Mutagenetix > Incidental Mutation

Incidental Mutation 'R5279:Ntn1'

404125

Institutional Source

Beutler Lab

Gene Symbol

Ntn1

Ensembl Gene

ENSMUSG00000020902

Gene Name

netrin 1

Synonyms

Netrin-1

MMRRC Submission

042839-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.723) question?

Stock #

R5279 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

68209364-68400823 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 68385712 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 137 (S137P)

Ref Sequence

ENSEMBL: ENSMUSP00000121193 (fasta)

Gene Model

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

AlphaFold

O09118

Predicted Effect

probably benign
Transcript: ENSMUST00000021284
AA Change: S137P

PolyPhen 2 Score 0.370 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000021284
Gene: ENSMUSG00000020902
AA Change: S137P

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: S137P

PolyPhen 2 Score 0.370 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000104314
Gene: ENSMUSG00000020902
AA Change: S137P

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
AA Change: S137P

PolyPhen 2 Score 0.370 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000121193
Gene: ENSMUSG00000020902
AA Change: S137P

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

Meta Mutation Damage Score

0.1901

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.4%

Validation Efficiency

99% (73/74)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca17	C	A	17: 24,289,414	G1049V	probably damaging	Het
Afdn	G	A	17: 13,888,952	R1579H	probably damaging	Het
Ankrd28	T	A	14: 31,735,006	N386Y	probably damaging	Het
Atf7ip	T	A	6: 136,603,379	Y1100*	probably null	Het
Atp9b	T	A	18: 80,912,858	E3V	probably damaging	Het
AW554918	T	G	18: 25,175,431	D60E	possibly damaging	Het
Baz2b	G	T	2: 59,932,152	Q927K	probably damaging	Het
Birc6	A	G	17: 74,650,047	R3659G	probably damaging	Het
C8a	T	G	4: 104,845,988	N291H	probably damaging	Het
Calcoco1	G	A	15: 102,710,985	L390F	probably damaging	Het
Carmil3	A	G	14: 55,501,571	D894G	probably damaging	Het
Cdc20	A	G	4: 118,433,514	Y430H	probably damaging	Het
Cdc6	A	T	11: 98,912,262	I316F	probably damaging	Het
Cenpu	T	A	8: 46,578,910		probably null	Het
Csmd2	T	A	4: 128,456,914	V1592D	probably benign	Het
Csmd3	G	T	15: 48,791,944		probably null	Het
Dnah7c	T	C	1: 46,519,269	F512L	probably benign	Het
Fam136a	T	A	6: 86,366,704	L61Q	probably damaging	Het
Fpgs	A	C	2: 32,692,767		probably benign	Het
Fzd4	G	A	7: 89,407,673	M309I	probably benign	Het
Gad2	A	G	2: 22,673,957	T391A	probably benign	Het
Gm11563	A	T	11: 99,658,713	S72T	unknown	Het
Gm5155	T	A	7: 17,873,289		noncoding transcript	Het
Gon4l	A	G	3: 88,887,637	I716V	probably benign	Het
Itga9	T	C	9: 118,628,205	V128A	probably damaging	Het
Kat6a	CGCAGCAGCAGCAGCAGCA	CGCAGCAGCAGCA	8: 22,939,648		probably benign	Het
Lrrc9	T	A	12: 72,495,594	D1063E	possibly damaging	Het
Lyst	T	A	13: 13,648,802	L1453*	probably null	Het
Mcm3ap	T	C	10: 76,507,539	V1755A	probably damaging	Het
Mrc1	T	C	2: 14,310,058	S985P	probably damaging	Het
Mst1	A	C	9: 108,082,215	K233N	probably damaging	Het
Nr2c2ap	G	A	8: 70,132,003	D42N	probably damaging	Het
Pard3	T	C	8: 127,460,386		probably null	Het
Pcdh15	T	A	10: 74,594,183	D1210E	probably damaging	Het
Pcdhga5	T	C	18: 37,694,721	L74P	probably benign	Het
Pcsk5	T	C	19: 17,595,658		probably null	Het
Pdia3	T	C	2: 121,414,003		probably benign	Het
Pikfyve	A	T	1: 65,196,699	R177*	probably null	Het
Pklr	A	G	3: 89,143,259	E409G	probably damaging	Het
Plod2	T	C	9: 92,581,323	Y154H	probably damaging	Het
Psmc3	T	A	2: 91,054,322	D6E	probably benign	Het
Ptpru	T	A	4: 131,820,023	N205I	possibly damaging	Het
Rbm6	T	C	9: 107,778,014	E1006G	probably benign	Het
Rgl2	T	C	17: 33,935,948	V642A	probably benign	Het
Rnf8	T	A	17: 29,626,706	H104Q	possibly damaging	Het
Robo4	CGG	CG	9: 37,411,490		probably null	Het
Rpa1	T	C	11: 75,313,344	N269S	probably damaging	Het
Sdk2	A	G	11: 113,867,031	M519T	probably benign	Het
Snx30	A	G	4: 59,885,070	S237G	probably benign	Het
Spx	A	G	6: 142,414,040	N36S	probably damaging	Het
Stard7	T	C	2: 127,295,496	Y289H	probably damaging	Het
Sugp2	T	C	8: 70,257,107		probably benign	Het
Susd4	C	T	1: 182,887,478	T288I	probably damaging	Het
Tceanc2	T	A	4: 107,177,629		probably null	Het
Tm4sf4	T	G	3: 57,433,738	V97G	probably benign	Het
Tmtc1	C	T	6: 148,355,131		probably benign	Het
Trappc11	C	T	8: 47,505,304		probably benign	Het
Triobp	G	T	15: 78,994,391	V398F	possibly damaging	Het
Ttll9	T	A	2: 152,962,544	S2T	possibly damaging	Het
Ttn	T	C	2: 76,900,976		probably benign	Het
Tyw3	A	G	3: 154,594,471	C80R	probably damaging	Het
Usp24	T	C	4: 106,385,424	V1177A	possibly damaging	Het
Vmn1r65	A	G	7: 6,008,755	V160A	probably damaging	Het
Vmn2r104	T	A	17: 20,041,884	H328L	probably benign	Het
Vmn2r65	A	C	7: 84,940,641	I689S	probably damaging	Het
Wrn	A	G	8: 33,241,101	Y1068H	probably damaging	Het
Xpo4	C	A	14: 57,613,409	S346I	probably benign	Het
Zc3h3	T	A	15: 75,839,590	T341S	probably benign	Het
Zxdc	T	C	6: 90,370,437	M260T	possibly damaging	Het

Other mutations in Ntn1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00155:Ntn1	APN	11	68226619	splice site	probably benign
IGL00972:Ntn1	APN	11	68213272	missense	possibly damaging	0.83
IGL01695:Ntn1	APN	11	68226604	missense	probably benign	0.00
IGL01731:Ntn1	APN	11	68385418	missense	probably damaging	1.00
IGL02008:Ntn1	APN	11	68213263	missense	probably damaging	1.00
IGL02584:Ntn1	APN	11	68277530	missense	probably damaging	1.00
IGL02664:Ntn1	APN	11	68385469	missense	probably benign	0.06
R0363:Ntn1	UTSW	11	68385543	missense	probably benign	0.44
R1201:Ntn1	UTSW	11	68213226	missense	probably damaging	0.96
R1268:Ntn1	UTSW	11	68213133	small deletion	probably benign
R1913:Ntn1	UTSW	11	68213185	missense	probably damaging	1.00
R2245:Ntn1	UTSW	11	68385294	missense	probably benign	0.12
R2248:Ntn1	UTSW	11	68277572	missense	possibly damaging	0.95
R2359:Ntn1	UTSW	11	68385612	missense	probably damaging	1.00
R2862:Ntn1	UTSW	11	68385864	missense	probably benign	0.00
R3830:Ntn1	UTSW	11	68385793	missense	probably damaging	1.00
R3851:Ntn1	UTSW	11	68385793	missense	probably damaging	1.00
R3852:Ntn1	UTSW	11	68385793	missense	probably damaging	1.00
R4413:Ntn1	UTSW	11	68385910	missense	probably damaging	1.00
R4870:Ntn1	UTSW	11	68213026	small deletion	probably benign
R4871:Ntn1	UTSW	11	68213026	small deletion	probably benign
R4952:Ntn1	UTSW	11	68213026	small deletion	probably benign
R5001:Ntn1	UTSW	11	68260532	missense	probably damaging	1.00
R6217:Ntn1	UTSW	11	68213332	missense	possibly damaging	0.91
R6505:Ntn1	UTSW	11	68213199	missense	probably damaging	1.00
R6669:Ntn1	UTSW	11	68385750	missense	probably benign	0.00
R7172:Ntn1	UTSW	11	68385667	missense	probably damaging	1.00
R7411:Ntn1	UTSW	11	68386089	missense	probably benign	0.15
R8314:Ntn1	UTSW	11	68385624	missense	probably damaging	1.00
R9216:Ntn1	UTSW	11	68226571	missense	possibly damaging	0.76
R9385:Ntn1	UTSW	11	68385187	missense	probably damaging	1.00
R9442:Ntn1	UTSW	11	68257659	intron	probably benign
R9697:Ntn1	UTSW	11	68277530	missense	probably damaging	1.00
R9752:Ntn1	UTSW	11	68385886	missense	possibly damaging	0.80
X0027:Ntn1	UTSW	11	68385636	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATAGTAATAGGAGTCGCGCG -3'
(R):5'- ACTTTGTCAACGCGGCCTTC -3'

Sequencing Primer
(F):5'- TGAAAGCCACGCGGATGTC -3'
(R):5'- CTACTGCGTGGTGAGCGAG -3'

Posted On

2016-07-22