Mutagenetix > Incidental Mutation

Incidental Mutation 'R3832:Slit3'

274070

Institutional Source

Beutler Lab

Gene Symbol

Slit3

Ensembl Gene

ENSMUSG00000056427

Gene Name

slit guidance ligand 3

Synonyms

Slit1, b2b2362.1Clo

MMRRC Submission

040887-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.871) question?

Stock #

R3832 (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 35579509 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Cysteine at position 1229 (S1229C)

Ref Sequence

ENSEMBL: ENSMUSP00000066857 (fasta)

Gene Model

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

AlphaFold

Q9WVB4

Predicted Effect

probably null
Transcript: ENSMUST00000069837
AA Change: S1229C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427
AA Change: S1229C

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

probably null
Transcript: ENSMUST00000069837
AA Change: S1229C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000066857
Gene: ENSMUSG00000056427
AA Change: S1229C

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

Meta Mutation Damage Score

0.7421

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.7%

Validation Efficiency

98% (54/55)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts20	A	C	15: 94,229,339 (GRCm39)	C927G	probably damaging	Het
Afdn	T	A	17: 14,116,436 (GRCm39)	D190E	probably benign	Het
Aldh1a7	T	C	19: 20,685,602 (GRCm39)	Y316C	probably damaging	Het
Arhgef38	T	C	3: 132,912,686 (GRCm39)	R118G	possibly damaging	Het
Bcar3	A	G	3: 122,220,298 (GRCm39)	D65G	probably damaging	Het
Cacna1i	T	C	15: 80,240,388 (GRCm39)	F370S	probably damaging	Het
Cacnb2	A	T	2: 14,986,236 (GRCm39)	I338F	probably damaging	Het
Cblc	T	C	7: 19,526,097 (GRCm39)	M238V	probably damaging	Het
Ccdc3	A	G	2: 5,233,953 (GRCm39)	N259S	probably benign	Het
Cep55	A	G	19: 38,041,560 (GRCm39)		probably benign	Het
Col6a1	T	C	10: 76,546,951 (GRCm39)	D757G	unknown	Het
Csmd3	CCTTTGCGCTT	CCTT	15: 47,604,632 (GRCm39)		probably null	Het
Cyb5d2	G	T	11: 72,686,349 (GRCm39)	S80R	possibly damaging	Het
Cyfip2	T	C	11: 46,152,333 (GRCm39)	D485G	probably benign	Het
Cyp27b1	G	T	10: 126,886,929 (GRCm39)	V382L	probably damaging	Het
Erich3	G	A	3: 154,467,998 (GRCm39)	V817M	probably damaging	Het
Gdf6	T	C	4: 9,844,568 (GRCm39)	S31P	probably benign	Het
Gtsf1	T	C	15: 103,333,902 (GRCm39)	I25V	probably damaging	Het
Hephl1	T	C	9: 14,981,044 (GRCm39)	E796G	probably damaging	Het
Iglv2	A	T	16: 19,079,593 (GRCm39)	M1K	probably null	Het
Kif26b	GAAA	GAA	1: 178,744,181 (GRCm39)		probably null	Het
Klhl28	C	A	12: 64,998,195 (GRCm39)	G433V	probably damaging	Het
Lipn	T	C	19: 34,046,933 (GRCm39)		probably null	Het
Lypd10	T	A	7: 24,413,712 (GRCm39)	S243T	probably benign	Het
Mapk7	A	G	11: 61,380,680 (GRCm39)	S641P	possibly damaging	Het
Med22	A	G	2: 26,800,379 (GRCm39)	S17P	probably damaging	Het
Or14c44	A	T	7: 86,062,401 (GRCm39)	Y277F	probably damaging	Het
Or14j5	T	C	17: 38,162,071 (GRCm39)	V196A	probably benign	Het
Otud1	G	C	2: 19,662,951 (GRCm39)	A27P	possibly damaging	Het
Pcdhga6	A	T	18: 37,841,479 (GRCm39)	N400Y	probably damaging	Het
Pdgfd	T	C	9: 6,359,762 (GRCm39)	S278P	probably damaging	Het
Pdzd7	A	T	19: 45,028,693 (GRCm39)	V150E	probably damaging	Het
Peak1	T	C	9: 56,165,667 (GRCm39)	S754G	probably benign	Het
Phf14	A	G	6: 11,933,873 (GRCm39)		probably null	Het
Phlpp1	G	A	1: 106,320,327 (GRCm39)	E1441K	probably damaging	Het
Piezo2	A	G	18: 63,214,733 (GRCm39)		probably null	Het
Pikfyve	G	A	1: 65,283,579 (GRCm39)	V739I	probably damaging	Het
Plcg1	T	G	2: 160,596,357 (GRCm39)	M651R	possibly damaging	Het
Prex2	T	C	1: 11,226,588 (GRCm39)		probably benign	Het
Pus3	G	C	9: 35,477,874 (GRCm39)	G369R	probably benign	Het
Rab11fip1	G	A	8: 27,642,774 (GRCm39)	T675I	probably benign	Het
Scarf1	T	C	11: 75,406,078 (GRCm39)	C121R	probably damaging	Het
Sco1	T	C	11: 66,944,605 (GRCm39)	V76A	probably damaging	Het
Slc39a8	T	A	3: 135,554,894 (GRCm39)	C113S	probably damaging	Het
Snd1	G	T	6: 28,531,403 (GRCm39)		probably benign	Het
Tbc1d9	A	G	8: 83,960,292 (GRCm39)	S182G	probably damaging	Het
Tecta	A	C	9: 42,250,329 (GRCm39)	F1816C	probably damaging	Het
Tekt1	T	C	11: 72,245,645 (GRCm39)	N170S	probably benign	Het
Trim47	T	C	11: 115,998,783 (GRCm39)	T279A	probably benign	Het
Ttll4	A	G	1: 74,725,550 (GRCm39)	K653E	probably damaging	Het
Vcam1	T	C	3: 115,908,140 (GRCm39)	T641A	possibly damaging	Het
Vmn1r16	A	G	6: 57,300,212 (GRCm39)	F137L	probably benign	Het
Vmn2r17	T	A	5: 109,576,262 (GRCm39)	W378R	probably damaging	Het
Zfp777	T	C	6: 48,021,149 (GRCm39)	T158A	probably benign	Het
Zp1	T	C	19: 10,893,888 (GRCm39)	D439G	probably damaging	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
R3833:Slit3	UTSW	11	35,579,509 (GRCm39)	missense	probably null	1.00
R3839:Slit3	UTSW	11	35,399,064 (GRCm39)	missense	probably benign	0.10
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'- CATCTGAAGAGGGTGCTAGG -3'
(R):5'- GTAATGAGGTGTCATCTCCCAC -3'

Sequencing Primer
(F):5'- CTAGGCATGGGTCAGGTGAG -3'
(R):5'- ACATGGGCCTGCCTTCC -3'

Posted On

2015-04-02