Mutagenetix > Incidental Mutation

Incidental Mutation 'R5304:Lrrtm4'

404424

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm4

Ensembl Gene

ENSMUSG00000052581

Gene Name

leucine rich repeat transmembrane neuronal 4

Synonyms

7530419J18Rik

MMRRC Submission

042887-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.109) question?

Stock #

R5304 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

79995860-80787124 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 79999683 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Leucine at position 365 (Q365L)

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 benign
Transcript: ENSMUST00000074662
AA Change: Q364L

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: Q364L

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: Q364L

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: Q364L

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: Q364L

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: Q364L

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: Q364L

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: Q364L

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: Q365L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: Q365L

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: ENSMUST00000147663
AA Change: Q365L

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: Q365L

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

Meta Mutation Damage Score

0.0726

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.5%
20x: 95.9%

Validation Efficiency

99% (87/88)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adcy1	C	T	11: 7,014,198 (GRCm39)	A200V	probably benign	Het
Adgrv1	T	C	13: 81,726,372 (GRCm39)	D551G	possibly damaging	Het
Aldh3a2	A	G	11: 61,144,538 (GRCm39)	V340A	probably damaging	Het
Amy1	C	A	3: 113,352,013 (GRCm39)	C393F	probably damaging	Het
Ankrd16	T	C	2: 11,794,545 (GRCm39)	V310A	probably benign	Het
Arhgef15	T	C	11: 68,838,063 (GRCm39)	S686G	probably null	Het
Arid4b	T	A	13: 14,361,514 (GRCm39)	N659K	probably benign	Het
Asz1	C	T	6: 18,076,619 (GRCm39)	R191Q	probably benign	Het
Atp2a3	A	G	11: 72,879,383 (GRCm39)	I947V	probably damaging	Het
AW011738	G	A	4: 156,287,969 (GRCm39)		probably benign	Het
Bfsp1	G	T	2: 143,669,211 (GRCm39)	T456K	probably benign	Het
Cdc25c	T	C	18: 34,883,864 (GRCm39)	T40A	possibly damaging	Het
Cdh20	G	A	1: 110,036,569 (GRCm39)	C583Y	probably damaging	Het
Ceacam23	A	C	7: 17,636,617 (GRCm39)	E231D	probably benign	Het
Cfap54	A	T	10: 92,656,968 (GRCm39)	L3028Q	probably damaging	Het
Chd1	A	G	17: 15,975,213 (GRCm39)	S1088G	probably benign	Het
Chd1	A	T	17: 15,990,530 (GRCm39)	H1694L	possibly damaging	Het
Cstf3	G	T	2: 104,493,735 (GRCm39)	E580*	probably null	Het
Dip2a	A	T	10: 76,130,357 (GRCm39)	M622K	possibly damaging	Het
Dlgap1	A	T	17: 71,122,202 (GRCm39)	H877L	probably damaging	Het
Egfr	G	T	11: 16,834,260 (GRCm39)	M122I	probably benign	Het
Etfbkmt	T	A	6: 149,048,704 (GRCm39)	D114E	probably damaging	Het
Eva1c	T	C	16: 90,666,551 (GRCm39)	L158P	probably damaging	Het
Exo1	G	A	1: 175,720,542 (GRCm39)	V287M	probably damaging	Het
Fam171a1	T	C	2: 3,226,654 (GRCm39)	Y471H	probably damaging	Het
Fermt1	T	A	2: 132,783,986 (GRCm39)	T8S	probably benign	Het
Fgfr2	G	T	7: 129,769,504 (GRCm39)	P630T	probably damaging	Het
Fmo5	G	A	3: 97,558,938 (GRCm39)	G466E	probably damaging	Het
Hcn4	A	G	9: 58,751,215 (GRCm39)	I280M	probably benign	Het
Ifi208	A	C	1: 173,511,174 (GRCm39)	K443T	probably benign	Het
Irs3	A	G	5: 137,643,003 (GRCm39)	F145S	probably benign	Het
Kirrel1	T	A	3: 86,996,902 (GRCm39)	H300L	probably benign	Het
Krit1	A	G	5: 3,869,326 (GRCm39)	Q340R	probably damaging	Het
Lipo5	T	C	19: 33,445,149 (GRCm39)	D140G	unknown	Het
Lrwd1	G	T	5: 136,160,004 (GRCm39)	T353K	possibly damaging	Het
Lsm14a	A	T	7: 34,053,154 (GRCm39)	S240R	possibly damaging	Het
Map3k5	A	G	10: 19,983,984 (GRCm39)	I870V	probably benign	Het
Matcap2	A	T	9: 22,335,528 (GRCm39)	T49S	probably benign	Het
Mmp17	A	T	5: 129,671,678 (GRCm39)	E76V	probably null	Het
Mphosph10	A	G	7: 64,038,732 (GRCm39)	F272L	probably damaging	Het
Mtcl2	G	A	2: 156,865,737 (GRCm39)	Q1127*	probably null	Het
Myh10	A	G	11: 68,655,071 (GRCm39)	K380R	probably damaging	Het
Myo3b	C	T	2: 70,257,232 (GRCm39)	P1282L	probably damaging	Het
Nemp2	T	C	1: 52,682,238 (GRCm39)		probably benign	Het
Ola1	T	C	2: 73,029,778 (GRCm39)	I114V	probably damaging	Het
Or4c3d	T	A	2: 89,882,257 (GRCm39)	H137L	probably benign	Het
Or8k28	T	A	2: 86,285,779 (GRCm39)	T279S	probably damaging	Het
Pabpc4	T	G	4: 123,184,100 (GRCm39)	D204E	probably benign	Het
Pigr	A	T	1: 130,777,230 (GRCm39)	M679L	probably benign	Het
Pik3c2b	A	T	1: 132,998,146 (GRCm39)	M341L	possibly damaging	Het
Plin4	T	A	17: 56,413,132 (GRCm39)	T498S	probably benign	Het
Ppp2r5e	A	G	12: 75,562,459 (GRCm39)	S15P	possibly damaging	Het
Prdm13	T	C	4: 21,678,984 (GRCm39)	Y502C	probably damaging	Het
Ptprk	T	C	10: 28,468,050 (GRCm39)		probably null	Het
Rapgef6	T	C	11: 54,548,200 (GRCm39)	S505P	probably benign	Het
Rgmb	G	T	17: 16,040,990 (GRCm39)	S199*	probably null	Het
Rgsl1	T	C	1: 153,703,238 (GRCm39)	T173A	probably damaging	Het
Rhobtb1	G	T	10: 69,105,742 (GRCm39)	K102N	probably damaging	Het
Ripor2	A	T	13: 24,858,649 (GRCm39)	D147V	probably damaging	Het
Rsad2	A	T	12: 26,500,681 (GRCm39)	V202E	probably damaging	Het
Slc1a6	A	G	10: 78,629,141 (GRCm39)	N186S	probably damaging	Het
Sorbs3	G	A	14: 70,422,345 (GRCm39)	R622*	probably null	Het
Spag9	C	A	11: 93,959,838 (GRCm39)	D342E	probably damaging	Het
Srgap3	T	C	6: 112,743,900 (GRCm39)	Y446C	probably damaging	Het
Thsd7b	C	T	1: 129,605,980 (GRCm39)	R574*	probably null	Het
Tmem74	A	T	15: 43,730,217 (GRCm39)	Y275*	probably null	Het
Topors	A	T	4: 40,262,541 (GRCm39)	S248T	possibly damaging	Het
Trpm1	A	T	7: 63,858,694 (GRCm39)	Y239F	probably benign	Het
Ttn	T	A	2: 76,548,527 (GRCm39)	Y30179F	possibly damaging	Het
Ugt2b34	A	T	5: 87,040,724 (GRCm39)	F399L	probably damaging	Het
Ush2a	A	T	1: 188,088,995 (GRCm39)	I317F	probably damaging	Het
Usp1	T	C	4: 98,822,855 (GRCm39)	V723A	probably benign	Het
Usp34	T	G	11: 23,293,616 (GRCm39)	L237V	probably damaging	Het
Vgf	A	T	5: 137,061,140 (GRCm39)	D434V	probably damaging	Het
Vmn1r179	A	G	7: 23,628,100 (GRCm39)	N97S	probably benign	Het
Vps13a	A	G	19: 16,687,751 (GRCm39)	L899P	possibly damaging	Het
Vps33b	A	T	7: 79,924,001 (GRCm39)	I41F	probably damaging	Het
Zap70	A	T	1: 36,817,299 (GRCm39)	H210L	probably damaging	Het
Zc3h8	T	C	2: 128,770,835 (GRCm39)	D300G	probably benign	Het
Zfp958	C	A	8: 4,676,196 (GRCm39)	H55N	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
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
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'- AGGAGACTGTCAATGCATGG -3'
(R):5'- CTGCGATGATTTTGTGAAACGAC -3'

Sequencing Primer
(F):5'- GAGACTGTCAATGCATGGATATCC -3'
(R):5'- TTGTGAAACGACACGTGCTC -3'

Posted On

2016-07-22