Mutagenetix > Incidental Mutation

Incidental Mutation 'R9709:Lrrtm4'

729966

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm4

Ensembl Gene

ENSMUSG00000052581

Gene Name

leucine rich repeat transmembrane neuronal 4

Synonyms

7530419J18Rik

MMRRC Submission

Accession Numbers

Essential gene?

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

Stock #

R9709 (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 80786154 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 587 (E587G)

Ref Sequence

ENSEMBL: ENSMUSP00000117263 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000126399] [ENSMUST00000133918] [ENSMUST00000147663]

AlphaFold

Q80XG9

Predicted Effect

probably damaging
Transcript: ENSMUST00000126399
AA Change: E586G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000121124
Gene: ENSMUSG00000052581
AA Change: E586G

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: ENSMUST00000133918
AA Change: E586G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000115016
Gene: ENSMUSG00000052581
AA Change: E586G

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: ENSMUST00000147663
AA Change: E587G

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000117263
Gene: ENSMUSG00000052581
AA Change: E587G

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: 99.5%
20x: 98.3%

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: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810062G17Rik	T	C	3: 36,530,356 (GRCm39)	S25P	unknown	Het
4921539E11Rik	A	G	4: 103,092,678 (GRCm39)	I268T	unknown	Het
4930507D05Rik	T	A	10: 62,285,581 (GRCm39)	C102S	unknown	Het
Abca14	T	A	7: 119,888,739 (GRCm39)	Y1228*	probably null	Het
Abca17	T	C	17: 24,517,934 (GRCm39)	I792V	probably benign	Het
Abca6	C	A	11: 110,102,589 (GRCm39)	L878F	probably benign	Het
Adk	C	A	14: 21,126,386 (GRCm39)	T4N	probably benign	Het
Ankrd40cl	G	A	11: 94,175,560 (GRCm39)	S65N	probably benign	Het
Atg2b	A	T	12: 105,611,140 (GRCm39)	F1264I	probably damaging	Het
Atl3	T	G	19: 7,507,921 (GRCm39)	S358A	probably benign	Het
Atp8a2	T	A	14: 60,271,187 (GRCm39)	Y248F	probably damaging	Het
Bcas3	T	C	11: 85,474,749 (GRCm39)	V785A	probably damaging	Het
Cckar	C	T	5: 53,860,201 (GRCm39)		probably null	Het
Cdc42se2	A	G	11: 54,614,417 (GRCm39)	F47L	probably benign	Het
Cfap58	T	C	19: 47,963,992 (GRCm39)	L540P	probably damaging	Het
Copg1	A	G	6: 87,868,957 (GRCm39)	E117G	probably benign	Het
Cstpp1	T	C	2: 91,112,099 (GRCm39)	Q250R	probably benign	Het
Cul2	C	T	18: 3,431,560 (GRCm39)	T655M	probably damaging	Het
Ddi2	T	C	4: 141,412,429 (GRCm39)	Q161R	probably benign	Het
Dffb	T	C	4: 154,059,121 (GRCm39)	Y52C	probably damaging	Het
Dll1	T	C	17: 15,591,198 (GRCm39)	Q249R	probably benign	Het
Dnmt3a	T	A	12: 3,957,701 (GRCm39)	I894N	probably damaging	Het
Fshr	G	A	17: 89,293,265 (GRCm39)	T471I	probably damaging	Het
Gabpb1	C	T	2: 126,500,488 (GRCm39)	V4I	probably benign	Het
Gbp9	T	C	5: 105,231,542 (GRCm39)	Q348R	probably damaging	Het
Gm21149	G	A	5: 15,677,110 (GRCm39)	S248F	unknown	Het
Gpr152	C	A	19: 4,192,640 (GRCm39)	H60Q	probably benign	Het
Hdac9	A	G	12: 34,362,602 (GRCm39)	S612P	probably benign	Het
Hhipl2	A	G	1: 183,199,747 (GRCm39)	D102G	possibly damaging	Het
Hspa9	A	G	18: 35,073,294 (GRCm39)	V530A	possibly damaging	Het
Igfbp7	T	C	5: 77,549,384 (GRCm39)	N173S	unknown	Het
Ighv1-75	A	G	12: 115,797,791 (GRCm39)	S44P	possibly damaging	Het
Iqgap3	C	A	3: 88,016,176 (GRCm39)	F986L	probably damaging	Het
Itgax	G	T	7: 127,735,500 (GRCm39)	G523W	probably damaging	Het
Itih3	A	G	14: 30,637,587 (GRCm39)		probably null	Het
Kcnb2	T	C	1: 15,780,523 (GRCm39)	I465T	probably benign	Het
Kmt2b	A	G	7: 30,279,228 (GRCm39)	V1478A	probably damaging	Het
Ky	A	T	9: 102,419,411 (GRCm39)	I473F	probably damaging	Het
Lbr	A	G	1: 181,666,034 (GRCm39)	V25A	probably damaging	Het
Ldlr	A	G	9: 21,657,135 (GRCm39)	T751A	probably benign	Het
Lvrn	A	C	18: 47,006,847 (GRCm39)		probably null	Het
Mast2	A	T	4: 116,173,044 (GRCm39)	C594S	probably damaging	Het
Mast4	A	G	13: 102,910,711 (GRCm39)	V644A	probably damaging	Het
Mcm5	T	C	8: 75,842,604 (GRCm39)	Y293H	probably damaging	Het
Mthfd2	A	T	6: 83,283,665 (GRCm39)	V339E	possibly damaging	Het
Muc4	A	T	16: 32,590,644 (GRCm39)	I881F		Het
Myo7a	A	G	7: 97,743,536 (GRCm39)	S372P	possibly damaging	Het
Nbea	T	A	3: 55,693,879 (GRCm39)	K2180*	probably null	Het
Neb	T	C	2: 52,101,507 (GRCm39)	D4621G	probably damaging	Het
Nefh	C	T	11: 4,890,042 (GRCm39)	S859N	probably benign	Het
Nek2	T	A	1: 191,563,289 (GRCm39)	H384Q	possibly damaging	Het
Nfkb2	A	G	19: 46,298,782 (GRCm39)	E645G	probably benign	Het
Nin	G	T	12: 70,149,468 (GRCm39)	P47Q		Het
Nit1	C	A	1: 171,171,307 (GRCm39)	K178N	probably benign	Het
Nrap	C	A	19: 56,317,452 (GRCm39)	K1433N	probably damaging	Het
Nrap	T	C	19: 56,317,453 (GRCm39)	K1433R	probably benign	Het
Nup85	A	G	11: 115,457,463 (GRCm39)	Y55C	possibly damaging	Het
Or2a14	G	T	6: 43,130,469 (GRCm39)	V77F	possibly damaging	Het
Pde1b	A	G	15: 103,411,985 (GRCm39)	K29E	probably benign	Het
Pheta2	G	T	15: 82,227,537 (GRCm39)	D19Y	probably damaging	Het
Pheta2	C	G	15: 82,227,535 (GRCm39)	A18G	probably damaging	Het
Pik3cg	A	T	12: 32,226,687 (GRCm39)	Y1067N	probably benign	Het
Pkd1l1	C	T	11: 8,799,016 (GRCm39)	G2249S	probably damaging	Het
Plppr4	T	A	3: 117,121,976 (GRCm39)	T201S	possibly damaging	Het
Polr1e	A	G	4: 45,018,678 (GRCm39)	T3A	probably benign	Het
Polr1has	A	T	17: 37,275,249 (GRCm39)	R7S	probably benign	Het
Pou6f2	G	T	13: 18,414,389 (GRCm39)	Q129K	unknown	Het
Ppil4	T	A	10: 7,675,341 (GRCm39)	D163E	probably benign	Het
Pradc1	A	G	6: 85,424,952 (GRCm39)	F82L	probably benign	Het
Psd3	T	C	8: 68,194,414 (GRCm39)	K784R	probably null	Het
Ptgs1	C	A	2: 36,141,204 (GRCm39)	S550R	probably damaging	Het
Pxylp1	A	G	9: 96,711,030 (GRCm39)	L153P	probably damaging	Het
Rgs10	A	C	7: 127,975,729 (GRCm39)	F146C	probably damaging	Het
Rimbp2	G	A	5: 128,874,875 (GRCm39)	P239S	probably damaging	Het
Rp1	A	G	1: 4,112,255 (GRCm39)	Y1199H	unknown	Het
Rrp12	A	T	19: 41,857,231 (GRCm39)	M1181K	probably benign	Het
Rundc3b	T	C	5: 8,570,982 (GRCm39)	N279S	probably benign	Het
Sbf2	G	T	7: 110,027,514 (GRCm39)	P494Q	probably damaging	Het
Scnn1b	A	G	7: 121,509,693 (GRCm39)	T281A	probably benign	Het
Scube2	A	T	7: 109,430,971 (GRCm39)	N409K	probably damaging	Het
Serpina3m	A	C	12: 104,359,008 (GRCm39)	D340A	probably damaging	Het
Sez6	G	A	11: 77,865,121 (GRCm39)	E623K	possibly damaging	Het
Sgpp2	T	C	1: 78,367,200 (GRCm39)	I111T	probably benign	Het
Shprh	C	T	10: 11,038,574 (GRCm39)	T443I	possibly damaging	Het
Sis	T	A	3: 72,799,074 (GRCm39)	Y1726F	possibly damaging	Het
Slc17a9	T	C	2: 180,374,321 (GRCm39)	L129P	probably damaging	Het
Slc1a5	T	A	7: 16,527,729 (GRCm39)	F342I	probably benign	Het
Slc4a4	T	A	5: 89,188,205 (GRCm39)		probably null	Het
Slco3a1	T	C	7: 73,952,957 (GRCm39)	E534G	possibly damaging	Het
Smok2b	A	T	17: 13,454,052 (GRCm39)	I71F	possibly damaging	Het
Tmbim7	A	T	5: 3,711,809 (GRCm39)	H18L	probably damaging	Het
Tmem151a	A	T	19: 5,131,876 (GRCm39)	Y443*	probably null	Het
Tnks1bp1	T	G	2: 84,902,125 (GRCm39)	S1674A	probably benign	Het
Trappc11	T	A	8: 47,946,348 (GRCm39)	I1095F	probably damaging	Het
Trim11	A	G	11: 58,872,864 (GRCm39)	R183G	possibly damaging	Het
Trim29	A	G	9: 43,231,797 (GRCm39)	D348G	probably benign	Het
Ttc28	A	T	5: 111,433,637 (GRCm39)	S2224C	probably damaging	Het
Vps13d	C	T	4: 144,875,915 (GRCm39)	V1537M		Het
Zfp1005	T	A	2: 150,110,305 (GRCm39)	C332S	possibly damaging	Het
Zfp184	A	G	13: 22,143,665 (GRCm39)	D457G	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
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
Z1177:Lrrtm4	UTSW	6	79,999,700 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AGCTATGACCAACCAGTGATTG -3'
(R):5'- GCAAAGGAAGTTCTGGGTCC -3'

Sequencing Primer
(F):5'- CCAGTGATTGGGTACTGCCAG -3'
(R):5'- AGGTTTATCAGCTGCCCAAC -3'

Posted On

2022-10-06