Mutagenetix > Incidental Mutation

Incidental Mutation 'R7048:Lrrtm1'

547432

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm1

Ensembl Gene

ENSMUSG00000060780

Gene Name

leucine rich repeat transmembrane neuronal 1

Synonyms

4632401D06Rik

MMRRC Submission

045146-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7048 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

77219672-77234774 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 77221152 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 203 (N203S)

Ref Sequence

ENSEMBL: ENSMUSP00000124373 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000020400] [ENSMUST00000075340] [ENSMUST00000159616] [ENSMUST00000159626] [ENSMUST00000160894] [ENSMUST00000161677] [ENSMUST00000161811] [ENSMUST00000161846]

AlphaFold

Q8K377

Predicted Effect

probably damaging
Transcript: ENSMUST00000020400
AA Change: N203S

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

SMART Domains

Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: N203S

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART
LRR	184	207	6.96e0	SMART
LRR	208	236	1.76e2	SMART
LRR	255	278	4.71e1	SMART
LRR	279	302	1.03e1	SMART
Blast:LRRCT	314	364	4e-13	BLAST
transmembrane domain	428	450	N/A	INTRINSIC
low complexity region	467	475	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000075340

SMART Domains

Protein: ENSMUSP00000074809
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	18	337	2e-104	PFAM
Pfam:Vinculin	331	866	7.7e-222	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000159616
AA Change: N203S

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

SMART Domains

Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: N203S

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART
LRR	184	207	6.96e0	SMART
LRR	208	236	1.76e2	SMART
LRR	255	278	4.71e1	SMART
LRR	279	302	1.03e1	SMART
Blast:LRRCT	314	364	4e-13	BLAST
transmembrane domain	428	450	N/A	INTRINSIC
low complexity region	467	475	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000159626

SMART Domains

Protein: ENSMUSP00000124376
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	18	337	3.4e-105	PFAM
Pfam:Vinculin	330	914	6.6e-214	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000160894

SMART Domains

Protein: ENSMUSP00000124764
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	31	352	2.1e-104	PFAM
Pfam:Vinculin	343	927	4.6e-213	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000161677
AA Change: N203S

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

SMART Domains

Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: N203S

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART
LRR	184	207	6.96e0	SMART
LRR	208	236	1.76e2	SMART
LRR	255	278	4.71e1	SMART
LRR	279	302	1.03e1	SMART
Blast:LRRCT	314	364	4e-13	BLAST
transmembrane domain	428	450	N/A	INTRINSIC
low complexity region	467	475	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000161811

SMART Domains

Protein: ENSMUSP00000124948
Gene: ENSMUSG00000060780

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
LRRNT	38	70	1.06e0	SMART
LRR	64	87	5.56e0	SMART
LRR	88	111	1.03e1	SMART
LRR_TYP	112	135	2.71e-2	SMART
LRR_TYP	136	159	1.98e-4	SMART
LRR_TYP	160	183	9.44e-2	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000161846

SMART Domains

Protein: ENSMUSP00000123714
Gene: ENSMUSG00000063063

Domain	Start	End	E-Value	Type
Pfam:Vinculin	31	350	5.3e-105	PFAM
Pfam:Vinculin	344	879	2.1e-222	PFAM

Meta Mutation Damage Score

0.1333

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

97% (66/68)

MGI Phenotype

PHENOTYPE: Mice homozygous for a null mutation are viable and fertile with grossly normal brain morphology. Mice homozygous for another knock-out allele exhibit impaired cognitive function and altered hippocampal synapse morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrl2	T	C	3: 148,552,565 (GRCm39)	D629G	probably damaging	Het
Akap11	T	A	14: 78,749,954 (GRCm39)	Q811L		Het
Ank2	T	A	3: 126,819,267 (GRCm39)	Q468L	probably benign	Het
Ano3	A	T	2: 110,513,116 (GRCm39)	Y626*	probably null	Het
Ap1m1	A	G	8: 73,003,642 (GRCm39)	N114S	probably damaging	Het
Asb3	T	A	11: 31,051,121 (GRCm39)	I525N	probably damaging	Het
Atg4a-ps	A	G	3: 103,552,672 (GRCm39)	I223T	probably damaging	Het
B3gnt7	T	C	1: 86,233,308 (GRCm39)	Y68H	probably benign	Het
Bbs5	T	C	2: 69,484,705 (GRCm39)	I125T	probably benign	Het
Cd180	A	G	13: 102,841,431 (GRCm39)	N159S	probably damaging	Het
Cd37	T	C	7: 44,887,888 (GRCm39)		probably benign	Het
Cdk14	T	A	5: 5,143,005 (GRCm39)	Q242L	probably damaging	Het
Clcn1	T	C	6: 42,284,477 (GRCm39)	V605A	probably damaging	Het
Cped1	G	A	6: 22,119,469 (GRCm39)	M309I	probably benign	Het
Cyp2r1	A	T	7: 114,151,971 (GRCm39)	Y120N	probably damaging	Het
Ddx3y	A	T	Y: 1,279,491 (GRCm39)	S124R	probably benign	Het
Dlec1	A	T	9: 118,972,472 (GRCm39)		probably null	Het
Dnah17	T	C	11: 117,936,944 (GRCm39)	E3420G	possibly damaging	Het
Dnajc13	C	T	9: 104,080,613 (GRCm39)		probably null	Het
Dusp23	A	T	1: 172,459,253 (GRCm39)	Y136*	probably null	Het
Eif4b	A	G	15: 102,001,571 (GRCm39)		probably benign	Het
F13a1	A	G	13: 37,082,117 (GRCm39)	V529A	probably benign	Het
Fhl2	A	G	1: 43,162,808 (GRCm39)	Y236H	probably damaging	Het
Gm826	C	T	2: 160,169,026 (GRCm39)	W94*	probably null	Het
Gpsm2	C	T	3: 108,610,361 (GRCm39)	R33H	probably damaging	Het
Hmcn1	T	C	1: 150,475,404 (GRCm39)		probably null	Het
Ifit1bl2	T	C	19: 34,596,551 (GRCm39)	D355G	probably benign	Het
Itga8	A	G	2: 12,115,895 (GRCm39)	V77A	probably damaging	Het
Kcmf1	C	T	6: 72,826,450 (GRCm39)	R40K	probably damaging	Het
Kdm7a	T	C	6: 39,145,982 (GRCm39)	E315G	probably damaging	Het
Kmt2b	C	T	7: 30,268,731 (GRCm39)	G2666D	probably damaging	Het
Mdn1	A	G	4: 32,767,969 (GRCm39)	N5301D	probably benign	Het
Mest	T	G	6: 30,742,723 (GRCm39)	H108Q	probably damaging	Het
Mettl25b	A	G	3: 87,837,167 (GRCm39)	I36T	probably damaging	Het
Moxd1	C	A	10: 24,157,374 (GRCm39)	D335E	probably damaging	Het
Ncf2	A	C	1: 152,683,921 (GRCm39)	N47H	probably benign	Het
Npc1	A	G	18: 12,337,822 (GRCm39)		probably null	Het
Or14j2	A	T	17: 37,886,114 (GRCm39)	S67T	probably damaging	Het
Pcid2	A	G	8: 13,128,243 (GRCm39)	V386A	probably benign	Het
Phactr2	T	A	10: 13,121,168 (GRCm39)	T444S	probably benign	Het
Plekha7	T	C	7: 115,747,559 (GRCm39)	N710D	probably benign	Het
Ppp1r16b	C	T	2: 158,599,174 (GRCm39)	T382I	probably benign	Het
Pramel15	T	C	4: 144,103,754 (GRCm39)	D124G	probably benign	Het
Ptprz1	A	T	6: 22,961,622 (GRCm39)	Y111F	probably benign	Het
Rbbp8	A	G	18: 11,865,277 (GRCm39)	E722G	possibly damaging	Het
Rimbp3	A	G	16: 17,028,190 (GRCm39)	D538G	probably benign	Het
Rims1	A	G	1: 22,511,901 (GRCm39)	S551P	probably damaging	Het
Rsrc1	A	G	3: 67,088,164 (GRCm39)	D166G	probably damaging	Het
Selenon	T	C	4: 134,270,154 (GRCm39)	N350S	probably benign	Het
Sh3gl2	T	A	4: 85,295,802 (GRCm39)	L168H	probably damaging	Het
Smc3	T	C	19: 53,617,682 (GRCm39)	Y560H	probably benign	Het
Syce1	C	T	7: 140,359,281 (GRCm39)	D147N	possibly damaging	Het
Syt10	A	C	15: 89,675,008 (GRCm39)	V446G	probably damaging	Het
Taar1	T	C	10: 23,796,722 (GRCm39)	L140P	probably benign	Het
Tfpi2	C	A	6: 3,968,032 (GRCm39)	C36F	probably damaging	Het
Thoc5	G	A	11: 4,876,237 (GRCm39)		probably null	Het
Tnrc6c	T	A	11: 117,612,800 (GRCm39)	N319K	probably benign	Het
Trhr2	C	T	8: 123,085,418 (GRCm39)	D189N	probably damaging	Het
Trim42	A	T	9: 97,245,474 (GRCm39)	F442Y	probably damaging	Het
Ubap2	G	A	4: 41,196,033 (GRCm39)	T949I	possibly damaging	Het
Ugt1a8	T	C	1: 88,016,024 (GRCm39)	F146L	probably benign	Het
Vmn2r80	C	A	10: 79,030,153 (GRCm39)	Q660K	probably damaging	Het
Vstm2b	C	T	7: 40,578,800 (GRCm39)	T258I	possibly damaging	Het
Washc2	T	C	6: 116,197,544 (GRCm39)	L259P	possibly damaging	Het
Zscan18	A	T	7: 12,508,671 (GRCm39)		probably benign	Het
Zzef1	T	G	11: 72,757,525 (GRCm39)	Y1193*	probably null	Het

Other mutations in Lrrtm1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00927:Lrrtm1	APN	6	77,221,046 (GRCm39)	missense	probably benign	0.00
IGL01011:Lrrtm1	APN	6	77,221,218 (GRCm39)	splice site	probably null
IGL01125:Lrrtm1	APN	6	77,221,436 (GRCm39)	missense	probably damaging	1.00
IGL01924:Lrrtm1	APN	6	77,221,169 (GRCm39)	missense	possibly damaging	0.81
IGL02508:Lrrtm1	APN	6	77,221,574 (GRCm39)	missense	probably damaging	1.00
IGL03005:Lrrtm1	APN	6	77,221,139 (GRCm39)	missense	probably damaging	1.00
IGL03076:Lrrtm1	APN	6	77,221,568 (GRCm39)	missense	probably damaging	1.00
R0077:Lrrtm1	UTSW	6	77,220,855 (GRCm39)	missense	probably damaging	1.00
R0540:Lrrtm1	UTSW	6	77,221,611 (GRCm39)	missense	probably damaging	1.00
R0607:Lrrtm1	UTSW	6	77,221,611 (GRCm39)	missense	probably damaging	1.00
R0927:Lrrtm1	UTSW	6	77,221,843 (GRCm39)	missense	probably damaging	1.00
R1742:Lrrtm1	UTSW	6	77,221,074 (GRCm39)	missense	probably damaging	1.00
R1762:Lrrtm1	UTSW	6	77,221,680 (GRCm39)	missense	probably benign
R1933:Lrrtm1	UTSW	6	77,221,949 (GRCm39)	splice site	probably null
R1934:Lrrtm1	UTSW	6	77,221,949 (GRCm39)	splice site	probably null
R2180:Lrrtm1	UTSW	6	77,221,329 (GRCm39)	missense	probably damaging	1.00
R2267:Lrrtm1	UTSW	6	77,220,996 (GRCm39)	missense	probably damaging	0.97
R2914:Lrrtm1	UTSW	6	77,221,962 (GRCm39)	missense	probably damaging	0.99
R2937:Lrrtm1	UTSW	6	77,220,635 (GRCm39)	missense	probably benign	0.03
R2938:Lrrtm1	UTSW	6	77,220,635 (GRCm39)	missense	probably benign	0.03
R4604:Lrrtm1	UTSW	6	77,221,127 (GRCm39)	missense	probably damaging	1.00
R4908:Lrrtm1	UTSW	6	77,221,661 (GRCm39)	missense	probably benign	0.01
R4910:Lrrtm1	UTSW	6	77,221,884 (GRCm39)	missense	probably damaging	1.00
R5739:Lrrtm1	UTSW	6	77,221,872 (GRCm39)	missense	probably damaging	0.99
R6604:Lrrtm1	UTSW	6	77,221,221 (GRCm39)	missense	possibly damaging	0.70
R6845:Lrrtm1	UTSW	6	77,220,864 (GRCm39)	missense	probably benign	0.02
R7203:Lrrtm1	UTSW	6	77,220,584 (GRCm39)	missense	probably damaging	1.00
R7783:Lrrtm1	UTSW	6	77,221,236 (GRCm39)	missense	probably damaging	1.00
R7826:Lrrtm1	UTSW	6	77,221,095 (GRCm39)	splice site	probably null
R8164:Lrrtm1	UTSW	6	77,221,199 (GRCm39)	missense	probably damaging	1.00
R8303:Lrrtm1	UTSW	6	77,221,662 (GRCm39)	missense	probably benign	0.03
R8856:Lrrtm1	UTSW	6	77,221,807 (GRCm39)	missense	possibly damaging	0.85
R9221:Lrrtm1	UTSW	6	77,221,596 (GRCm39)	missense	probably damaging	1.00
R9564:Lrrtm1	UTSW	6	77,221,536 (GRCm39)	missense	probably benign	0.00
R9749:Lrrtm1	UTSW	6	77,220,855 (GRCm39)	missense	probably damaging	1.00
RF018:Lrrtm1	UTSW	6	77,221,334 (GRCm39)	missense	possibly damaging	0.63

Predicted Primers

PCR Primer
(F):5'- TCCTATAACAAGCTGCAGGC -3'
(R):5'- AACGGTCTCGAACACATGG -3'

Sequencing Primer
(F):5'- AGGCGCTAGCTCCGGATC -3'
(R):5'- GTATTCGATCTCGTTCCCAGACAAG -3'

Posted On

2019-05-13