Mutagenetix > Incidental Mutation

Incidental Mutation 'R0363:Ntn1'

30196

Institutional Source

Beutler Lab

Gene Symbol

Ntn1

Ensembl Gene

ENSMUSG00000020902

Gene Name

netrin 1

Synonyms

Netrin-1

MMRRC Submission

038569-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.673) question?

Stock #

R0363 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

68100190-68277652 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 68276369 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 193 (I193T)

Ref Sequence

ENSEMBL: ENSMUSP00000104314 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021284] [ENSMUST00000108674] [ENSMUST00000135141]

AlphaFold

O09118

Predicted Effect

probably benign
Transcript: ENSMUST00000021284
AA Change: I193T

PolyPhen 2 Score 0.435 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000021284
Gene: ENSMUSG00000020902
AA Change: I193T

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
LamNT	45	283	7.14e-148	SMART
EGF_Lam	285	338	2.44e-9	SMART
EGF_Lam	341	401	3.01e-9	SMART
EGF_Lam	404	451	8.43e-13	SMART
C345C	487	595	1.67e-37	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000108674
AA Change: I193T

PolyPhen 2 Score 0.435 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000104314
Gene: ENSMUSG00000020902
AA Change: I193T

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
LamNT	45	283	7.14e-148	SMART
EGF_Lam	285	338	2.44e-9	SMART
EGF_Lam	341	401	3.01e-9	SMART
EGF_Lam	404	451	8.43e-13	SMART
C345C	487	595	1.67e-37	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000135141

SMART Domains

Protein: ENSMUSP00000121193
Gene: ENSMUSG00000020902

Domain	Start	End	E-Value	Type
signal peptide	1	24	N/A	INTRINSIC
LamNT	45	159	6.8e-15	SMART

Meta Mutation Damage Score

0.1732

Coding Region Coverage

1x: 98.9%
3x: 97.8%
10x: 94.7%
20x: 86.5%

Validation Efficiency

98% (78/80)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Netrin is included in a family of laminin-related secreted proteins. The function of this gene has not yet been defined; however, netrin is thought to be involved in axon guidance and cell migration during development. Mutations and loss of expression of netrin suggest that variation in netrin may be involved in cancer development. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted mutations exhibit impaired axonal migration, abnormal semicircular canals, lack of corpus callosum, aberrant commissures, hypoplasia of the optic nerve, motor and balance defects, failure to suckle, and neonatal death. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522H14Rik	T	A	4: 109,381,520 (GRCm39)	Q86L	probably null	Het
Abhd2	A	G	7: 79,000,561 (GRCm39)	D262G	possibly damaging	Het
Abhd5	T	C	9: 122,197,211 (GRCm39)	F133L	possibly damaging	Het
Agap2	T	A	10: 126,926,834 (GRCm39)	V957E	probably damaging	Het
Ankrd12	T	C	17: 66,292,676 (GRCm39)	K919R	probably damaging	Het
Ap1m1	T	C	8: 73,006,738 (GRCm39)	S245P	probably benign	Het
Ap1m1	T	C	8: 73,010,568 (GRCm39)		probably benign	Het
Apcdd1	A	G	18: 63,070,168 (GRCm39)	Y145C	possibly damaging	Het
Apob	A	T	12: 8,060,136 (GRCm39)	N2840Y	probably damaging	Het
Arel1	A	G	12: 84,981,027 (GRCm39)	S327P	probably damaging	Het
Arhgap21	C	A	2: 20,885,944 (GRCm39)	R421L	probably damaging	Het
Ccdc85a	A	T	11: 28,533,400 (GRCm39)	I48N	probably damaging	Het
Chd6	A	G	2: 160,856,244 (GRCm39)	S672P	probably damaging	Het
Ciz1	G	C	2: 32,267,375 (GRCm39)		probably null	Het
Cmbl	G	A	15: 31,585,588 (GRCm39)		probably null	Het
Cmya5	A	G	13: 93,231,377 (GRCm39)	V1237A	possibly damaging	Het
Cntnap4	A	T	8: 113,583,143 (GRCm39)	K1074*	probably null	Het
Cntnap5b	A	G	1: 100,202,193 (GRCm39)	M347V	probably benign	Het
Col1a2	G	A	6: 4,518,822 (GRCm39)		probably benign	Het
Cuzd1	A	T	7: 130,917,991 (GRCm39)	M203K	probably benign	Het
Cyp3a16	T	C	5: 145,392,689 (GRCm39)		probably benign	Het
Dlgap3	A	G	4: 127,129,314 (GRCm39)	E892G	probably damaging	Het
Dnah7b	T	C	1: 46,275,948 (GRCm39)	S2612P	probably damaging	Het
Epas1	T	G	17: 87,113,276 (GRCm39)		probably benign	Het
Etv5	G	A	16: 22,230,458 (GRCm39)	A192V	probably benign	Het
Fa2h	T	A	8: 112,075,921 (GRCm39)	H234L	probably damaging	Het
Fcho1	T	C	8: 72,170,134 (GRCm39)	Y47C	probably damaging	Het
Flvcr1	T	A	1: 190,744,451 (GRCm39)		probably benign	Het
Il1rl1	CTTGTTGTTGTTGTTGTTG	CTTGTTGTTGTTGTTGTTGTTG	1: 40,481,734 (GRCm39)		probably benign	Het
Ino80	G	A	2: 119,213,441 (GRCm39)	R1249C	probably damaging	Het
Inpp4b	T	C	8: 82,610,886 (GRCm39)		probably benign	Het
Isy1	G	A	6: 87,796,167 (GRCm39)	R257W	probably damaging	Het
Kmt2a	A	G	9: 44,721,010 (GRCm39)		probably null	Het
Krt4	G	A	15: 101,833,081 (GRCm39)	R9C	possibly damaging	Het
Map1a	T	C	2: 121,132,525 (GRCm39)	S876P	probably damaging	Het
Mettl21e	A	G	1: 44,250,190 (GRCm39)		probably null	Het
Msh2	C	T	17: 88,024,904 (GRCm39)	T594M	probably benign	Het
Mtmr3	A	G	11: 4,437,536 (GRCm39)	S973P	probably damaging	Het
Muc5ac	A	T	7: 141,354,697 (GRCm39)	M889L	probably benign	Het
Nudt13	A	T	14: 20,359,851 (GRCm39)	I193F	probably damaging	Het
Or2n1	A	G	17: 38,486,338 (GRCm39)	D121G	probably damaging	Het
Or3a1	C	T	11: 74,225,925 (GRCm39)	G44D	probably damaging	Het
Or4b1b	A	T	2: 90,112,200 (GRCm39)	S240T	probably damaging	Het
Or5p73	A	T	7: 108,064,941 (GRCm39)	T137S	possibly damaging	Het
Otulin	A	G	15: 27,606,381 (GRCm39)	V344A	probably damaging	Het
P2rx7	C	T	5: 122,795,093 (GRCm39)	Q128*	probably null	Het
Pcdhb22	G	A	18: 37,652,213 (GRCm39)	R227H	probably benign	Het
Plekha5	G	A	6: 140,537,473 (GRCm39)	R646K	possibly damaging	Het
Pltp	C	T	2: 164,682,056 (GRCm39)	R394H	probably benign	Het
Ppip5k1	C	G	2: 121,177,836 (GRCm39)	A324P	probably damaging	Het
Pramel14	C	T	4: 143,718,221 (GRCm39)	M407I	probably benign	Het
Prdm13	A	C	4: 21,679,737 (GRCm39)	V251G	unknown	Het
Prkg1	T	C	19: 31,641,596 (GRCm39)	E29G	probably damaging	Het
Prrc2c	A	G	1: 162,525,380 (GRCm39)	S409P	unknown	Het
Rp1	T	A	1: 4,417,941 (GRCm39)	D1057V	probably damaging	Het
Rttn	G	A	18: 89,029,079 (GRCm39)	C599Y	probably damaging	Het
Shisa6	C	T	11: 66,416,153 (GRCm39)	R213Q	probably benign	Het
Slc3a1	T	C	17: 85,340,273 (GRCm39)	Y232H	probably damaging	Het
Slx4	G	A	16: 3,797,953 (GRCm39)	A1477V	probably damaging	Het
Ssrp1	T	G	2: 84,871,018 (GRCm39)	I218S	probably damaging	Het
St6galnac1	A	C	11: 116,659,756 (GRCm39)	S186A	probably benign	Het
Stab1	A	G	14: 30,880,965 (GRCm39)		probably benign	Het
Sycp2	T	C	2: 177,988,204 (GRCm39)		probably benign	Het
Syne2	T	A	12: 76,118,981 (GRCm39)	I5867N	probably damaging	Het
Taar7f	T	A	10: 23,925,839 (GRCm39)	D144E	probably damaging	Het
Tlcd5	A	T	9: 43,023,048 (GRCm39)	M84K	probably damaging	Het
Tmem87b	T	A	2: 128,673,153 (GRCm39)	S196T	probably damaging	Het
Tnfrsf21	A	G	17: 43,348,768 (GRCm39)	T127A	probably benign	Het
Trp73	A	G	4: 154,148,406 (GRCm39)	I336T	probably benign	Het
Ttl	A	G	2: 128,917,981 (GRCm39)	I148V	probably damaging	Het
Ttll7	T	C	3: 146,649,970 (GRCm39)	Y667H	probably benign	Het
Ubr4	A	G	4: 139,119,171 (GRCm39)	T152A	probably damaging	Het
Vmn1r58	A	T	7: 5,413,636 (GRCm39)	V198E	probably damaging	Het
Vps52	T	A	17: 34,181,091 (GRCm39)	F376L	probably benign	Het
Zfp1007	T	C	5: 109,824,754 (GRCm39)	E232G	probably benign	Het

Other mutations in Ntn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00155:Ntn1	APN	11	68,117,445 (GRCm39)	splice site	probably benign
IGL00972:Ntn1	APN	11	68,104,098 (GRCm39)	missense	possibly damaging	0.83
IGL01695:Ntn1	APN	11	68,117,430 (GRCm39)	missense	probably benign	0.00
IGL01731:Ntn1	APN	11	68,276,244 (GRCm39)	missense	probably damaging	1.00
IGL02008:Ntn1	APN	11	68,104,089 (GRCm39)	missense	probably damaging	1.00
IGL02584:Ntn1	APN	11	68,168,356 (GRCm39)	missense	probably damaging	1.00
IGL02664:Ntn1	APN	11	68,276,295 (GRCm39)	missense	probably benign	0.06
R1201:Ntn1	UTSW	11	68,104,052 (GRCm39)	missense	probably damaging	0.96
R1268:Ntn1	UTSW	11	68,103,959 (GRCm39)	small deletion	probably benign
R1913:Ntn1	UTSW	11	68,104,011 (GRCm39)	missense	probably damaging	1.00
R2245:Ntn1	UTSW	11	68,276,120 (GRCm39)	missense	probably benign	0.12
R2248:Ntn1	UTSW	11	68,168,398 (GRCm39)	missense	possibly damaging	0.95
R2359:Ntn1	UTSW	11	68,276,438 (GRCm39)	missense	probably damaging	1.00
R2862:Ntn1	UTSW	11	68,276,690 (GRCm39)	missense	probably benign	0.00
R3830:Ntn1	UTSW	11	68,276,619 (GRCm39)	missense	probably damaging	1.00
R3851:Ntn1	UTSW	11	68,276,619 (GRCm39)	missense	probably damaging	1.00
R3852:Ntn1	UTSW	11	68,276,619 (GRCm39)	missense	probably damaging	1.00
R4413:Ntn1	UTSW	11	68,276,736 (GRCm39)	missense	probably damaging	1.00
R4870:Ntn1	UTSW	11	68,103,852 (GRCm39)	small deletion	probably benign
R4871:Ntn1	UTSW	11	68,103,852 (GRCm39)	small deletion	probably benign
R4952:Ntn1	UTSW	11	68,103,852 (GRCm39)	small deletion	probably benign
R5001:Ntn1	UTSW	11	68,151,358 (GRCm39)	missense	probably damaging	1.00
R5279:Ntn1	UTSW	11	68,276,538 (GRCm39)	missense	probably benign	0.37
R6217:Ntn1	UTSW	11	68,104,158 (GRCm39)	missense	possibly damaging	0.91
R6505:Ntn1	UTSW	11	68,104,025 (GRCm39)	missense	probably damaging	1.00
R6669:Ntn1	UTSW	11	68,276,576 (GRCm39)	missense	probably benign	0.00
R7172:Ntn1	UTSW	11	68,276,493 (GRCm39)	missense	probably damaging	1.00
R7411:Ntn1	UTSW	11	68,276,915 (GRCm39)	missense	probably benign	0.15
R8314:Ntn1	UTSW	11	68,276,450 (GRCm39)	missense	probably damaging	1.00
R9216:Ntn1	UTSW	11	68,117,397 (GRCm39)	missense	possibly damaging	0.76
R9385:Ntn1	UTSW	11	68,276,013 (GRCm39)	missense	probably damaging	1.00
R9442:Ntn1	UTSW	11	68,148,485 (GRCm39)	intron	probably benign
R9697:Ntn1	UTSW	11	68,168,356 (GRCm39)	missense	probably damaging	1.00
R9752:Ntn1	UTSW	11	68,276,712 (GRCm39)	missense	possibly damaging	0.80
X0027:Ntn1	UTSW	11	68,276,462 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGTTGTGCCTACAGTCACACACC -3'
(R):5'- GACCTATGTGAGCCTGCAATTCTGC -3'

Sequencing Primer
(F):5'- CACTGCATAGTAATAGGAGTCGC -3'
(R):5'- GCAATTCTGCTCGCCGC -3'

Posted On

2013-04-24