Mutagenetix > Incidental Mutation

Incidental Mutation 'R0403:Ntng1'

35670

Institutional Source

Beutler Lab

Gene Symbol

Ntng1

Ensembl Gene

ENSMUSG00000059857

Gene Name

netrin G1

Synonyms

Lmnt1, A930010C08Rik

MMRRC Submission

038608-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0403 (G1)

Quality Score

145

Status

Validated

Chromosome

Chromosomal Location

109780040-110144011 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 109934611 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 282 (A282V)

Ref Sequence

ENSEMBL: ENSMUSP00000102180 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000072596] [ENSMUST00000106570] [ENSMUST00000106571] [ENSMUST00000106575] [ENSMUST00000128219] [ENSMUST00000131027] [ENSMUST00000133268] [ENSMUST00000138344] [ENSMUST00000138953] [ENSMUST00000156177]

AlphaFold

Q8R4G0

Predicted Effect

probably benign
Transcript: ENSMUST00000072596
AA Change: A282V

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000072397
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF_Lam	364	417	4.81e-8	SMART
EGF_Lam	420	462	5.74e-6	SMART
EGF	466	498	5.12e-3	SMART
low complexity region	522	537	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000106570
AA Change: A282V

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000102180
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	355	1.28e-3	SMART
EGF	388	420	5.12e-3	SMART
low complexity region	444	459	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106571
AA Change: A282V

PolyPhen 2 Score 0.424 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000102181
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF	408	440	5.12e-3	SMART
low complexity region	464	479	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000106575
AA Change: A282V

PolyPhen 2 Score 0.841 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000102185
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	355	3.33e-2	SMART
EGF_Lam	364	417	4.81e-8	SMART
EGF_Lam	420	462	5.74e-6	SMART
EGF	466	498	5.12e-3	SMART
low complexity region	522	537	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000128219
AA Change: A282V

PolyPhen 2 Score 0.363 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000116579
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
LamNT	59	295	1.5e-20	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000131027
AA Change: A282V

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000118800
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF_Lam	364	417	4.81e-8	SMART
EGF	421	453	5.12e-3	SMART
low complexity region	477	492	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000133268
AA Change: A282V

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000117371
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF	365	397	5.12e-3	SMART
low complexity region	421	436	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000138344
AA Change: A282V

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000120688
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF_Lam	364	406	5.74e-6	SMART
EGF	410	442	5.12e-3	SMART
low complexity region	466	481	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000138953
AA Change: A282V

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000116213
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF	407	439	5.12e-3	SMART
low complexity region	463	478	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000156177
AA Change: A282V

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000119534
Gene: ENSMUSG00000059857
AA Change: A282V

Domain	Start	End	E-Value	Type
LamNT	59	295	3.22e-18	SMART
EGF_Lam	297	354	6.86e-4	SMART
EGF	387	419	5.12e-3	SMART
low complexity region	443	458	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189335

Meta Mutation Damage Score

0.2142

Coding Region Coverage

1x: 98.0%
3x: 96.8%
10x: 93.2%
20x: 83.7%

Validation Efficiency

97% (110/113)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a preproprotein that is processed into a secreted protein containing eukaroytic growth factor (EGF)-like domains. This protein acts to guide axon growth during neuronal development. Polymorphisms in this gene may be associated with schizophrenia. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2015]
PHENOTYPE: Mice homozygous for a null allele survive into adulthood with no major alterations in gross brain cytoarchitecture or axonal projection. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ace	A	G	11: 105,973,880		probably null	Het
Adgrg3	C	T	8: 95,036,922	L284F	probably benign	Het
Alkbh8	T	A	9: 3,385,469	V587E	probably damaging	Het
Ap4b1	T	A	3: 103,818,839	C244S	probably damaging	Het
Ap4b1	T	A	3: 103,821,396	M590K	probably benign	Het
Arhgap15	C	T	2: 44,063,766	T168I	probably damaging	Het
Arntl2	T	A	6: 146,822,655	H348Q	probably damaging	Het
Atp8b1	A	G	18: 64,540,310	V997A	probably damaging	Het
Atrn	G	A	2: 130,906,859	C100Y	probably damaging	Het
Baiap2l2	C	A	15: 79,271,216	A151S	probably benign	Het
Baz2b	A	T	2: 59,969,377	D199E	possibly damaging	Het
Cblb	A	G	16: 52,152,626	D440G	probably benign	Het
Cdon	T	C	9: 35,473,500	V694A	probably benign	Het
Cep250	A	T	2: 155,992,349	R2065W	probably damaging	Het
Ces2b	G	T	8: 104,833,945	A131S	probably damaging	Het
Chrna9	A	T	5: 65,967,892	T59S	possibly damaging	Het
Cog3	T	A	14: 75,742,327		probably benign	Het
Cpa1	G	A	6: 30,641,857	V227I	probably benign	Het
Cyp3a25	A	T	5: 145,998,513	C98S	probably damaging	Het
D8Ertd738e	C	T	8: 84,249,601		probably null	Het
Ddx60	A	G	8: 61,994,541		probably benign	Het
Dhx16	T	C	17: 35,883,050		probably null	Het
Dnah9	T	A	11: 66,084,789	Q1478L	possibly damaging	Het
Dock10	T	C	1: 80,524,070	Y1434C	possibly damaging	Het
Enpp3	T	A	10: 24,804,436	D325V	probably damaging	Het
Entpd6	C	A	2: 150,760,170	T194K	possibly damaging	Het
Fam208b	A	T	13: 3,582,052	Y816*	probably null	Het
Fat2	A	T	11: 55,270,349	V3185E	probably benign	Het
Flrt1	A	G	19: 7,095,919	L421P	probably benign	Het
Fmn2	A	T	1: 174,694,278	Q1292L	probably damaging	Het
Fndc1	T	C	17: 7,775,588		probably null	Het
Fndc1	T	C	17: 7,753,723	D1459G	probably damaging	Het
Fzr1	A	G	10: 81,369,368	S265P	possibly damaging	Het
Gm13119	A	G	4: 144,362,646	N178S	probably benign	Het
Gm14085	T	C	2: 122,521,854	L364S	probably damaging	Het
Gpr142	G	A	11: 114,806,029	V134M	probably damaging	Het
Grid2ip	G	T	5: 143,357,620	V24L	possibly damaging	Het
Herc2	G	A	7: 56,159,417	R2555H	probably damaging	Het
Hpdl	A	T	4: 116,820,479	Y262N	possibly damaging	Het
Htr3a	A	G	9: 48,908,659	V57A	probably damaging	Het
Igfbp7	T	C	5: 77,355,591	I186V	probably benign	Het
Itga2b	C	T	11: 102,467,326		probably null	Het
Itgae	A	C	11: 73,123,183	D736A	possibly damaging	Het
Itpkc	T	A	7: 27,208,345	M645L	probably benign	Het
Jchain	T	C	5: 88,521,378	R139G	probably benign	Het
Kif13a	A	G	13: 46,791,401	V908A	probably damaging	Het
Kif1b	T	A	4: 149,181,967	K389*	probably null	Het
Klhl12	T	C	1: 134,485,856	Y360H	possibly damaging	Het
Knop1	G	A	7: 118,853,053	R148W	probably damaging	Het
Lpar1	T	A	4: 58,487,191	N27Y	probably damaging	Het
Lpar2	T	A	8: 69,824,152	V197D	probably damaging	Het
Lrrc74a	A	G	12: 86,740,979	N128S	probably damaging	Het
Lum	G	T	10: 97,572,043	V337F	probably benign	Het
Mag	T	C	7: 30,906,980	D344G	probably damaging	Het
Maip1	G	A	1: 57,407,196	A142T	probably benign	Het
Mlh3	A	G	12: 85,268,968	V148A	possibly damaging	Het
Nav3	A	G	10: 109,767,103	V1195A	probably damaging	Het
Ncor2	A	G	5: 125,033,337	S868P	possibly damaging	Het
Nek1	A	G	8: 61,106,855	E907G	probably damaging	Het
Nfam1	G	A	15: 83,016,379	T134I	probably benign	Het
Nr0b2	T	C	4: 133,553,759	V112A	probably damaging	Het
Nrp1	A	G	8: 128,457,969	N365S	probably damaging	Het
Nrsn2	T	C	2: 152,369,790	Y107C	probably damaging	Het
Nxf1	T	C	19: 8,765,028	I337T	probably damaging	Het
Obscn	C	T	11: 59,076,540	G479D	probably damaging	Het
Olfr45	T	C	7: 140,691,309	S135P	possibly damaging	Het
Oprd1	T	A	4: 132,113,768	D293V	probably benign	Het
P3h2	T	G	16: 25,969,950	N586H	possibly damaging	Het
Pcid2	T	C	8: 13,085,367	Y214C	probably damaging	Het
Pkd1l3	C	G	8: 109,623,649	D375E	possibly damaging	Het
Pkd1l3	G	A	8: 109,623,663	S380N	probably benign	Het
Ppic	C	A	18: 53,411,071	G81W	probably damaging	Het
Ppp2r1a	C	A	17: 20,957,041	P246T	probably damaging	Het
Ppp4r4	T	G	12: 103,584,102	S46A	probably benign	Het
Prkce	A	G	17: 86,168,653	T21A	probably damaging	Het
Prkg2	T	C	5: 98,994,645	E210G	possibly damaging	Het
Prss35	A	G	9: 86,756,037	M287V	probably damaging	Het
Psd	G	A	19: 46,320,972		probably benign	Het
Ptch2	A	T	4: 117,110,839	K843*	probably null	Het
Rab44	C	A	17: 29,145,261	T603K	probably damaging	Het
Rasal3	T	A	17: 32,392,790		probably null	Het
Rbbp6	A	G	7: 122,992,296	T526A	probably damaging	Het
Ros1	A	T	10: 52,143,438		probably benign	Het
Sec24b	T	A	3: 129,989,676	L1104F	possibly damaging	Het
Sec24b	A	G	3: 129,999,534	S685P	probably damaging	Het
Sema6a	G	A	18: 47,290,045		probably null	Het
Setmar	A	T	6: 108,075,962	H139L	probably benign	Het
Slc4a7	T	C	14: 14,766,808	V710A	probably benign	Het
Smarcc1	T	A	9: 110,237,808		probably null	Het
Smchd1	G	A	17: 71,394,902	L1032F	probably damaging	Het
Speg	T	C	1: 75,430,784		probably benign	Het
Tcea1	C	G	1: 4,889,503	R134G	probably benign	Het
Tchhl1	C	T	3: 93,471,029	Q347*	probably null	Het
Tecrl	A	T	5: 83,354,758		probably benign	Het
Tepsin	T	C	11: 120,093,682		probably benign	Het
Tmem40	G	A	6: 115,733,985		probably benign	Het
Tpr	G	A	1: 150,407,414		probably benign	Het
Ttll12	A	T	15: 83,580,658		probably benign	Het
Ttn	T	A	2: 76,909,608	D3529V	probably benign	Het
Usp34	T	A	11: 23,333,838	H177Q	possibly damaging	Het
Vsig10	T	A	5: 117,338,461	S327T	probably benign	Het
Zbtb4	T	A	11: 69,777,639	M396K	probably damaging	Het
Zfp352	C	T	4: 90,225,009	T462I	possibly damaging	Het
Zfp385b	T	C	2: 77,476,845	M145V	probably damaging	Het
Zfp780b	C	A	7: 27,971,689	V65F	possibly damaging	Het

Other mutations in Ntng1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02162:Ntng1	APN	3	109934995	nonsense	probably null
IGL02367:Ntng1	APN	3	110135513	splice site	probably null
IGL02448:Ntng1	APN	3	109934559	splice site	probably benign
IGL02487:Ntng1	APN	3	109935047	missense	probably damaging	0.98
IGL02500:Ntng1	APN	3	110135330	missense	probably damaging	1.00
IGL02578:Ntng1	APN	3	110135394	missense	probably benign	0.01
IGL03009:Ntng1	APN	3	109934702	missense	possibly damaging	0.89
IGL03096:Ntng1	APN	3	110135349	missense	probably benign	0.19
R0108:Ntng1	UTSW	3	109851755	splice site	probably benign
R0326:Ntng1	UTSW	3	110135503	nonsense	probably null
R0699:Ntng1	UTSW	3	109872295	missense	probably damaging	1.00
R0702:Ntng1	UTSW	3	109872254	missense	probably damaging	1.00
R1981:Ntng1	UTSW	3	109935010	missense	possibly damaging	0.61
R2096:Ntng1	UTSW	3	109832555	missense	probably damaging	0.99
R3739:Ntng1	UTSW	3	109934691	missense	probably damaging	1.00
R3963:Ntng1	UTSW	3	109934868	missense	probably damaging	1.00
R4484:Ntng1	UTSW	3	110143808	unclassified	probably benign
R4516:Ntng1	UTSW	3	109935013	missense	probably damaging	1.00
R4518:Ntng1	UTSW	3	109935013	missense	probably damaging	1.00
R4520:Ntng1	UTSW	3	109934996	missense	probably damaging	1.00
R4523:Ntng1	UTSW	3	109934996	missense	probably damaging	1.00
R4524:Ntng1	UTSW	3	109934996	missense	probably damaging	1.00
R4776:Ntng1	UTSW	3	109934713	missense	probably damaging	1.00
R4817:Ntng1	UTSW	3	109934868	missense	probably damaging	1.00
R4827:Ntng1	UTSW	3	110135411	missense	probably damaging	1.00
R4990:Ntng1	UTSW	3	110135261	critical splice donor site	probably null
R5067:Ntng1	UTSW	3	110135345	missense	possibly damaging	0.95
R5087:Ntng1	UTSW	3	110135329	nonsense	probably null
R5196:Ntng1	UTSW	3	109934983	missense	probably damaging	1.00
R5263:Ntng1	UTSW	3	109934872	missense	probably damaging	0.99
R5743:Ntng1	UTSW	3	110135420	missense	probably damaging	1.00
R6268:Ntng1	UTSW	3	109935035	missense	probably damaging	1.00
R6292:Ntng1	UTSW	3	110143886	unclassified	probably benign
R6419:Ntng1	UTSW	3	109782853	missense	possibly damaging	0.95
R6898:Ntng1	UTSW	3	109872218	missense	probably damaging	0.98
R7081:Ntng1	UTSW	3	109851789	missense	probably benign	0.00
R7090:Ntng1	UTSW	3	109935180	nonsense	probably null
R7134:Ntng1	UTSW	3	109935129	missense	probably benign
R7302:Ntng1	UTSW	3	109832617	missense	possibly damaging	0.94
R7353:Ntng1	UTSW	3	110135447	missense	probably damaging	1.00
R7408:Ntng1	UTSW	3	109853082	missense	probably benign	0.00
R7610:Ntng1	UTSW	3	109934825	missense	probably damaging	1.00
R7686:Ntng1	UTSW	3	109935014	missense	possibly damaging	0.80
R7972:Ntng1	UTSW	3	110135486	missense	probably benign	0.02
R9210:Ntng1	UTSW	3	109872317	missense	probably damaging	1.00
R9214:Ntng1	UTSW	3	109934605	missense	probably damaging	1.00
R9266:Ntng1	UTSW	3	110143607	unclassified	probably benign
R9266:Ntng1	UTSW	3	110143846	missense	unknown
R9364:Ntng1	UTSW	3	110135364	missense	probably damaging	0.97
R9593:Ntng1	UTSW	3	109934908	missense	probably damaging	1.00
R9596:Ntng1	UTSW	3	110135640	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- GCCAAAGGGTCTCAAAATGCCTTG -3'
(R):5'- CACGGTCTTGGAAATCATTTGCACG -3'

Sequencing Primer
(F):5'- AGAATATACTTGCATAGTGGTGCTCC -3'
(R):5'- TCCACTTCGAGATCAAAGACAGG -3'

Posted On

2013-05-09