	19: 45,565,458 (GRCm39)	D144G	probably damaging	Het
Efhb	A	G	17: 53,769,580 (GRCm39)	F243S	possibly damaging	Het
Eif2ak2	A	T	17: 79,178,662 (GRCm39)	Y137*	probably null	Het
Eif4e1b	A	G	13: 54,932,018 (GRCm39)	N34S	probably null	Het
F2rl3	A	G	8: 73,489,513 (GRCm39)	T247A	probably benign	Het
Fan1	A	T	7: 64,004,119 (GRCm39)	H782Q	probably damaging	Het
Fer1l5	T	C	1: 36,414,367 (GRCm39)		probably null	Het
Fer1l6	T	C	15: 58,509,806 (GRCm39)	S1423P	probably damaging	Het
Fetub	C	T	16: 22,751,081 (GRCm39)	R143C	probably damaging	Het
Fgfbp1	T	C	5: 44,136,704 (GRCm39)	D196G	possibly damaging	Het
Fxn	G	A	19: 24,239,407 (GRCm39)	R162C	probably damaging	Het
Fxr2	C	T	11: 69,543,099 (GRCm39)	T632M	probably benign	Het
Gab1	A	T	8: 81,606,161 (GRCm39)	Y24*	probably null	Het
Gcc2	T	C	10: 58,106,806 (GRCm39)	S681P	probably damaging	Het
Git2	T	C	5: 114,905,175 (GRCm39)	N94S	probably benign	Het
Gm5799	T	G	14: 43,782,088 (GRCm39)	L87V	probably damaging	Het
Golga7b	A	T	19: 42,251,886 (GRCm39)	D44V	probably benign	Het
Hace1	T	A	10: 45,546,539 (GRCm39)	I391N	possibly damaging	Het
Hmcn2	T	C	2: 31,274,127 (GRCm39)	S1416P	probably damaging	Het
Hoxa11	G	A	6: 52,222,681 (GRCm39)	R7C	probably damaging	Het
Igkv14-126	A	T	6: 67,873,475 (GRCm39)	T68S	possibly damaging	Het
Insyn2a	T	C	7: 134,520,377 (GRCm39)	D51G	probably damaging	Het
Itpr3	T	C	17: 27,305,934 (GRCm39)	I164T	probably damaging	Het
Kif22	A	G	7: 126,628,131 (GRCm39)	S540P	probably damaging	Het
Ldlr	T	A	9: 21,643,077 (GRCm39)	C34*	probably null	Het
Mad2l1	G	T	6: 66,514,612 (GRCm39)	G94C	possibly damaging	Het
Malrd1	C	A	2: 15,700,137 (GRCm39)	H661Q	probably damaging	Het
Mical3	T	A	6: 120,993,796 (GRCm39)		probably benign	Het
Mipep	T	A	14: 61,109,554 (GRCm39)	W644R	probably damaging	Het
Mycl	A	G	4: 122,893,713 (GRCm39)	D171G	probably damaging	Het
Myof	A	G	19: 37,901,805 (GRCm39)	F997L	possibly damaging	Het
Nagpa	C	T	16: 5,021,613 (GRCm39)	R46H	probably damaging	Het
Nf1	A	G	11: 79,456,801 (GRCm39)	Y629C	probably damaging	Het
Obscn	T	A	11: 58,888,033 (GRCm39)	E2164V	probably damaging	Het
Or52h1	A	T	7: 103,828,961 (GRCm39)	V218D	possibly damaging	Het
Or5ac23	A	G	16: 59,149,785 (GRCm39)	V29A	possibly damaging	Het
Or5w19	T	C	2: 87,698,904 (GRCm39)	S190P	possibly damaging	Het
Or8k25	T	C	2: 86,243,551 (GRCm39)	I282V	probably damaging	Het
Pcdh20	T	C	14: 88,705,488 (GRCm39)	E604G	probably benign	Het
Pcdhb7	G	A	18: 37,475,709 (GRCm39)	V282I	probably benign	Het
Pcnx4	A	G	12: 72,603,648 (GRCm39)	D523G	possibly damaging	Het
Pigx	G	A	16: 31,903,404 (GRCm39)	T219I	probably damaging	Het
Plch1	G	T	3: 63,648,210 (GRCm39)	P399Q	probably damaging	Het
Pvrig-ps	T	A	5: 138,340,537 (GRCm39)	F74I	possibly damaging	Het
Rsrp1	T	A	4: 134,654,113 (GRCm39)	I255K	probably damaging	Het
Scn1a	T	A	2: 66,107,962 (GRCm39)	Y1588F	possibly damaging	Het
Serpina9	T	A	12: 103,967,666 (GRCm39)	H243L	probably damaging	Het
Tapbp	T	C	17: 34,138,956 (GRCm39)	L41P	probably damaging	Het
Tbc1d16	T	A	11: 119,101,391 (GRCm39)	K40*	probably null	Het
Tbc1d2	C	T	4: 46,629,912 (GRCm39)	G252R	probably benign	Het
Tbc1d23	T	C	16: 57,051,713 (GRCm39)	E6G	possibly damaging	Het
Tdrd6	A	G	17: 43,940,643 (GRCm39)	V135A	probably damaging	Het
Tmem87a	A	T	2: 120,222,656 (GRCm39)		probably null	Het
Tnrc18	T	A	5: 142,750,928 (GRCm39)	K1217N	unknown	Het
Trim33	G	A	3: 103,244,848 (GRCm39)		probably null	Het
Ttn	T	A	2: 76,567,997 (GRCm39)	Y27632F	probably benign	Het
Tubgcp6	A	T	15: 89,006,994 (GRCm39)	D9E	probably benign	Het
Uaca	G	A	9: 60,777,326 (GRCm39)	R571Q	probably damaging	Het
Zfp655	T	A	5: 145,180,572 (GRCm39)	F143L	possibly damaging	Het

Other mutations in Lrrtm4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00498:Lrrtm4	APN	6	79,999,529 (GRCm39)	missense	probably damaging	1.00
IGL02043:Lrrtm4	APN	6	79,998,845 (GRCm39)	missense	possibly damaging	0.89
IGL02603:Lrrtm4	APN	6	79,999,967 (GRCm39)	missense	possibly damaging	0.92
IGL02614:Lrrtm4	APN	6	79,998,827 (GRCm39)	missense	probably benign	0.01
IGL02735:Lrrtm4	APN	6	80,786,031 (GRCm39)	missense	probably benign
IGL02812:Lrrtm4	APN	6	79,998,947 (GRCm39)	missense	probably damaging	1.00
IGL02885:Lrrtm4	APN	6	79,998,786 (GRCm39)	missense	probably damaging	1.00
IGL02956:Lrrtm4	APN	6	79,998,633 (GRCm39)	missense	probably benign	0.04
IGL03242:Lrrtm4	APN	6	79,999,071 (GRCm39)	missense	probably benign	0.22
R0504:Lrrtm4	UTSW	6	79,999,029 (GRCm39)	missense	probably damaging	1.00
R0537:Lrrtm4	UTSW	6	79,999,103 (GRCm39)	missense	probably benign	0.02
R0656:Lrrtm4	UTSW	6	79,998,953 (GRCm39)	missense	possibly damaging	0.87
R0698:Lrrtm4	UTSW	6	79,999,911 (GRCm39)	missense	probably damaging	1.00
R1651:Lrrtm4	UTSW	6	79,999,511 (GRCm39)	missense	probably benign	0.06
R2126:Lrrtm4	UTSW	6	79,998,722 (GRCm39)	missense	probably damaging	1.00
R2211:Lrrtm4	UTSW	6	79,999,623 (GRCm39)	missense	probably benign	0.00
R2363:Lrrtm4	UTSW	6	79,998,857 (GRCm39)	missense	probably damaging	1.00
R3732:Lrrtm4	UTSW	6	79,996,638 (GRCm39)	intron	probably benign
R3817:Lrrtm4	UTSW	6	79,999,044 (GRCm39)	missense	probably benign	0.00
R4814:Lrrtm4	UTSW	6	80,000,117 (GRCm39)	missense	possibly damaging	0.69
R5304:Lrrtm4	UTSW	6	79,999,683 (GRCm39)	missense	probably benign	0.01
R5318:Lrrtm4	UTSW	6	79,999,495 (GRCm39)	missense	probably damaging	1.00
R5327:Lrrtm4	UTSW	6	79,999,620 (GRCm39)	missense	probably damaging	1.00
R5931:Lrrtm4	UTSW	6	79,998,722 (GRCm39)	missense	probably damaging	0.99
R7597:Lrrtm4	UTSW	6	79,999,428 (GRCm39)	nonsense	probably null
R7793:Lrrtm4	UTSW	6	79,999,841 (GRCm39)	missense	probably damaging	0.97
R7875:Lrrtm4	UTSW	6	79,999,343 (GRCm39)	missense	possibly damaging	0.89
R8058:Lrrtm4	UTSW	6	79,999,528 (GRCm39)	missense	probably benign
R8238:Lrrtm4	UTSW	6	79,999,668 (GRCm39)	missense	probably damaging	0.97
R8324:Lrrtm4	UTSW	6	79,998,974 (GRCm39)	missense	probably damaging	1.00
R8751:Lrrtm4	UTSW	6	79,999,092 (GRCm39)	missense	probably damaging	1.00
R8859:Lrrtm4	UTSW	6	79,998,870 (GRCm39)	missense	probably damaging	1.00
R9142:Lrrtm4	UTSW	6	79,999,426 (GRCm39)	missense	probably damaging	1.00
R9633:Lrrtm4	UTSW	6	80,000,064 (GRCm39)	missense	probably damaging	1.00
R9709:Lrrtm4	UTSW	6	80,786,154 (GRCm39)	missense	probably damaging	0.96
Z1177:Lrrtm4	UTSW	6	79,999,700 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- TCGCAGACATCCCTGAGAAC -3'
(R):5'- AAAGTCAAGGTTCCGGCAGTC -3'

Sequencing Primer
(F):5'- CATCCCTGAGAACATTTCTGGAGG -3'
(R):5'- GGTTCCGGCAGTCTTGAAAAACC -3'

Posted On

2018-02-27