Mutagenetix > Incidental Mutation

Incidental Mutation 'R8058:Lrrtm4'

619534

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm4

Ensembl Gene

ENSMUSG00000052581

Gene Name

leucine rich repeat transmembrane neuronal 4

Synonyms

7530419J18Rik

MMRRC Submission

067495-MU

Accession Numbers

Essential gene?

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

Stock #

R8058 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

79995860-80787124 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 79999528 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Isoleucine at position 313 (M313I)

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: M312I

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

SMART Domains

Protein: ENSMUSP00000074232
Gene: ENSMUSG00000052581
AA Change: M312I

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: M312I

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

SMART Domains

Protein: ENSMUSP00000117445
Gene: ENSMUSG00000052581
AA Change: M312I

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: M312I

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

SMART Domains

Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: M312I

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 benign
Transcript: ENSMUST00000133918
AA Change: M312I

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

SMART Domains

Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: M312I

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: M313I

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

SMART Domains

Protein: ENSMUSP00000121621
Gene: ENSMUSG00000052581
AA Change: M313I

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: M313I

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

SMART Domains

Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: M313I

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: 98.8%

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca1	C	T	4: 53,081,954 (GRCm39)	D769N	possibly damaging	Het
Abcb6	A	G	1: 75,156,653 (GRCm39)	L37P	possibly damaging	Het
Abcg1	G	T	17: 31,324,504 (GRCm39)	A250S	probably benign	Het
Acsf3	C	T	8: 123,540,373 (GRCm39)	H524Y	possibly damaging	Het
Agbl4	A	G	4: 110,518,039 (GRCm39)	K110R	unknown	Het
Arfgap2	G	A	2: 91,096,644 (GRCm39)		probably null	Het
B4galt4	T	C	16: 38,586,383 (GRCm39)		probably null	Het
Bex6	G	T	16: 32,005,224 (GRCm39)	D11Y	probably damaging	Het
Bhlhe40	TG	TGG	6: 108,641,818 (GRCm39)	254	probably null	Het
C8b	A	T	4: 104,647,811 (GRCm39)	D334V	probably damaging	Het
Capn11	T	C	17: 45,954,681 (GRCm39)	Q152R	probably null	Het
Ccdc171	C	A	4: 83,499,003 (GRCm39)	Q234K	probably damaging	Het
Cemip2	C	A	19: 21,829,695 (GRCm39)	A1268E	probably benign	Het
Clec2h	A	G	6: 128,650,966 (GRCm39)	D82G	probably benign	Het
Creld2	A	G	15: 88,710,632 (GRCm39)	D349G	probably damaging	Het
D430041D05Rik	A	G	2: 103,979,128 (GRCm39)	*1415Q	probably null	Het
Dnmt3a	T	C	12: 3,952,768 (GRCm39)	V755A	possibly damaging	Het
Doc2a	G	T	7: 126,450,164 (GRCm39)	V201L	probably benign	Het
Fan1	T	A	7: 64,022,234 (GRCm39)	N340Y	probably damaging	Het
Fbn1	G	T	2: 125,193,889 (GRCm39)	D1359E	possibly damaging	Het
Fcnb	T	C	2: 27,969,707 (GRCm39)	Y120C	probably damaging	Het
Fras1	T	A	5: 96,842,778 (GRCm39)	D1665E	probably benign	Het
Fry	A	T	5: 150,419,232 (GRCm39)	D524V		Het
Garem1	A	G	18: 21,281,621 (GRCm39)	L245P	probably damaging	Het
Gdf6	A	G	4: 9,859,712 (GRCm39)	S265G	probably benign	Het
Gm5591	T	C	7: 38,218,363 (GRCm39)	I837V	probably benign	Het
Gpr61	T	C	3: 108,058,211 (GRCm39)	Y150C	probably damaging	Het
Grin2b	A	T	6: 135,710,225 (GRCm39)	L1107Q	probably damaging	Het
Helb	A	G	10: 119,941,483 (GRCm39)	S402P	probably benign	Het
Htt	A	G	5: 34,977,444 (GRCm39)	T777A	probably benign	Het
Iffo2	A	G	4: 139,341,164 (GRCm39)	D383G	probably benign	Het
Ikzf3	G	T	11: 98,407,753 (GRCm39)	Y29*	probably null	Het
Ints2	A	T	11: 86,146,179 (GRCm39)	M143K	probably benign	Het
Jmjd1c	T	C	10: 67,090,274 (GRCm39)	V2292A	not run	Het
Katnip	A	G	7: 125,442,188 (GRCm39)	E725G	probably benign	Het
Lamb1	C	A	12: 31,353,046 (GRCm39)	Q916K	probably benign	Het
Lum	A	G	10: 97,404,425 (GRCm39)	I107V	probably benign	Het
Ly6h	T	C	15: 75,437,061 (GRCm39)	E126G	probably benign	Het
Map3k5	G	A	10: 20,007,860 (GRCm39)	V1230M	probably damaging	Het
Mcoln1	T	C	8: 3,558,378 (GRCm39)	F211L	probably benign	Het
Mink1	G	A	11: 70,494,594 (GRCm39)	W258*	probably null	Het
Muc16	G	T	9: 18,571,298 (GRCm39)	S407*	probably null	Het
Ngef	G	A	1: 87,473,744 (GRCm39)	Q13*	probably null	Het
Nxpe5	T	A	5: 138,237,573 (GRCm39)	Y44*	probably null	Het
Or13d1	T	A	4: 52,971,106 (GRCm39)	L162M	probably benign	Het
Or4a77	A	G	2: 89,487,671 (GRCm39)	V38A	probably benign	Het
Or5t9	A	G	2: 86,660,052 (GRCm39)	R319G	probably benign	Het
Or7e178	T	A	9: 20,225,476 (GRCm39)	I247F	probably damaging	Het
Or8g24	A	T	9: 38,989,862 (GRCm39)	Y60N	probably damaging	Het
Or8h8	C	A	2: 86,753,151 (GRCm39)	A242S	probably benign	Het
Orc3	C	A	4: 34,595,223 (GRCm39)	E249*	probably null	Het
Otogl	A	T	10: 107,598,287 (GRCm39)	C2288S	probably damaging	Het
Pde1b	A	G	15: 103,433,238 (GRCm39)	E249G	probably damaging	Het
Phf2	T	C	13: 48,976,558 (GRCm39)	E219G	unknown	Het
Rbm19	T	A	5: 120,278,440 (GRCm39)		probably null	Het
Rcc2	G	A	4: 140,429,586 (GRCm39)	C40Y	probably benign	Het
Sbk2	A	G	7: 4,960,289 (GRCm39)	Y294H	possibly damaging	Het
Selenoo	T	C	15: 88,976,942 (GRCm39)	I198T	possibly damaging	Het
Sema3f	T	C	9: 107,559,800 (GRCm39)	E729G	probably benign	Het
Serpinb1b	A	T	13: 33,269,293 (GRCm39)	T9S	probably benign	Het
Sfxn4	T	C	19: 60,832,690 (GRCm39)	T235A	probably damaging	Het
Shc4	A	T	2: 125,491,154 (GRCm39)	Y461*	probably null	Het
Slc22a15	T	C	3: 101,771,926 (GRCm39)	D391G	probably benign	Het
Slc22a23	G	T	13: 34,489,167 (GRCm39)	Y239*	probably null	Het
Slc24a2	G	A	4: 86,909,750 (GRCm39)	A656V	probably damaging	Het
Slc2a5	A	T	4: 150,227,590 (GRCm39)	I470F	probably damaging	Het
Sptbn4	T	C	7: 27,063,694 (GRCm39)	E2249G	possibly damaging	Het
Tas2r139	A	T	6: 42,118,753 (GRCm39)	Q295L	probably benign	Het
Tdrd7	C	A	4: 46,034,309 (GRCm39)	S1051R	probably benign	Het
Tnfrsf18	G	A	4: 156,112,802 (GRCm39)	A163T	probably benign	Het
Ube3b	T	C	5: 114,544,846 (GRCm39)	V596A	possibly damaging	Het
Vmn2r10	T	A	5: 109,149,955 (GRCm39)	N363I	probably benign	Het
Vmn2r15	T	A	5: 109,440,956 (GRCm39)	I301F	probably damaging	Het
Yod1	C	T	1: 130,646,806 (GRCm39)	Q228*	probably null	Het
Zfp433	A	T	10: 81,556,124 (GRCm39)	K209*	probably null	Het
Zfp865	G	A	7: 5,033,445 (GRCm39)	V477I	probably benign	Het
Zfp937	T	A	2: 150,081,421 (GRCm39)	Y484N	probably benign	Het
Zfp951	T	G	5: 104,962,312 (GRCm39)	H418P	probably 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
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
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'- GTCAGTCAAGGCCTAACATGG -3'
(R):5'- TTTGAGGCGCCAGATGTGATC -3'

Sequencing Primer
(F):5'- AACATGGACCTGGAGTTCCTTGC -3'
(R):5'- CGCCAGATGTGATCGTTCTG -3'

Posted On

2020-01-23