Mutagenetix > Incidental Mutations

Incidental Mutation 'R0432:Slit1'

38882

Institutional Source

Beutler Lab

Gene Symbol

Slit1

Ensembl Gene

ENSMUSG00000025020

Gene Name

slit guidance ligand 1

Synonyms

Slil1

MMRRC Submission

038634-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0432 (G1)

Quality Score

162

Status

Validated

Chromosome

Chromosomal Location

41600257-41743665 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 41743293 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 39 (T39I)

Ref Sequence

ENSEMBL: ENSMUSP00000128381 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025993] [ENSMUST00000166496] [ENSMUST00000169141] [ENSMUST00000171586]

Predicted Effect

probably damaging
Transcript: ENSMUST00000025993
AA Change: T39I

PolyPhen 2 Score 0.971 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000025993
Gene: ENSMUSG00000025020
AA Change: T39I

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
LRRNT	33	65	5.68e-9	SMART
LRR	59	83	4.58e1	SMART
LRR	84	107	4.7e0	SMART
LRR_TYP	108	131	1.95e-3	SMART
LRR	133	155	6.05e0	SMART
LRR	157	179	3.98e1	SMART
LRR_TYP	180	203	3.44e-4	SMART
LRRCT	215	264	3.51e-6	SMART
LRRNT	281	313	3e-8	SMART
LRR	307	331	6.41e1	SMART
LRR_TYP	332	355	8.22e-2	SMART
LRR_TYP	356	379	9.08e-4	SMART
LRR	380	403	2.82e0	SMART
LRR_TYP	404	427	5.42e-2	SMART
LRRCT	439	488	5.78e-7	SMART
LRRNT	512	544	1.04e-7	SMART
LRR_TYP	564	587	3.39e-3	SMART
LRR	589	611	2.08e1	SMART
LRR_TYP	612	635	1.56e-2	SMART
LRR_TYP	636	659	4.11e-2	SMART
LRRCT	671	720	2.89e-7	SMART
LRRNT	733	765	4.87e-8	SMART
LRR	783	806	1.22e1	SMART
LRR_TYP	807	830	9.73e-4	SMART
LRR_TYP	831	854	9.58e-3	SMART
LRRCT	866	915	5.6e-14	SMART
EGF	928	962	5.08e-7	SMART
EGF	967	1003	1.74e-5	SMART
EGF_CA	1005	1041	1.05e-8	SMART
EGF	1046	1081	1.21e-4	SMART
EGF_CA	1083	1119	3.64e-8	SMART
FOLN	1086	1108	8.44e0	SMART
FOLN	1127	1149	1.4e0	SMART
EGF	1127	1160	1.78e-2	SMART
LamG	1183	1319	4.43e-38	SMART
EGF	1338	1371	6.76e-3	SMART
EGF	1377	1410	3.38e-3	SMART
FOLN	1418	1440	2.25e1	SMART
EGF	1418	1451	1.28e-3	SMART
CT	1462	1531	3.15e-4	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000157595

Predicted Effect

probably damaging
Transcript: ENSMUST00000166496
AA Change: T39I

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000128381
Gene: ENSMUSG00000025020
AA Change: T39I

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
LRRNT	33	65	5.68e-9	SMART
LRR	59	83	4.58e1	SMART
LRR	84	107	4.7e0	SMART
LRR_TYP	108	131	1.95e-3	SMART
LRR	133	155	6.05e0	SMART
LRR	157	179	3.98e1	SMART
LRR_TYP	180	203	3.44e-4	SMART
LRRCT	215	264	3.51e-6	SMART
LRRNT	281	313	3e-8	SMART
LRR	307	331	6.41e1	SMART
LRR_TYP	332	355	8.22e-2	SMART
LRR_TYP	356	379	9.08e-4	SMART
LRR	380	403	2.82e0	SMART
LRR_TYP	404	427	5.42e-2	SMART
LRRCT	439	488	5.78e-7	SMART
LRRNT	512	544	1.04e-7	SMART
LRR_TYP	564	587	3.39e-3	SMART
LRR	589	611	2.08e1	SMART
LRR_TYP	612	635	1.56e-2	SMART
LRR_TYP	636	659	4.11e-2	SMART
LRRCT	671	720	2.89e-7	SMART
LRRNT	733	765	4.87e-8	SMART
LRR	783	806	1.22e1	SMART
LRR_TYP	807	830	9.73e-4	SMART
LRR_TYP	831	854	9.58e-3	SMART
LRRCT	866	915	5.6e-14	SMART
EGF	928	962	5.08e-7	SMART
EGF	967	1003	1.74e-5	SMART
EGF_CA	1005	1041	1.05e-8	SMART
EGF	1046	1081	1.21e-4	SMART
EGF_CA	1083	1119	3.64e-8	SMART
FOLN	1086	1108	8.44e0	SMART
FOLN	1127	1149	1.4e0	SMART
EGF	1127	1160	1.78e-2	SMART
LamG	1183	1319	4.43e-38	SMART
EGF	1338	1371	6.76e-3	SMART
EGF	1377	1410	3.38e-3	SMART
low complexity region	1437	1458	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000169141
AA Change: T39I

PolyPhen 2 Score 0.971 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000129034
Gene: ENSMUSG00000025020
AA Change: T39I

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
LRRNT	33	65	5.68e-9	SMART
LRR	59	83	4.58e1	SMART
LRR	84	107	4.7e0	SMART
LRR_TYP	108	131	1.95e-3	SMART
LRR	133	155	6.05e0	SMART
LRR	157	179	3.98e1	SMART
LRR_TYP	180	203	3.44e-4	SMART
LRRCT	215	264	3.51e-6	SMART
LRRNT	281	313	3e-8	SMART
LRR	307	331	6.41e1	SMART
LRR_TYP	332	355	8.22e-2	SMART
LRR_TYP	356	379	9.08e-4	SMART
LRR	380	403	2.82e0	SMART
LRR_TYP	404	427	5.42e-2	SMART
LRRCT	439	488	5.78e-7	SMART
LRRNT	512	544	1.04e-7	SMART
LRR_TYP	564	587	3.39e-3	SMART
LRR	589	611	2.08e1	SMART
LRR_TYP	612	635	1.56e-2	SMART
LRR_TYP	636	659	4.11e-2	SMART
LRRCT	671	720	2.89e-7	SMART
LRRNT	733	765	4.87e-8	SMART
LRR	783	806	1.22e1	SMART
LRR_TYP	807	830	9.73e-4	SMART
LRR_TYP	831	854	9.58e-3	SMART
LRRCT	866	915	5.6e-14	SMART
EGF	928	962	5.08e-7	SMART
EGF	967	1003	1.74e-5	SMART
EGF_CA	1005	1041	1.05e-8	SMART
EGF	1046	1081	1.21e-4	SMART
EGF_CA	1083	1119	3.64e-8	SMART
FOLN	1086	1108	8.44e0	SMART
FOLN	1127	1149	1.4e0	SMART
EGF	1127	1160	1.78e-2	SMART
LamG	1183	1319	4.43e-38	SMART
EGF	1338	1371	6.76e-3	SMART
EGF	1377	1410	3.38e-3	SMART
FOLN	1418	1440	2.25e1	SMART
EGF	1418	1451	1.28e-3	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000171586
AA Change: T39I

PolyPhen 2 Score 0.693 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000126139
Gene: ENSMUSG00000025020
AA Change: T39I

Domain	Start	End	E-Value	Type
signal peptide	1	32	N/A	INTRINSIC
LRRNT	33	65	5.68e-9	SMART
LRR	59	83	4.58e1	SMART
LRR	84	107	4.7e0	SMART
LRR_TYP	108	131	2.24e-3	SMART
LRR	133	155	3.98e1	SMART
LRR_TYP	156	179	3.44e-4	SMART
LRRCT	191	240	3.51e-6	SMART
LRRNT	257	289	3e-8	SMART
LRR	283	307	6.41e1	SMART
LRR_TYP	308	331	8.22e-2	SMART
LRR_TYP	332	355	9.08e-4	SMART
LRR	356	379	2.82e0	SMART

Meta Mutation Damage Score

0.2259

Coding Region Coverage

1x: 99.2%
3x: 98.3%
10x: 96.3%
20x: 92.9%

Validation Efficiency

99% (91/92)

MGI Phenotype

PHENOTYPE: Mice homozygous for a reporter allele exhibit normal interneuron numbers and morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310061I04Rik	A	G	17: 35,895,816	L110P	probably damaging	Het
4930522L14Rik	A	T	5: 109,736,919	C358S	probably damaging	Het
9330182L06Rik	G	T	5: 9,440,966	G659*	probably null	Het
Abca8b	C	A	11: 109,980,015	V104F	possibly damaging	Het
Afap1l2	T	C	19: 56,917,119		probably benign	Het
Ahctf1	A	C	1: 179,784,161	I548R	probably damaging	Het
Alox12b	G	T	11: 69,169,556	G646V	probably damaging	Het
Aoah	C	T	13: 20,911,198		probably benign	Het
Arhgap39	C	T	15: 76,734,886	D833N	probably damaging	Het
Atxn1l	A	G	8: 109,731,693	W646R	probably damaging	Het
Cabp2	T	C	19: 4,084,903	I28T	possibly damaging	Het
Cacna1b	G	A	2: 24,687,704	T719I	probably damaging	Het
Camk1d	A	T	2: 5,445,135	H70Q	probably damaging	Het
Car1	T	C	3: 14,770,176	T170A	probably benign	Het
Ccdc162	T	C	10: 41,541,860	T2113A	probably benign	Het
Cdc5l	G	A	17: 45,415,684	R321W	probably damaging	Het
Cdh17	T	A	4: 11,771,273	C18*	probably null	Het
Cdk17	A	T	10: 93,237,790		probably benign	Het
Chd9	T	A	8: 90,994,450		probably benign	Het
Chrm5	T	A	2: 112,479,655	K372M	possibly damaging	Het
Clasp2	A	G	9: 113,909,419	T423A	probably benign	Het
Col11a1	A	G	3: 114,205,901		probably benign	Het
Col27a1	T	C	4: 63,225,611	M512T	possibly damaging	Het
Dclk3	A	G	9: 111,484,935	D693G	probably damaging	Het
Dcun1d3	T	A	7: 119,857,950	K180*	probably null	Het
Dmxl2	T	C	9: 54,416,951	R876G	probably benign	Het
Dnmbp	A	T	19: 43,854,857	Y432*	probably null	Het
Eml2	C	T	7: 19,179,531	Q125*	probably null	Het
Faap100	A	C	11: 120,373,876		probably benign	Het
Foxp2	T	C	6: 15,254,279		probably benign	Het
Gda	A	G	19: 21,417,107	Y129H	probably damaging	Het
Gga3	G	A	11: 115,590,524	R207C	probably damaging	Het
Glg1	T	C	8: 111,182,569	I496M	probably damaging	Het
Glt6d1	C	A	2: 25,794,727		probably null	Het
Gm10322	A	T	10: 59,616,208	H49L	possibly damaging	Het
Golga5	G	T	12: 102,476,208	V269F	possibly damaging	Het
Gramd3	G	A	18: 56,474,069	C85Y	probably benign	Het
Grhl1	C	T	12: 24,582,919	P153L	probably benign	Het
Hdac9	T	C	12: 34,437,222	Q60R	probably damaging	Het
Hdlbp	T	C	1: 93,425,332	I414V	probably damaging	Het
Itpk1	C	T	12: 102,606,078		probably benign	Het
Itsn1	T	A	16: 91,815,520	Y266N	probably damaging	Het
Lipe	G	A	7: 25,398,488	P10L	probably benign	Het
Lrrc8a	A	G	2: 30,257,067	E631G	probably damaging	Het
Lvrn	T	A	18: 46,905,299	N973K	possibly damaging	Het
Man2c1	T	A	9: 57,135,597	H250Q	probably damaging	Het
Mup3	T	C	4: 62,085,282	T117A	probably benign	Het
Myo6	A	C	9: 80,273,974		probably benign	Het
Nbn	T	A	4: 15,983,951		probably benign	Het
Ncapg	T	A	5: 45,672,428	N157K	probably damaging	Het
Olfr1024	T	A	2: 85,904,157	N299I	probably damaging	Het
Olfr1137	G	A	2: 87,711,430	H159Y	probably benign	Het
Olfr1154	T	C	2: 87,902,960	T239A	probably damaging	Het
Olfr1178	C	T	2: 88,392,033	T262I	probably damaging	Het
Olfr1434	T	A	19: 12,283,903	M285K	probably damaging	Het
P4ha1	T	A	10: 59,348,257	Y180*	probably null	Het
Pcdhb19	T	A	18: 37,499,535	F794L	probably benign	Het
Pdxdc1	T	A	16: 13,854,400	I379F	probably damaging	Het
Psme3	T	A	11: 101,320,442	S185T	possibly damaging	Het
Ptgr1	A	G	4: 58,978,045	S116P	probably damaging	Het
Ptpn23	A	T	9: 110,389,010		probably null	Het
Rabgap1l	A	C	1: 160,722,205	I277R	probably benign	Het
Rapgef1	C	T	2: 29,679,816	T93I	possibly damaging	Het
Rbp3	A	T	14: 33,954,773	D226V	probably damaging	Het
Rnf144a	A	T	12: 26,339,329	C38S	probably damaging	Het
Rptor	C	T	11: 119,780,553	Q281*	probably null	Het
Rragd	T	C	4: 33,004,332	L208S	probably damaging	Het
Slc12a4	T	C	8: 105,959,488	E41G	probably damaging	Het
Slc16a1	G	T	3: 104,653,419	V347F	probably benign	Het
Sra1	T	C	18: 36,677,503	N98S	probably benign	Het
Ssx2ip	T	C	3: 146,426,429	L215P	probably damaging	Het
Syne2	A	T	12: 75,949,064	H2126L	probably damaging	Het
Tep1	TTTCTTCTTCTT	TTTCTTCTT	14: 50,866,823		probably benign	Het
Tgfbi	T	C	13: 56,632,191		probably benign	Het
Tmem232	T	C	17: 65,256,503	M632V	probably damaging	Het
Tmem81	C	G	1: 132,507,829	I124M	probably damaging	Het
Tnnt3	T	G	7: 142,512,086	D153E	probably benign	Het
Tnrc6b	T	A	15: 80,923,446		probably benign	Het
Tpsab1	A	G	17: 25,343,824		probably benign	Het
Usp34	T	A	11: 23,401,505	V1431D	probably damaging	Het
Wdr49	G	T	3: 75,450,022	R285S	possibly damaging	Het
Wdr7	A	G	18: 63,796,249	Y1052C	probably damaging	Het
Zan	A	T	5: 137,382,316		probably benign	Het
Zfp652	G	A	11: 95,763,739	V323I	possibly damaging	Het
Zfp740	A	G	15: 102,212,659	T136A	possibly damaging	Het
Zfp82	C	T	7: 30,056,329	E443K	probably damaging	Het
Zfp874b	A	G	13: 67,481,836	S10P	probably damaging	Het
Zmynd19	A	G	2: 24,958,122	Y110C	probably benign	Het

Other mutations in Slit1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00162:Slit1	APN	19	41650835	missense	probably damaging	1.00
IGL00515:Slit1	APN	19	41624501	missense	probably damaging	0.97
IGL00909:Slit1	APN	19	41602255	missense	possibly damaging	0.89
IGL00953:Slit1	APN	19	41602300	missense	probably damaging	1.00
IGL01116:Slit1	APN	19	41606385	missense	possibly damaging	0.93
IGL01457:Slit1	APN	19	41611044	missense	probably damaging	1.00
IGL01688:Slit1	APN	19	41729106	missense	probably damaging	1.00
IGL01720:Slit1	APN	19	41634214	missense	probably benign	0.01
IGL01925:Slit1	APN	19	41608378	missense	probably damaging	0.98
IGL02008:Slit1	APN	19	41646140	missense	probably damaging	0.99
IGL02312:Slit1	APN	19	41601680	missense	possibly damaging	0.66
IGL02398:Slit1	APN	19	41602237	missense	probably damaging	1.00
IGL02542:Slit1	APN	19	41627248	missense	probably damaging	1.00
IGL02559:Slit1	APN	19	41721085	missense	probably benign	0.01
IGL02609:Slit1	APN	19	41602304	missense	probably damaging	0.99
IGL02623:Slit1	APN	19	41651683	missense	probably damaging	0.98
IGL02729:Slit1	APN	19	41603334	missense	probably damaging	1.00
IGL03230:Slit1	APN	19	41729085	missense	probably damaging	1.00
IGL03387:Slit1	APN	19	41603442	missense	possibly damaging	0.57
PIT4576001:Slit1	UTSW	19	41624549	missense	possibly damaging	0.52
R0366:Slit1	UTSW	19	41611031	missense	probably damaging	1.00
R0496:Slit1	UTSW	19	41608311	splice site	probably benign
R0722:Slit1	UTSW	19	41608435	missense	probably damaging	1.00
R1468:Slit1	UTSW	19	41608384	missense	probably damaging	1.00
R1468:Slit1	UTSW	19	41608384	missense	probably damaging	1.00
R1488:Slit1	UTSW	19	41608385	missense	probably damaging	1.00
R1615:Slit1	UTSW	19	41650671	splice site	probably benign
R1694:Slit1	UTSW	19	41637592	missense	possibly damaging	0.69
R1762:Slit1	UTSW	19	41603335	missense	probably damaging	1.00
R1842:Slit1	UTSW	19	41721038	critical splice donor site	probably null
R1844:Slit1	UTSW	19	41625573	missense	probably damaging	1.00
R1940:Slit1	UTSW	19	41630776	missense	probably damaging	1.00
R2087:Slit1	UTSW	19	41637483	missense	probably benign	0.00
R2094:Slit1	UTSW	19	41606380	missense	probably damaging	0.99
R2095:Slit1	UTSW	19	41606380	missense	probably damaging	0.99
R2104:Slit1	UTSW	19	41602247	missense	possibly damaging	0.69
R2305:Slit1	UTSW	19	41611016	missense	probably benign	0.03
R2972:Slit1	UTSW	19	41611016	missense	probably benign	0.03
R2973:Slit1	UTSW	19	41611016	missense	probably benign	0.03
R2974:Slit1	UTSW	19	41611016	missense	probably benign	0.03
R3159:Slit1	UTSW	19	41604373	missense	probably benign
R3752:Slit1	UTSW	19	41646967	critical splice donor site	probably null
R4095:Slit1	UTSW	19	41608486	intron	probably benign
R4282:Slit1	UTSW	19	41614417	missense	probably benign
R4417:Slit1	UTSW	19	41614469	missense	probably damaging	1.00
R4607:Slit1	UTSW	19	41616793	missense	probably benign	0.10
R4729:Slit1	UTSW	19	41647020	missense	probably damaging	1.00
R4756:Slit1	UTSW	19	41649013	missense	probably damaging	1.00
R4764:Slit1	UTSW	19	41721044	nonsense	probably null
R4849:Slit1	UTSW	19	41649544	missense	probably benign	0.17
R4874:Slit1	UTSW	19	41729054	critical splice donor site	probably null
R5581:Slit1	UTSW	19	41616663	critical splice donor site	probably null
R5699:Slit1	UTSW	19	41625520	critical splice donor site	probably null
R5888:Slit1	UTSW	19	41743296	missense	probably damaging	1.00
R5906:Slit1	UTSW	19	41606374	missense	probably damaging	1.00
R6176:Slit1	UTSW	19	41637595	missense	probably damaging	1.00
R6277:Slit1	UTSW	19	41600509	missense	possibly damaging	0.81
R6702:Slit1	UTSW	19	41614870	missense	possibly damaging	0.95
R6860:Slit1	UTSW	19	41616715	missense	probably benign	0.10
R7015:Slit1	UTSW	19	41629886	nonsense	probably null
R7172:Slit1	UTSW	19	41634666	missense	probably damaging	1.00
R7512:Slit1	UTSW	19	41600635	missense	probably damaging	1.00
R7568:Slit1	UTSW	19	41601635	missense	probably damaging	1.00
R7614:Slit1	UTSW	19	41634200	missense	probably damaging	1.00
R7650:Slit1	UTSW	19	41629924	missense	probably damaging	1.00
R7687:Slit1	UTSW	19	41650689	missense	probably benign	0.03
R7732:Slit1	UTSW	19	41604408	missense	probably benign	0.01
R7947:Slit1	UTSW	19	41610808	missense	probably damaging	1.00
R7947:Slit1	UTSW	19	41610809	missense	probably benign
R8171:Slit1	UTSW	19	41727073	missense	probably damaging	0.97
R8217:Slit1	UTSW	19	41624520	missense	possibly damaging	0.60
X0023:Slit1	UTSW	19	41601640	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACCAAGGCACTGACTCCTCTACTG -3'
(R):5'- TAAGACGCCTTTCCTGGGTCTACG -3'

Sequencing Primer
(F):5'- ACTCCTCTACTGGCGACG -3'
(R):5'- TTCCTGGGTCTACGCACAG -3'

Posted On

2013-05-23