Mutagenetix > Incidental Mutation

Incidental Mutation 'R4776:Ntng1'

367904

Institutional Source

Beutler Lab

Gene Symbol

Ntng1

Ensembl Gene

ENSMUSG00000059857

Gene Name

netrin G1

Synonyms

Lmnt1, A930010C08Rik

MMRRC Submission

042413-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4776 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

109780040-110144011 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 109934713 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Valine at position 248 (D248V)

Ref Sequence

ENSEMBL: ENSMUSP00000116579 (fasta)

Gene Model

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

AlphaFold

Q8R4G0

Predicted Effect

probably damaging
Transcript: ENSMUST00000072596
AA Change: D248V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000072397
Gene: ENSMUSG00000059857
AA Change: D248V

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: D248V

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

SMART Domains

Protein: ENSMUSP00000102180
Gene: ENSMUSG00000059857
AA Change: D248V

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 damaging
Transcript: ENSMUST00000106571
AA Change: D248V

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000102181
Gene: ENSMUSG00000059857
AA Change: D248V

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

probably damaging
Transcript: ENSMUST00000106575
AA Change: D248V

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

SMART Domains

Protein: ENSMUSP00000102185
Gene: ENSMUSG00000059857
AA Change: D248V

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 damaging
Transcript: ENSMUST00000128219
AA Change: D248V

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

SMART Domains

Protein: ENSMUSP00000116579
Gene: ENSMUSG00000059857
AA Change: D248V

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000131027
AA Change: D248V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000118800
Gene: ENSMUSG00000059857
AA Change: D248V

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 damaging
Transcript: ENSMUST00000133268
AA Change: D248V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000117371
Gene: ENSMUSG00000059857
AA Change: D248V

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 damaging
Transcript: ENSMUST00000138344
AA Change: D248V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000120688
Gene: ENSMUSG00000059857
AA Change: D248V

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 damaging
Transcript: ENSMUST00000138953
AA Change: D248V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000116213
Gene: ENSMUSG00000059857
AA Change: D248V

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 damaging
Transcript: ENSMUST00000156177
AA Change: D248V

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000119534
Gene: ENSMUSG00000059857
AA Change: D248V

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

0.7956

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 93.9%

Validation Efficiency

98% (94/96)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310035C23Rik	T	A	1: 105,719,535	Y683*	probably null	Het
2610028H24Rik	A	T	10: 76,457,512	M156L	probably benign	Het
4930470P17Rik	C	T	2: 170,579,724	A79T	unknown	Het
4930522L14Rik	A	G	5: 109,736,873	I373T	probably benign	Het
A830010M20Rik	C	A	5: 107,510,451	A1117E	probably damaging	Het
Amotl1	G	A	9: 14,593,373	Q217*	probably null	Het
Ankrd28	A	T	14: 31,732,054	C254S	probably damaging	Het
Ap2a1	A	G	7: 44,901,546		probably benign	Het
Arfgef3	A	T	10: 18,654,247	S245T	probably benign	Het
Arntl	A	T	7: 113,285,037	K94I	probably damaging	Het
Atp1b2	A	T	11: 69,601,561	D224E	probably damaging	Het
Boc	G	A	16: 44,487,721	R924W	probably damaging	Het
Car14	C	T	3: 95,898,873	G292D	probably benign	Het
Cenpb	T	C	2: 131,178,183		probably benign	Het
Ces1b	A	T	8: 93,063,030	D423E	possibly damaging	Het
Cfap54	T	A	10: 92,972,694	N1373I	possibly damaging	Het
Chrdl2	T	C	7: 100,006,541		probably benign	Het
Cic	T	G	7: 25,282,883	S12A	possibly damaging	Het
Csmd2	A	T	4: 128,442,892	Q1421L	probably benign	Het
D630039A03Rik	T	C	4: 57,910,452	H120R	possibly damaging	Het
Dicer1	T	A	12: 104,692,446	D1779V	probably damaging	Het
Dock9	G	T	14: 121,610,097	H1016N	possibly damaging	Het
Dxo	T	C	17: 34,838,998	L352P	probably damaging	Het
Eif2b5	T	A	16: 20,500,233	F78I	probably damaging	Het
Eri2	A	G	7: 119,784,946		probably benign	Het
Fam208b	A	G	13: 3,570,391	F2170S	probably damaging	Het
Fbxw7	T	G	3: 84,925,689	L13V	possibly damaging	Het
Fgf7	T	A	2: 126,035,783	C23*	probably null	Het
Fubp1	T	A	3: 152,222,068		probably null	Het
Gm2663	A	T	6: 40,995,953	I240N	probably damaging	Het
Gnb1l	C	T	16: 18,548,096	Q140*	probably null	Het
Gnptab	G	A	10: 88,436,528	R1010Q	probably damaging	Het
Gtf2h1	G	A	7: 46,822,878	W544*	probably null	Het
Gucy2c	C	T	6: 136,722,514	E586K	probably damaging	Het
Hc	T	A	2: 35,039,734	E232V	probably benign	Het
Ifi207	T	A	1: 173,730,056	D372V	unknown	Het
Igkv8-28	A	T	6: 70,144,118	V15E	probably benign	Het
Il1rap	A	G	16: 26,692,799	S198G	possibly damaging	Het
Lct	A	G	1: 128,300,387	I1123T	probably damaging	Het
Lhcgr	T	C	17: 88,742,697	E467G	probably damaging	Het
Macf1	C	T	4: 123,476,015	R86K	probably benign	Het
Maml3	T	A	3: 51,856,532	Q337L	probably benign	Het
March10	T	A	11: 105,390,037	D474V	probably benign	Het
March2	G	T	17: 33,709,916	T2K	probably damaging	Het
Mast1	A	G	8: 84,937,193		probably null	Het
Med12l	T	C	3: 59,233,212	I868T	probably damaging	Het
Msrb1	T	C	17: 24,740,173	S100P	probably damaging	Het
Nlrp4c	T	C	7: 6,066,126	L342P	probably benign	Het
Nrxn3	T	A	12: 90,331,956	V417E	possibly damaging	Het
Oaz3	T	C	3: 94,434,998	Q117R	probably benign	Het
Olfr1311	A	G	2: 112,020,931	Y308H	probably benign	Het
Olfr444	A	G	6: 42,955,521	I8V	probably benign	Het
Olfr589	A	G	7: 103,155,414	L111P	probably benign	Het
Osbpl3	A	C	6: 50,300,973	S767A	probably benign	Het
Pafah1b1	A	T	11: 74,685,871		probably benign	Het
Pard6b	A	G	2: 168,098,788	T232A	probably damaging	Het
Paxip1	A	T	5: 27,765,206	C596S	probably damaging	Het
Pnpla6	T	C	8: 3,523,818	V422A	probably benign	Het
Psmd6	A	T	14: 14,120,932		probably benign	Het
Rock2	T	A	12: 16,977,740	C1353S	probably damaging	Het
Rpl31-ps17	C	T	12: 54,701,612		noncoding transcript	Het
Sel1l	T	A	12: 91,813,893	H658L	probably damaging	Het
Sh3yl1	T	A	12: 30,940,314	L105Q	probably damaging	Het
Shroom3	G	T	5: 92,943,086	V1151F	probably damaging	Het
Sirt1	T	C	10: 63,335,722	K227E	probably benign	Het
Slc25a34	A	T	4: 141,623,588	F37I	possibly damaging	Het
Slc39a5	T	A	10: 128,397,049	I378F	probably damaging	Het
Smarcad1	A	T	6: 65,098,824	D731V	probably null	Het
Sox6	T	G	7: 115,541,670	K483N	probably damaging	Het
Sp140	T	A	1: 85,610,828	D95E	possibly damaging	Het
Srgap1	G	T	10: 121,792,351	D882E	probably benign	Het
Syne4	T	C	7: 30,316,833		probably benign	Het
Tec	T	C	5: 72,768,776	Y289C	probably benign	Het
Tmem102	A	T	11: 69,804,802	Y115N	probably damaging	Het
Tns2	C	T	15: 102,108,934	R281C	probably damaging	Het
Trav17	T	A	14: 53,806,640	M1K	probably null	Het
Trdn	T	A	10: 33,399,082		probably null	Het
Trp53	A	T	11: 69,586,921	I8F	probably benign	Het
Ttn	T	A	2: 76,754,662	D22064V	probably damaging	Het
Ube3c	G	A	5: 29,632,838		probably null	Het
Ulk1	C	T	5: 110,788,947		probably null	Het
Upp1	T	C	11: 9,135,976	V271A	probably damaging	Het
Vmn2r4	T	C	3: 64,388,661	E901G	probably damaging	Het
Vmn2r96	G	A	17: 18,597,508	G449D	probably damaging	Het
Vps37b	T	C	5: 124,006,612	K165E	probably damaging	Het
Vwf	A	T	6: 125,566,305	I185F	possibly damaging	Het
Wasf2	A	G	4: 133,185,004	T56A	probably benign	Het
Zdhhc23	C	G	16: 43,973,589	D241H	possibly damaging	Het
Zfp276	T	C	8: 123,254,884	S57P	probably benign	Het
Zxdc	A	G	6: 90,370,518	H287R	probably 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
R0403:Ntng1	UTSW	3	109934611	missense	probably damaging	0.97
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
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'- TCAAGATGGGCATGTGTTCTC -3'
(R):5'- GAACATGGCAGCCCTATCAG -3'

Sequencing Primer
(F):5'- CAAGATGGGCATGTGTTCTCTTACC -3'
(R):5'- ACATGGCAGCCCTATCAGTATTATGC -3'

Posted On

2015-12-29