Mutagenetix > Incidental Mutation

Incidental Mutation 'R8324:Lrrtm4'

643980

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm4

Ensembl Gene

ENSMUSG00000052581

Gene Name

leucine rich repeat transmembrane neuronal 4

Synonyms

7530419J18Rik

MMRRC Submission

067725-MU

Accession Numbers

Essential gene?

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

Stock #

R8324 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

79995860-80787124 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 79998974 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 129 (T129A)

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 damaging
Transcript: ENSMUST00000074662
AA Change: T128A

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

SMART Domains

Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: T128A

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: T128A

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

SMART Domains

Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: T128A

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: T128A

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

SMART Domains

Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: T128A

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

probably damaging
Transcript: ENSMUST00000133918
AA Change: T128A

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

SMART Domains

Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: T128A

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: T129A

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

SMART Domains

Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: T129A

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 damaging
Transcript: ENSMUST00000147663
AA Change: T129A

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

SMART Domains

Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: T129A

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	T	C	11: 9,240,395 (GRCm39)	S753P	probably damaging	Het
Acan	A	G	7: 78,740,804 (GRCm39)	E390G	probably damaging	Het
Antxr2	T	C	5: 98,086,368 (GRCm39)	N413S	probably damaging	Het
Bace2	C	T	16: 97,158,108 (GRCm39)	A36V	possibly damaging	Het
Caprin1	G	A	2: 103,613,526 (GRCm39)	R79*	probably null	Het
Cdan1	A	G	2: 120,557,806 (GRCm39)	V507A	probably benign	Het
Cdkl3	T	A	11: 51,913,706 (GRCm39)		probably null	Het
Chst5	A	T	8: 112,617,140 (GRCm39)	L160Q	probably benign	Het
Col11a1	C	G	3: 113,958,059 (GRCm39)	P1111R	probably damaging	Het
Col6a6	T	A	9: 105,632,853 (GRCm39)	E1470D	probably benign	Het
Cpped1	T	A	16: 11,623,340 (GRCm39)	T274S	probably benign	Het
Ctnnbl1	G	A	2: 157,621,735 (GRCm39)	E75K	probably damaging	Het
Cyp4f40	T	C	17: 32,878,502 (GRCm39)	S15P	probably benign	Het
Ddx46	T	C	13: 55,811,727 (GRCm39)	S643P	probably damaging	Het
Defb34	A	G	8: 19,173,814 (GRCm39)	Q16R	probably null	Het
Dhrs2	T	A	14: 55,476,221 (GRCm39)	V147E	probably damaging	Het
Dnah5	G	T	15: 28,347,011 (GRCm39)	R2498L	probably damaging	Het
Dpp10	T	A	1: 123,781,901 (GRCm39)	I93F	probably benign	Het
Eef1e1	T	A	13: 38,839,045 (GRCm39)	D104V	probably damaging	Het
Egfr	A	G	11: 16,808,971 (GRCm39)	Y55C	probably damaging	Het
Egfr	A	C	11: 16,858,885 (GRCm39)	I955L	probably damaging	Het
Ehbp1l1	C	A	19: 5,770,026 (GRCm39)	V426F	possibly damaging	Het
Elp1	C	T	4: 56,772,491 (GRCm39)	E877K	probably damaging	Het
Fam234a	C	T	17: 26,437,672 (GRCm39)	V108I	probably benign	Het
Fzd8	T	A	18: 9,214,688 (GRCm39)	M590K	probably damaging	Het
Gm13287	T	C	4: 88,721,875 (GRCm39)	S129P	probably damaging	Het
Heatr5b	A	G	17: 79,062,793 (GRCm39)	S1919P	possibly damaging	Het
Hspg2	C	G	4: 137,246,290 (GRCm39)	P1023A	possibly damaging	Het
Itpr2	T	C	6: 146,229,896 (GRCm39)	E1233G	probably damaging	Het
Kcnmb4	A	G	10: 116,254,219 (GRCm39)	L186P	probably damaging	Het
Krt72	T	A	15: 101,690,580 (GRCm39)	Y224F	probably damaging	Het
Loxhd1	T	C	18: 77,427,275 (GRCm39)		probably null	Het
Lrguk	A	G	6: 34,079,506 (GRCm39)	T914A	probably benign	Het
Mmp13	A	T	9: 7,276,636 (GRCm39)	I244F	possibly damaging	Het
Mob1a	T	A	6: 83,306,956 (GRCm39)	L41Q	probably damaging	Het
Mtcl1	T	C	17: 66,743,212 (GRCm39)	R426G	probably damaging	Het
Mybbp1a	T	C	11: 72,336,114 (GRCm39)		probably null	Het
Myh9	A	G	15: 77,673,117 (GRCm39)		probably null	Het
Myo1d	T	A	11: 80,448,347 (GRCm39)	D926V	probably damaging	Het
Ncapg	T	G	5: 45,853,010 (GRCm39)	H825Q	probably damaging	Het
Olfml1	T	C	7: 107,189,570 (GRCm39)	S212P	probably benign	Het
Or52p1	G	A	7: 104,267,321 (GRCm39)	R145H	probably benign	Het
Pak2	T	C	16: 31,871,029 (GRCm39)	N51S	probably benign	Het
Papln	T	C	12: 83,833,393 (GRCm39)	Y1132H	probably damaging	Het
Pax3	T	A	1: 78,170,426 (GRCm39)	R134S	probably damaging	Het
Pdzrn4	A	G	15: 92,668,818 (GRCm39)	E990G	probably damaging	Het
Peak1	A	T	9: 56,114,760 (GRCm39)	W1394R	probably damaging	Het
Pkn2	T	C	3: 142,534,771 (GRCm39)	N285D	probably benign	Het
Pramel13	A	C	4: 144,122,427 (GRCm39)	L39R	probably damaging	Het
Prrc2a	A	G	17: 35,375,960 (GRCm39)	S897P	possibly damaging	Het
Rad51	A	G	2: 118,954,312 (GRCm39)	T131A	possibly damaging	Het
Rc3h2	T	A	2: 37,290,738 (GRCm39)	T255S	possibly damaging	Het
Repin1	G	T	6: 48,574,279 (GRCm39)	E403*	probably null	Het
Rictor	T	A	15: 6,775,043 (GRCm39)	V125E	probably damaging	Het
Rps6ka5	C	T	12: 100,524,746 (GRCm39)	D664N	possibly damaging	Het
Rreb1	T	A	13: 38,131,597 (GRCm39)	W1584R	probably damaging	Het
Rxra	T	C	2: 27,631,195 (GRCm39)	I142T	probably damaging	Het
Sall2	T	C	14: 52,550,343 (GRCm39)	T951A	probably benign	Het
Slc15a2	T	G	16: 36,579,669 (GRCm39)	N359T	probably damaging	Het
Slc23a1	C	T	18: 35,755,588 (GRCm39)	G436E	probably damaging	Het
Slc6a13	T	C	6: 121,314,373 (GRCm39)	*603Q	probably null	Het
Sptb	T	C	12: 76,665,936 (GRCm39)	D894G	possibly damaging	Het
Srgn	A	G	10: 62,343,444 (GRCm39)	L17P	probably damaging	Het
Tmprss9	T	C	10: 80,733,205 (GRCm39)		probably null	Het
Trav9n-4	T	C	14: 53,532,403 (GRCm39)	F86L	probably benign	Het
Trp63	A	G	16: 25,695,484 (GRCm39)	Y482C	unknown	Het
Ttc9b	G	T	7: 27,353,394 (GRCm39)	A15S	probably damaging	Het
Urb1	A	T	16: 90,588,078 (GRCm39)	I410N	probably damaging	Het
Vmn2r82	A	T	10: 79,214,727 (GRCm39)	K237*	probably null	Het
Wwox	G	A	8: 115,215,745 (GRCm39)		probably null	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
R6195:Lrrtm4	UTSW	6	79,998,939 (GRCm39)	missense	probably damaging	1.00
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
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'- AGACATCCCTGAGAACATTTCTG -3'
(R):5'- CAGAAAGTCAAGGTTCCGGC -3'

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

Posted On

2020-09-02