Mutagenetix > Incidental Mutation

Incidental Mutation 'R9299:Lrtm1'

704812

Institutional Source

Beutler Lab

Gene Symbol

Lrtm1

Ensembl Gene

ENSMUSG00000045776

Gene Name

leucine-rich repeats and transmembrane domains 1

Synonyms

A930016D02Rik

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.088) question?

Stock #

R9299 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

28740165-28755599 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 28743714 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 61 (P61S)

Ref Sequence

ENSEMBL: ENSMUSP00000061828 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000022567] [ENSMUST00000055662] [ENSMUST00000224708] [ENSMUST00000224760]

AlphaFold

Q8BXQ3

Predicted Effect

probably benign
Transcript: ENSMUST00000022567

SMART Domains

Protein: ENSMUSP00000022567
Gene: ENSMUSG00000021991

Domain	Start	End	E-Value	Type
low complexity region	14	27	N/A	INTRINSIC
Blast:WNT1	28	103	2e-33	BLAST
Pfam:VWA_N	113	229	6.8e-40	PFAM
VWA	254	439	4.13e-24	SMART
Pfam:Cache_1	452	548	3e-32	PFAM
low complexity region	1070	1088	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000055662
AA Change: P61S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000061828
Gene: ENSMUSG00000045776
AA Change: P61S

Domain	Start	End	E-Value	Type
LRRNT	32	66	4.41e-6	SMART
LRR	65	84	2.33e2	SMART
LRR	85	108	2.67e-1	SMART
LRR	109	131	1.15e1	SMART
LRR_TYP	133	156	3.89e-3	SMART
LRRCT	192	245	8.63e-6	SMART
transmembrane domain	297	319	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000224708
AA Change: P88S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

Predicted Effect

probably damaging
Transcript: ENSMUST00000224760
AA Change: P61S

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

Meta Mutation Damage Score

0.6179

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (60/60)

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017B05Rik	G	T	9: 57,163,792 (GRCm39)	R861S	possibly damaging	Het
Abca12	T	A	1: 71,359,042 (GRCm39)	N588I	possibly damaging	Het
Adamts9	A	G	6: 92,773,976 (GRCm39)	Y1727H	probably benign	Het
Ahnak	G	A	19: 8,989,824 (GRCm39)		probably benign	Het
Alad	C	T	4: 62,429,760 (GRCm39)		probably null	Het
Anapc15-ps	C	A	10: 95,509,077 (GRCm39)	D68Y	probably damaging	Het
Arhgap45	T	C	10: 79,862,565 (GRCm39)	S645P	possibly damaging	Het
Atp9a	A	T	2: 168,554,666 (GRCm39)	M1K	probably null	Het
B020004C17Rik	A	T	14: 57,254,230 (GRCm39)	I118F	probably damaging	Het
Capn13	T	A	17: 73,633,467 (GRCm39)		probably null	Het
Ccdc7a	T	C	8: 129,616,319 (GRCm39)	Q928R	probably benign	Het
Cdc42bpa	C	A	1: 179,972,073 (GRCm39)	L1292I	probably damaging	Het
Clec2e	A	C	6: 129,072,092 (GRCm39)	F96V	probably benign	Het
Cmklr1	G	C	5: 113,752,043 (GRCm39)	H319Q	probably benign	Het
Cnot1	T	C	8: 96,468,448 (GRCm39)	I1460M	probably damaging	Het
Cyc1	T	C	15: 76,228,506 (GRCm39)	V45A	probably benign	Het
Cyp4a10	A	G	4: 115,376,947 (GRCm39)	M104V	probably benign	Het
Cyth1	C	T	11: 118,059,837 (GRCm39)		probably benign	Het
Dnhd1	T	A	7: 105,369,806 (GRCm39)	N4410K	probably benign	Het
Dok4	T	A	8: 95,593,469 (GRCm39)	T106S	probably benign	Het
Dpcd	C	A	19: 45,566,009 (GRCm39)	Q203K	probably damaging	Het
Dph1	T	A	11: 75,070,622 (GRCm39)	Q339L	possibly damaging	Het
Dpy19l3	G	T	7: 35,424,752 (GRCm39)	S187*	probably null	Het
Eva1a	G	T	6: 82,069,047 (GRCm39)	A125S	probably damaging	Het
Fam24b	T	A	7: 130,927,949 (GRCm39)	Y80F	probably benign	Het
Frem2	T	C	3: 53,563,980 (GRCm39)	T176A	probably benign	Het
Gal3st3	A	T	19: 5,356,868 (GRCm39)	N81I	probably damaging	Het
Gm12888	G	A	4: 121,182,044 (GRCm39)	S16F	unknown	Het
Hsf5	T	A	11: 87,526,770 (GRCm39)	C481S	probably benign	Het
Ifi211	T	A	1: 173,735,288 (GRCm39)	Q47L	probably damaging	Het
Il17re	A	T	6: 113,440,971 (GRCm39)	M202L	probably benign	Het
Krtap5-3	T	A	7: 141,756,267 (GRCm39)	H175Q	unknown	Het
Ksr2	G	A	5: 117,885,399 (GRCm39)		probably null	Het
Ltk	A	T	2: 119,584,721 (GRCm39)	S487R	possibly damaging	Het
Mis18bp1	A	T	12: 65,185,538 (GRCm39)	D876E	possibly damaging	Het
Nalf1	T	C	8: 9,820,156 (GRCm39)	Y288C	probably damaging	Het
Or8b39	A	G	9: 37,996,785 (GRCm39)	T218A	probably benign	Het
Paqr7	A	G	4: 134,234,311 (GRCm39)	N56S	probably benign	Het
Pcdhb22	G	T	18: 37,651,885 (GRCm39)	E118*	probably null	Het
Pcdhb4	G	A	18: 37,442,264 (GRCm39)	A525T	probably benign	Het
Pik3cb	A	G	9: 98,943,844 (GRCm39)	F653S	probably damaging	Het
Pla2g4e	T	A	2: 120,002,204 (GRCm39)	D617V	probably damaging	Het
Plekha1	T	A	7: 130,511,348 (GRCm39)	C311S	possibly damaging	Het
Poteg	A	G	8: 27,940,287 (GRCm39)	Y156C	probably benign	Het
Rev3l	T	C	10: 39,723,999 (GRCm39)	S2644P	probably damaging	Het
Rnf40	T	A	7: 127,188,172 (GRCm39)	S2T	probably benign	Het
Rrp8	T	C	7: 105,383,384 (GRCm39)	D294G	probably damaging	Het
Slc6a21	T	C	7: 44,937,130 (GRCm39)	V252A		Het
Slx9	C	A	10: 77,351,535 (GRCm39)	A14S	possibly damaging	Het
Socs1	T	C	16: 10,602,578 (GRCm39)	D53G	possibly damaging	Het
St6galnac6	G	T	2: 32,502,345 (GRCm39)	R78L	probably benign	Het
Tbce	T	C	13: 14,194,398 (GRCm39)	K87R	probably benign	Het
Tep1	T	C	14: 51,081,988 (GRCm39)		probably benign	Het
Thada	T	C	17: 84,749,205 (GRCm39)	M589V	probably benign	Het
Thsd7a	A	G	6: 12,504,131 (GRCm39)	F341S		Het
Tmem82	A	T	4: 141,343,861 (GRCm39)	C136*	probably null	Het
Tmprss11a	A	T	5: 86,570,361 (GRCm39)	C199*	probably null	Het
Zbtb48	T	C	4: 152,105,147 (GRCm39)	N505S	possibly damaging	Het
Zfp385b	A	T	2: 77,246,115 (GRCm39)	V304E	probably damaging	Het

Other mutations in Lrtm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02191:Lrtm1	APN	14	28,743,906 (GRCm39)	missense	probably benign	0.00
R0102:Lrtm1	UTSW	14	28,744,184 (GRCm39)	splice site	probably benign
R0102:Lrtm1	UTSW	14	28,744,184 (GRCm39)	splice site	probably benign
R0602:Lrtm1	UTSW	14	28,744,179 (GRCm39)	splice site	probably benign
R5214:Lrtm1	UTSW	14	28,743,651 (GRCm39)	missense	possibly damaging	0.58
R5253:Lrtm1	UTSW	14	28,743,801 (GRCm39)	missense	probably benign	0.13
R5787:Lrtm1	UTSW	14	28,743,947 (GRCm39)	missense	possibly damaging	0.89
R5937:Lrtm1	UTSW	14	28,743,787 (GRCm39)	missense	possibly damaging	0.90
R6238:Lrtm1	UTSW	14	28,749,628 (GRCm39)	missense	probably benign	0.02
R6850:Lrtm1	UTSW	14	28,749,407 (GRCm39)	missense	probably benign	0.00
R7304:Lrtm1	UTSW	14	28,744,075 (GRCm39)	missense	probably damaging	0.97
R7363:Lrtm1	UTSW	14	28,743,850 (GRCm39)	missense	probably damaging	1.00
R7385:Lrtm1	UTSW	14	28,749,673 (GRCm39)	missense	probably benign	0.00
R8181:Lrtm1	UTSW	14	28,743,894 (GRCm39)	missense	probably damaging	1.00
RF036:Lrtm1	UTSW	14	28,743,400 (GRCm39)	frame shift	probably null
RF063:Lrtm1	UTSW	14	28,743,400 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- GAATTCCTTGGCTGATGGCG -3'
(R):5'- TCTATGGAAAGCAGGGAATTTTGGG -3'

Sequencing Primer
(F):5'- GCTGATGGCGACCACATTTCATAC -3'
(R):5'- GGTTACATTTAAAACCCGCAAATGTG -3'

Posted On

2022-03-25