Mutagenetix > Incidental Mutation

Incidental Mutation 'R1742:Lrrtm1'

200415

Institutional Source

Beutler Lab

Gene Symbol

Lrrtm1

Ensembl Gene

ENSMUSG00000060780

Gene Name

leucine rich repeat transmembrane neuronal 1

Synonyms

4632401D06Rik

MMRRC Submission

039774-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1742 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

77219672-77234774 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 77221074 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Glutamine at position 177 (P177Q)

Ref Sequence

ENSEMBL: ENSMUSP00000124948 (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: P177Q

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

SMART Domains

Protein: ENSMUSP00000020400
Gene: ENSMUSG00000060780
AA Change: P177Q

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: P177Q

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

SMART Domains

Protein: ENSMUSP00000125207
Gene: ENSMUSG00000060780
AA Change: P177Q

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: P177Q

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

SMART Domains

Protein: ENSMUSP00000124373
Gene: ENSMUSG00000060780
AA Change: P177Q

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 damaging
Transcript: ENSMUST00000161811
AA Change: P177Q

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

SMART Domains

Protein: ENSMUSP00000124948
Gene: ENSMUSG00000060780
AA Change: P177Q

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

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.4%
20x: 92.7%

Validation Efficiency

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankhd1	C	A	18: 36,758,318 (GRCm39)	A1004E	probably damaging	Het
Arfgef2	A	G	2: 166,708,900 (GRCm39)	S1071G	probably damaging	Het
Arhgef5	T	A	6: 43,257,133 (GRCm39)	I1228N	probably damaging	Het
Auh	G	A	13: 52,989,532 (GRCm39)	P308L	probably benign	Het
Bptf	A	G	11: 107,001,777 (GRCm39)	V445A	probably damaging	Het
Btf3	C	T	13: 98,452,804 (GRCm39)	M1I	probably null	Het
Bves	C	T	10: 45,223,961 (GRCm39)	T207M	probably damaging	Het
Ccdc171	T	A	4: 83,599,521 (GRCm39)	S779T	probably damaging	Het
Ccdc54	T	C	16: 50,410,601 (GRCm39)	K222E	possibly damaging	Het
Cebpe	A	G	14: 54,949,057 (GRCm39)	V120A	probably benign	Het
Clhc1	T	A	11: 29,507,647 (GRCm39)		probably null	Het
Col22a1	C	T	15: 71,673,762 (GRCm39)	G985S	unknown	Het
Col6a3	T	A	1: 90,741,516 (GRCm39)	I639F	probably damaging	Het
Cryga	C	A	1: 65,142,280 (GRCm39)	V38L	probably benign	Het
Dll3	T	C	7: 27,993,848 (GRCm39)	T530A	probably benign	Het
Dnaaf9	A	T	2: 130,582,315 (GRCm39)		probably null	Het
Dnah7a	G	A	1: 53,495,843 (GRCm39)	P3205S	probably benign	Het
Dpp10	T	A	1: 123,372,935 (GRCm39)	Y224F	probably damaging	Het
Eif1ad10	C	T	12: 88,216,453 (GRCm39)	D140N	unknown	Het
Fcrl2	T	C	3: 87,166,350 (GRCm39)	T142A	possibly damaging	Het
Fyttd1	C	T	16: 32,725,923 (GRCm39)	R175*	probably null	Het
Gm10277	TC	T	11: 77,676,828 (GRCm39)		probably null	Het
Gpr33	T	C	12: 52,071,045 (GRCm39)		probably null	Het
Gse1	T	A	8: 121,293,689 (GRCm39)	V205E	probably damaging	Het
Herc4	C	A	10: 63,123,728 (GRCm39)	N461K	probably benign	Het
Ifi206	G	A	1: 173,309,537 (GRCm39)	T153I	probably benign	Het
Iqca1	T	C	1: 90,025,773 (GRCm39)	I341V	probably benign	Het
Itsn1	T	G	16: 91,613,847 (GRCm39)		probably null	Het
Kcnk5	T	A	14: 20,191,925 (GRCm39)	Y412F	probably benign	Het
Lemd1	T	A	1: 132,156,036 (GRCm39)	I26K	probably damaging	Het
Lipc	A	T	9: 70,727,811 (GRCm39)	L12Q	probably damaging	Het
Mcph1	G	A	8: 18,657,379 (GRCm39)	G73R	probably benign	Het
Msantd5f6	T	C	4: 73,319,447 (GRCm39)	D99G	probably damaging	Het
Myh11	A	T	16: 14,037,908 (GRCm39)	L899Q	probably damaging	Het
Myo18a	G	T	11: 77,732,293 (GRCm39)	R822L	probably damaging	Het
Nav3	T	C	10: 109,605,074 (GRCm39)	T1000A	probably benign	Het
Nox4	T	C	7: 86,945,026 (GRCm39)	V94A	possibly damaging	Het
Or10ag53	T	A	2: 87,083,122 (GRCm39)	N280K	probably benign	Het
Or4c123	G	T	2: 89,126,768 (GRCm39)	P282H	probably damaging	Het
Or7g32	A	G	9: 19,389,337 (GRCm39)	S67P	probably damaging	Het
Oxr1	T	C	15: 41,713,955 (GRCm39)	L679P	probably damaging	Het
Pcdhb17	T	C	18: 37,619,629 (GRCm39)	I473T	probably damaging	Het
Pgbd5	T	A	8: 125,107,046 (GRCm39)	E165D	probably damaging	Het
Pgpep1l	A	T	7: 67,886,802 (GRCm39)	V169D	probably damaging	Het
Phf12	C	T	11: 77,900,312 (GRCm39)	T136I	probably benign	Het
Pif1	T	A	9: 65,495,132 (GRCm39)	M14K	probably benign	Het
Pigr	A	G	1: 130,772,823 (GRCm39)	E347G	probably damaging	Het
Plekha3	G	A	2: 76,513,223 (GRCm39)	E103K	possibly damaging	Het
Ptgs2	A	G	1: 149,980,150 (GRCm39)	I363V	probably damaging	Het
Rasl11a	T	A	5: 146,783,805 (GRCm39)		probably null	Het
Recql	T	C	6: 142,310,298 (GRCm39)	T511A	probably damaging	Het
Rgl2	T	A	17: 34,156,197 (GRCm39)		probably null	Het
Rpp25l	T	C	4: 41,712,763 (GRCm39)	Y4C	probably damaging	Het
Sass6	T	G	3: 116,401,126 (GRCm39)	C156G	probably damaging	Het
Sgta	T	G	10: 80,882,111 (GRCm39)	N288T	probably damaging	Het
Slco1a4	T	A	6: 141,770,771 (GRCm39)	T282S	probably benign	Het
Smad4	T	C	18: 73,808,968 (GRCm39)	R100G	probably damaging	Het
Sox8	C	T	17: 25,786,915 (GRCm39)	V263M	probably damaging	Het
Sp8	A	G	12: 118,813,552 (GRCm39)	H469R	probably benign	Het
Spata1	A	T	3: 146,175,378 (GRCm39)		probably null	Het
Taar7a	G	A	10: 23,869,117 (GRCm39)	S88F	probably damaging	Het
Tnks2	T	C	19: 36,853,661 (GRCm39)	L749S	probably damaging	Het
Tollip	C	A	7: 141,446,592 (GRCm39)	R19L	probably damaging	Het
Tox2	G	A	2: 163,067,446 (GRCm39)	R55H	probably benign	Het
Vmn2r27	T	C	6: 124,177,636 (GRCm39)	E456G	possibly damaging	Het
Vmn2r77	T	A	7: 86,444,543 (GRCm39)	N65K	probably benign	Het
Vwf	T	C	6: 125,644,513 (GRCm39)	M2456T	probably benign	Het
Zfp526	A	G	7: 24,923,939 (GRCm39)	N66S	possibly damaging	Het
Zic1	T	C	9: 91,243,629 (GRCm39)	Y446C	probably damaging	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
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
R7048:Lrrtm1	UTSW	6	77,221,152 (GRCm39)	missense	probably damaging	1.00
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'- TGCGCCGAGTTAAGGAACTCAC -3'
(R):5'- CAGTCGAGAGAGCTGACCACAATG -3'

Sequencing Primer
(F):5'- TCACGCTGAGTTCCAACCAG -3'
(R):5'- TTATTCCGCCTCAGGCAGAG -3'

Posted On

2014-05-23