Mutagenetix > Incidental Mutation

Incidental Mutation 'R3839:Slit3'

277060

Institutional Source

Beutler Lab

Gene Symbol

Slit3

Ensembl Gene

ENSMUSG00000056427

Gene Name

slit guidance ligand 3

Synonyms

Slit1, b2b2362.1Clo

MMRRC Submission

040892-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.871) question?

Stock #

R3839 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

35012283-35599334 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 35399064 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 143 (N143I)

Ref Sequence

ENSEMBL: ENSMUSP00000066857 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000069837]

AlphaFold

Q9WVB4

Predicted Effect

probably benign
Transcript: ENSMUST00000069837
AA Change: N143I

PolyPhen 2 Score 0.099 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427
AA Change: N143I

Domain	Start	End	E-Value	Type
low complexity region	2	23	N/A	INTRINSIC
LRRNT	33	65	2.12e-8	SMART
LRR	59	83	1.37e2	SMART
LRR_TYP	84	107	1.12e-3	SMART
LRR_TYP	108	131	7.78e-3	SMART
LRR_TYP	132	155	5.42e-2	SMART
LRR	156	179	5.88e0	SMART
LRR	180	203	7.55e-1	SMART
LRRCT	215	264	1.33e-6	SMART
LRRNT	279	311	6.79e-7	SMART
LRR	305	329	1.16e2	SMART
LRR	330	353	1.26e1	SMART
LRR_TYP	354	377	2.79e-4	SMART
LRR	378	401	4.05e-1	SMART
LRR	402	425	4.05e-1	SMART
LRRCT	437	486	7.75e-8	SMART
LRRNT	504	536	1.95e-7	SMART
LRR_TYP	556	579	7.49e-5	SMART
LRR	581	603	6.41e1	SMART
LRR_TYP	604	627	2.53e-2	SMART
LRR	628	651	1.76e-1	SMART
LRRCT	663	712	2.52e-7	SMART
LRRNT	724	756	3e-8	SMART
LRR	774	797	2.14e0	SMART
LRR_TYP	798	821	2.95e-3	SMART
LRR_TYP	822	845	2.43e-4	SMART
LRRCT	857	906	1.12e-13	SMART
EGF	919	953	6.86e-4	SMART
EGF	958	994	8.84e-7	SMART
EGF	999	1032	1.13e-4	SMART
EGF	1037	1072	2.3e-5	SMART
EGF_CA	1074	1110	5.92e-8	SMART
EGF	1122	1155	3.79e-6	SMART
LamG	1178	1314	3.16e-34	SMART
EGF	1331	1365	2.19e-2	SMART
EGF	1371	1403	1.13e-4	SMART
EGF	1411	1444	5.57e-4	SMART
CT	1455	1523	4.56e-5	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153098

Meta Mutation Damage Score

0.9367

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.8%
20x: 96.4%

Validation Efficiency

98% (48/49)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is secreted, likely interacting with roundabout homolog receptors to effect cell migration. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]
PHENOTYPE: Mice homozygous for a gene trap allele show congenital diaphragmatic hernia (CDH), variable renal defects and enlarged heart right ventricles. Mice homozygous for either of two reporter alleles show diaphragm dysgenesis and die prematurely; those with end-stage CDH show dyspnea and lung congestion. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700028I16Rik	A	G	10: 82,648,219 (GRCm39)		noncoding transcript	Het
Abraxas2	T	A	7: 132,484,867 (GRCm39)	S303R	probably benign	Het
Ackr3	G	A	1: 90,141,850 (GRCm39)	S103N	probably damaging	Het
Arhgef25	T	C	10: 127,025,605 (GRCm39)	T12A	probably benign	Het
Aspm	C	T	1: 139,405,792 (GRCm39)	H1560Y	probably benign	Het
Atg10	A	T	13: 91,085,499 (GRCm39)	I150K	probably damaging	Het
AW551984	T	C	9: 39,509,204 (GRCm39)		probably benign	Het
Cald1	A	T	6: 34,722,700 (GRCm39)	D122V	probably damaging	Het
Cc2d2a	T	C	5: 43,876,056 (GRCm39)	V1011A	probably benign	Het
Cdh9	G	T	15: 16,823,524 (GRCm39)	E169*	probably null	Het
Cmbl	T	C	15: 31,582,144 (GRCm39)	V47A	probably damaging	Het
Col9a2	C	G	4: 120,911,455 (GRCm39)	R599G	probably damaging	Het
Ctnnd2	T	A	15: 31,009,174 (GRCm39)		probably null	Het
Cyp4a10	A	C	4: 115,382,544 (GRCm39)	E278A	possibly damaging	Het
Ddx56	T	C	11: 6,217,712 (GRCm39)	D3G	probably benign	Het
Dnajb2	G	A	1: 75,218,124 (GRCm39)		probably null	Het
Eif3d	T	A	15: 77,848,300 (GRCm39)	T211S	probably benign	Het
Fam13c	C	T	10: 70,378,478 (GRCm39)	S336L	probably damaging	Het
Garnl3	C	T	2: 32,879,558 (GRCm39)	G923S	probably benign	Het
Gcnt4	A	T	13: 97,083,522 (GRCm39)	R273*	probably null	Het
Gldc	T	A	19: 30,096,075 (GRCm39)		probably benign	Het
Glra2	C	T	X: 164,072,612 (GRCm39)	V85I	probably benign	Het
Gm10608	CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	CAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA	9: 118,989,784 (GRCm39)		probably null	Het
Gpam	T	C	19: 55,068,890 (GRCm39)	N450S	probably benign	Het
Gpr156	T	A	16: 37,808,962 (GRCm39)	V228D	probably damaging	Het
Hivep2	C	A	10: 14,004,713 (GRCm39)	T437K	probably benign	Het
Hmgcr	A	G	13: 96,795,597 (GRCm39)	I324T	probably benign	Het
Itga3	A	G	11: 94,948,095 (GRCm39)		probably null	Het
Itih1	T	A	14: 30,657,785 (GRCm39)	N429Y	probably damaging	Het
Klhl40	A	G	9: 121,609,482 (GRCm39)	Y453C	possibly damaging	Het
Mid1ip1	T	C	X: 10,584,620 (GRCm39)	V51A	possibly damaging	Het
Msn	C	A	X: 95,203,805 (GRCm39)	Q303K	probably damaging	Het
Nap1l1	T	A	10: 111,331,183 (GRCm39)		probably null	Het
Rala	A	T	13: 18,067,759 (GRCm39)	C91S	probably damaging	Het
Rps9	A	G	7: 3,709,823 (GRCm39)		probably benign	Het
Sdr16c5	C	A	4: 4,006,601 (GRCm39)	M230I	probably damaging	Het
Sec14l3	A	G	11: 4,021,544 (GRCm39)		probably null	Het
Senp2	T	C	16: 21,828,485 (GRCm39)	S32P	probably damaging	Het
Skor1	A	C	9: 63,051,730 (GRCm39)	S746R	probably damaging	Het
Slc17a4	C	T	13: 24,085,752 (GRCm39)	R387H	probably benign	Het
Slc47a1	G	T	11: 61,243,884 (GRCm39)		probably benign	Het
Tpbg	T	C	9: 85,725,167 (GRCm39)		probably benign	Het
Tubb2a	G	T	13: 34,259,294 (GRCm39)	N165K	probably benign	Het
Usp14	A	G	18: 10,024,532 (GRCm39)		probably null	Het
Vmn2r109	A	G	17: 20,774,704 (GRCm39)	V217A	probably damaging	Het
Zfp108	A	G	7: 23,959,981 (GRCm39)	I191V	probably benign	Het

Other mutations in Slit3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00731:Slit3	APN	11	35,512,981 (GRCm39)	missense	probably damaging	1.00
IGL01324:Slit3	APN	11	35,501,529 (GRCm39)	missense	probably damaging	1.00
IGL01612:Slit3	APN	11	35,591,211 (GRCm39)	missense	possibly damaging	0.95
IGL02145:Slit3	APN	11	35,520,569 (GRCm39)	missense	probably damaging	0.99
IGL02146:Slit3	APN	11	35,125,675 (GRCm39)	missense	possibly damaging	0.71
IGL02430:Slit3	APN	11	35,068,601 (GRCm39)	splice site	probably null
IGL02528:Slit3	APN	11	35,469,801 (GRCm39)	missense	probably benign
IGL02530:Slit3	APN	11	35,598,969 (GRCm39)	makesense	probably null
IGL02640:Slit3	APN	11	35,591,172 (GRCm39)	missense	probably benign	0.10
IGL02819:Slit3	APN	11	35,062,417 (GRCm39)	missense	possibly damaging	0.71
IGL02839:Slit3	APN	11	35,539,874 (GRCm39)	missense	possibly damaging	0.46
IGL03150:Slit3	APN	11	35,399,084 (GRCm39)	missense	possibly damaging	0.88
IGL03161:Slit3	APN	11	35,591,241 (GRCm39)	missense	probably benign	0.10
IGL03336:Slit3	APN	11	35,560,928 (GRCm39)	missense	probably damaging	0.97
Bloated	UTSW	11	35,524,779 (GRCm39)	missense	possibly damaging	0.55
Quellung	UTSW	11	35,542,647 (GRCm39)	critical splice donor site	probably null
IGL02988:Slit3	UTSW	11	35,598,890 (GRCm39)	missense	probably damaging	0.99
PIT4791001:Slit3	UTSW	11	35,552,072 (GRCm39)	missense	possibly damaging	0.85
R0013:Slit3	UTSW	11	35,598,745 (GRCm39)	missense	probably benign
R0013:Slit3	UTSW	11	35,598,745 (GRCm39)	missense	probably benign
R0334:Slit3	UTSW	11	35,469,928 (GRCm39)	missense	probably damaging	0.97
R0385:Slit3	UTSW	11	35,591,109 (GRCm39)	missense	probably damaging	0.98
R0840:Slit3	UTSW	11	35,514,263 (GRCm39)	splice site	probably benign
R1065:Slit3	UTSW	11	35,012,462 (GRCm39)	missense	possibly damaging	0.86
R1364:Slit3	UTSW	11	35,560,934 (GRCm39)	missense	probably benign
R1476:Slit3	UTSW	11	35,577,126 (GRCm39)	missense	probably damaging	0.97
R1508:Slit3	UTSW	11	35,461,448 (GRCm39)	missense	probably damaging	1.00
R1665:Slit3	UTSW	11	35,125,733 (GRCm39)	missense	possibly damaging	0.71
R1692:Slit3	UTSW	11	35,550,171 (GRCm39)	missense	probably damaging	1.00
R1696:Slit3	UTSW	11	35,566,750 (GRCm39)	missense	probably damaging	0.99
R1727:Slit3	UTSW	11	35,520,659 (GRCm39)	missense	probably damaging	1.00
R1752:Slit3	UTSW	11	35,455,480 (GRCm39)	missense	probably damaging	0.98
R1970:Slit3	UTSW	11	35,521,668 (GRCm39)	critical splice acceptor site	probably null
R2077:Slit3	UTSW	11	35,435,575 (GRCm39)	missense	possibly damaging	0.88
R2126:Slit3	UTSW	11	35,579,506 (GRCm39)	missense	probably damaging	1.00
R2143:Slit3	UTSW	11	35,503,088 (GRCm39)	splice site	probably null
R2162:Slit3	UTSW	11	35,579,509 (GRCm39)	missense	probably null	1.00
R2873:Slit3	UTSW	11	35,435,620 (GRCm39)	nonsense	probably null
R3813:Slit3	UTSW	11	35,566,806 (GRCm39)	missense	probably damaging	1.00
R3831:Slit3	UTSW	11	35,579,509 (GRCm39)	missense	probably null	1.00
R3832:Slit3	UTSW	11	35,579,509 (GRCm39)	missense	probably null	1.00
R3833:Slit3	UTSW	11	35,579,509 (GRCm39)	missense	probably null	1.00
R4152:Slit3	UTSW	11	35,589,147 (GRCm39)	missense	probably damaging	0.98
R4387:Slit3	UTSW	11	35,574,875 (GRCm39)	missense	probably benign	0.12
R4795:Slit3	UTSW	11	35,542,647 (GRCm39)	critical splice donor site	probably null
R4910:Slit3	UTSW	11	35,523,549 (GRCm39)	missense	probably damaging	0.99
R4933:Slit3	UTSW	11	35,579,420 (GRCm39)	missense	probably damaging	1.00
R5048:Slit3	UTSW	11	35,479,812 (GRCm39)	missense	probably damaging	1.00
R5106:Slit3	UTSW	11	35,503,194 (GRCm39)	missense	probably damaging	1.00
R5138:Slit3	UTSW	11	35,479,812 (GRCm39)	missense	probably damaging	1.00
R5218:Slit3	UTSW	11	35,575,002 (GRCm39)	critical splice donor site	probably null
R5338:Slit3	UTSW	11	35,512,975 (GRCm39)	missense	probably benign
R5354:Slit3	UTSW	11	35,566,740 (GRCm39)	missense	probably damaging	1.00
R5436:Slit3	UTSW	11	35,598,738 (GRCm39)	missense	probably benign	0.05
R5896:Slit3	UTSW	11	35,598,932 (GRCm39)	missense	probably damaging	0.99
R5933:Slit3	UTSW	11	35,520,578 (GRCm39)	missense	probably benign	0.04
R5963:Slit3	UTSW	11	35,591,063 (GRCm39)	missense	probably damaging	1.00
R5964:Slit3	UTSW	11	35,591,063 (GRCm39)	missense	probably damaging	1.00
R6125:Slit3	UTSW	11	35,461,560 (GRCm39)	critical splice donor site	probably null
R6153:Slit3	UTSW	11	35,591,310 (GRCm39)	missense	possibly damaging	0.69
R6484:Slit3	UTSW	11	35,552,125 (GRCm39)	missense	probably benign
R6526:Slit3	UTSW	11	35,552,119 (GRCm39)	missense	probably benign	0.33
R6797:Slit3	UTSW	11	35,524,779 (GRCm39)	missense	possibly damaging	0.55
R6887:Slit3	UTSW	11	35,435,633 (GRCm39)	splice site	probably null
R7067:Slit3	UTSW	11	35,399,057 (GRCm39)	missense	probably benign	0.04
R7150:Slit3	UTSW	11	35,461,546 (GRCm39)	missense	probably damaging	1.00
R7228:Slit3	UTSW	11	35,490,245 (GRCm39)	missense	probably damaging	1.00
R7232:Slit3	UTSW	11	35,501,516 (GRCm39)	missense	possibly damaging	0.87
R7418:Slit3	UTSW	11	35,577,255 (GRCm39)	missense	possibly damaging	0.64
R7545:Slit3	UTSW	11	35,591,139 (GRCm39)	missense	possibly damaging	0.52
R7727:Slit3	UTSW	11	35,574,871 (GRCm39)	missense	probably damaging	1.00
R7820:Slit3	UTSW	11	35,591,235 (GRCm39)	missense	probably benign	0.23
R8177:Slit3	UTSW	11	35,469,919 (GRCm39)	missense	probably damaging	0.99
R8179:Slit3	UTSW	11	35,554,903 (GRCm39)	missense	probably benign	0.31
R8416:Slit3	UTSW	11	35,399,062 (GRCm39)	missense	probably benign	0.08
R8417:Slit3	UTSW	11	35,501,438 (GRCm39)	missense	probably damaging	0.99
R8476:Slit3	UTSW	11	35,520,596 (GRCm39)	missense	possibly damaging	0.70
R8785:Slit3	UTSW	11	35,560,968 (GRCm39)	missense	probably damaging	0.98
R8955:Slit3	UTSW	11	35,589,207 (GRCm39)	missense	probably damaging	0.97
R9040:Slit3	UTSW	11	35,594,136 (GRCm39)	missense	probably damaging	0.98
R9068:Slit3	UTSW	11	35,574,917 (GRCm39)	missense	probably damaging	1.00
R9088:Slit3	UTSW	11	35,012,463 (GRCm39)	missense	possibly damaging	0.86
R9266:Slit3	UTSW	11	35,598,808 (GRCm39)	missense	probably damaging	0.98
R9539:Slit3	UTSW	11	35,589,155 (GRCm39)	nonsense	probably null
R9636:Slit3	UTSW	11	35,594,088 (GRCm39)	missense	probably damaging	0.97
X0028:Slit3	UTSW	11	35,455,464 (GRCm39)	missense	probably damaging	0.99
Z1176:Slit3	UTSW	11	35,598,751 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- AATGCCTGCCCTGAAGCAAG -3'
(R):5'- AAGCTCCCCATGTTCCAAG -3'

Sequencing Primer
(F):5'- CCATTTCTGCAGAACAATGTGC -3'
(R):5'- ATGTTCCAAGCCACCAGGAGTG -3'

Posted On

2015-04-06