Mutagenetix > Incidental Mutation

Incidental Mutation 'R5023:Slitrk3'

391090

Institutional Source

Beutler Lab

Gene Symbol

Slitrk3

Ensembl Gene

ENSMUSG00000048304

Gene Name

SLIT and NTRK-like family, member 3

Synonyms

ST3

MMRRC Submission

042614-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.715) question?

Stock #

R5023 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

72954598-72965136 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 72957981 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 264 (T264A)

Ref Sequence

ENSEMBL: ENSMUSP00000141236 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000059407] [ENSMUST00000192477]

AlphaFold

Q810B9

Predicted Effect

probably benign
Transcript: ENSMUST00000059407
AA Change: T264A

PolyPhen 2 Score 0.244 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000088561
Gene: ENSMUSG00000048304
AA Change: T264A

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
Blast:LRRNT	44	79	3e-11	BLAST
LRR	101	124	2.08e1	SMART
LRR	125	148	6.05e0	SMART
LRR	149	172	3.97e0	SMART
LRR_TYP	173	196	1.67e-2	SMART
LRR	197	220	2.69e2	SMART
LRRCT	233	283	4.56e-5	SMART
low complexity region	332	350	N/A	INTRINSIC
LRRNT	373	411	4.17e0	SMART
LRR	432	455	1.62e0	SMART
LRR_TYP	456	479	2.61e-4	SMART
LRR	480	503	2.82e0	SMART
LRR_TYP	504	527	6.99e-5	SMART
LRRCT	563	613	3.22e-5	SMART
transmembrane domain	658	680	N/A	INTRINSIC
low complexity region	713	724	N/A	INTRINSIC
low complexity region	836	843	N/A	INTRINSIC
low complexity region	846	858	N/A	INTRINSIC
low complexity region	870	888	N/A	INTRINSIC
Blast:LRRCT	906	943	2e-16	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000192477
AA Change: T264A

PolyPhen 2 Score 0.244 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000141236
Gene: ENSMUSG00000048304
AA Change: T264A

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
Blast:LRRNT	44	79	3e-11	BLAST
LRR	101	124	2.08e1	SMART
LRR	125	148	6.05e0	SMART
LRR	149	172	3.97e0	SMART
LRR_TYP	173	196	1.67e-2	SMART
LRR	197	220	2.69e2	SMART
LRRCT	233	283	4.56e-5	SMART
low complexity region	332	350	N/A	INTRINSIC
LRRNT	373	411	4.17e0	SMART
LRR	432	455	1.62e0	SMART
LRR_TYP	456	479	2.61e-4	SMART
LRR	480	503	2.82e0	SMART
LRR_TYP	504	527	6.99e-5	SMART
LRRCT	563	613	3.22e-5	SMART
transmembrane domain	658	680	N/A	INTRINSIC
low complexity region	713	724	N/A	INTRINSIC
low complexity region	836	843	N/A	INTRINSIC
low complexity region	846	858	N/A	INTRINSIC
low complexity region	870	888	N/A	INTRINSIC
Blast:LRRCT	906	943	2e-16	BLAST

Meta Mutation Damage Score

0.0612

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

98% (127/129)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Slitrk family of structurally related transmembrane proteins that are involved in controlling neurite outgrowth. The encoded protein contains two leucine-rich repeat (LRR) domains and a C-terminal domain that is partially similar to Trk neurotrophin receptor protein. Enhanced expression of this gene was found in tissue from several different types of tumors. Alternative splicing results in multiple transcript variants, all encoding the same protein. [provided by RefSeq, Jan 2016]
PHENOTYPE: Mice homozygous for a knock-out mice exhibit reduced inhibitory synapse density, decreased miniature inhibitory postsynaptic current frequency and increased susceptibility to spontaneous and pharmacologically-induced seizures. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 124 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	A	T	11: 72,057,581 (GRCm39)	H739Q	probably benign	Het
Abca3	C	T	17: 24,593,274 (GRCm39)	R224C	probably damaging	Het
Abca8b	A	G	11: 109,865,814 (GRCm39)		probably null	Het
Adam1b	C	T	5: 121,639,222 (GRCm39)	V608M	probably damaging	Het
Ank2	A	G	3: 126,735,520 (GRCm39)		probably benign	Het
Ankrd17	A	C	5: 90,430,727 (GRCm39)	L1019R	probably damaging	Het
Arih1	T	C	9: 59,393,515 (GRCm39)	N39S	unknown	Het
Best3	G	A	10: 116,824,647 (GRCm39)	V38I	probably benign	Het
Bicc1	A	G	10: 70,783,713 (GRCm39)	S393P	possibly damaging	Het
C1d	T	A	11: 17,216,674 (GRCm39)	N135K	probably benign	Het
Cage1	G	T	13: 38,195,387 (GRCm39)	S778*	probably null	Het
Capn7	T	A	14: 31,074,383 (GRCm39)	V262E	probably damaging	Het
Ccdc190	A	G	1: 169,760,656 (GRCm39)	R95G	probably damaging	Het
Cd163	C	T	6: 124,302,247 (GRCm39)	T937I	probably damaging	Het
Cdh18	G	A	15: 23,259,752 (GRCm39)	S194N	probably damaging	Het
Ceacam23	A	T	7: 17,636,631 (GRCm39)	D236V	probably damaging	Het
Clec4b2	A	T	6: 123,177,915 (GRCm39)	S77C	probably null	Het
Ctsw	T	A	19: 5,516,077 (GRCm39)	D237V	probably damaging	Het
Cyp2c68	G	A	19: 39,700,951 (GRCm39)	T289I	probably benign	Het
Cyp4f39	A	G	17: 32,700,078 (GRCm39)	Y133C	probably damaging	Het
Dlg5	T	C	14: 24,186,690 (GRCm39)	E1847G	probably damaging	Het
Dnah7a	C	A	1: 53,686,407 (GRCm39)	E248*	probably null	Het
Eef2kmt	T	A	16: 5,065,463 (GRCm39)	D248V	probably damaging	Het
Ewsr1	T	C	11: 5,038,054 (GRCm39)	T113A	possibly damaging	Het
Fbxo4	A	G	15: 4,007,238 (GRCm39)		probably null	Het
Fbxo43	A	T	15: 36,163,075 (GRCm39)	M44K	probably benign	Het
Fchsd1	A	G	18: 38,097,863 (GRCm39)	I340T	possibly damaging	Het
Fgf5	C	A	5: 98,409,874 (GRCm39)	A141E	probably damaging	Het
Gfm1	T	C	3: 67,380,877 (GRCm39)	V664A	probably damaging	Het
Glp2r	T	C	11: 67,631,858 (GRCm39)	T121A	possibly damaging	Het
Gm10803	A	C	2: 93,394,517 (GRCm39)	L96F	probably damaging	Het
Gm14569	T	C	X: 35,694,470 (GRCm39)	D1413G	probably benign	Het
Gm15455	T	C	1: 33,876,432 (GRCm39)		noncoding transcript	Het
Gm1818	G	C	12: 48,602,318 (GRCm39)		noncoding transcript	Het
Gnb2	G	A	5: 137,528,202 (GRCm39)		probably null	Het
Gpc4	G	A	X: 51,163,440 (GRCm39)	R148C	probably damaging	Het
Gpx5	C	T	13: 21,472,915 (GRCm39)	V140I	probably damaging	Het
Gtpbp1	A	T	15: 79,603,422 (GRCm39)	Q637L	possibly damaging	Het
H2-T9	A	G	17: 36,420,307 (GRCm39)		probably benign	Het
Herc1	A	T	9: 66,377,608 (GRCm39)	K3458M	possibly damaging	Het
Hhat	A	T	1: 192,409,647 (GRCm39)	L138Q	probably damaging	Het
Hipk1	G	T	3: 103,684,823 (GRCm39)	T264N	probably damaging	Het
Hjurp	A	T	1: 88,202,772 (GRCm39)	Y71N	possibly damaging	Het
Hnf4g	G	T	3: 3,709,647 (GRCm39)	A144S	probably damaging	Het
Hook3	TAGAG	TAG	8: 26,522,047 (GRCm39)		probably null	Het
Ifi204	G	A	1: 173,579,306 (GRCm39)	T513I	possibly damaging	Het
Ino80b	G	T	6: 83,102,023 (GRCm39)	S26R	probably damaging	Het
Ints9	T	A	14: 65,217,677 (GRCm39)	L68H	probably damaging	Het
Isx	C	T	8: 75,619,342 (GRCm39)	T178I	probably benign	Het
Kel	A	G	6: 41,665,045 (GRCm39)	L255P	probably damaging	Het
Klf11	T	A	12: 24,705,358 (GRCm39)	S271T	probably benign	Het
Klhl20	A	C	1: 160,936,790 (GRCm39)		probably null	Het
Lama2	G	A	10: 27,066,500 (GRCm39)	T1127I	probably damaging	Het
Larp1b	T	A	3: 40,988,420 (GRCm39)	N81K	possibly damaging	Het
Lsm11	T	C	11: 45,835,666 (GRCm39)	D25G	probably damaging	Het
Map3k20	T	A	2: 72,232,689 (GRCm39)		probably benign	Het
Mbd6	C	T	10: 127,122,310 (GRCm39)	V173I	probably benign	Het
Milr1	A	G	11: 106,657,791 (GRCm39)	D131G	possibly damaging	Het
Mybpc1	T	G	10: 88,379,636 (GRCm39)	D635A	probably damaging	Het
Myh7b	G	C	2: 155,474,293 (GRCm39)	R1669S	possibly damaging	Het
Ndufa7	A	G	17: 34,043,577 (GRCm39)		probably benign	Het
Ndufs3	C	A	2: 90,729,004 (GRCm39)	A161S	probably benign	Het
Neo1	T	C	9: 58,897,554 (GRCm39)	D134G	probably damaging	Het
Nme4	G	A	17: 26,312,642 (GRCm39)	T129I	probably benign	Het
Npffr2	A	T	5: 89,730,546 (GRCm39)	T159S	probably benign	Het
Nup153	A	T	13: 46,834,585 (GRCm39)		probably benign	Het
Or3a10	T	A	11: 73,935,881 (GRCm39)	D73V	probably damaging	Het
Or51ac3	A	C	7: 103,214,378 (GRCm39)	M36R	possibly damaging	Het
Pate2	T	C	9: 35,597,407 (GRCm39)		probably benign	Het
Pcca	A	G	14: 123,027,810 (GRCm39)	N73D	probably damaging	Het
Pip5k1c	G	A	10: 81,146,723 (GRCm39)		probably null	Het
Pkhd1l1	A	T	15: 44,391,587 (GRCm39)	H1551L	probably benign	Het
Pkhd1l1	G	A	15: 44,445,623 (GRCm39)	M3768I	probably benign	Het
Ppa2	A	G	3: 133,076,195 (GRCm39)	M275V	probably benign	Het
Ptpn23	G	A	9: 110,217,624 (GRCm39)	T744I	probably benign	Het
Ptprv	A	T	1: 135,052,244 (GRCm39)		noncoding transcript	Het
Rad17	A	T	13: 100,781,571 (GRCm39)	H75Q	possibly damaging	Het
Rbm44	T	C	1: 91,096,820 (GRCm39)		probably null	Het
Rbpj	C	T	5: 53,806,757 (GRCm39)	R201W	probably damaging	Het
Rbpjl	C	A	2: 164,252,209 (GRCm39)	L215I	probably damaging	Het
Ror1	A	G	4: 100,283,129 (GRCm39)	E398G	probably benign	Het
Scamp3	T	A	3: 89,089,600 (GRCm39)		probably benign	Het
Selenot	CATGTATG	CATGTATGTATG	3: 58,495,874 (GRCm39)		probably null	Het
Siglec15	A	G	18: 78,091,890 (GRCm39)	C104R	probably damaging	Het
Sis	T	C	3: 72,841,455 (GRCm39)	I787V	probably benign	Het
Slc17a8	T	C	10: 89,412,422 (GRCm39)	D521G	probably benign	Het
Slc7a10	T	A	7: 34,896,780 (GRCm39)	M172K	possibly damaging	Het
Slco4c1	G	A	1: 96,768,953 (GRCm39)	P303L	probably damaging	Het
Smg8	A	C	11: 86,976,963 (GRCm39)	V206G	probably damaging	Het
Smg9	A	G	7: 24,105,297 (GRCm39)	K137R	possibly damaging	Het
Srrm2	C	A	17: 24,038,291 (GRCm39)		probably benign	Het
Sult2a2	T	A	7: 13,468,785 (GRCm39)	Y84N	possibly damaging	Het
Syngr2	A	T	11: 117,703,336 (GRCm39)	I34F	probably benign	Het
Tank	G	A	2: 61,408,979 (GRCm39)		probably benign	Het
Tead4	T	C	6: 128,271,134 (GRCm39)		probably benign	Het
Tesl1	G	A	X: 23,773,480 (GRCm39)	G327E	probably damaging	Het
Tex36	A	T	7: 133,197,019 (GRCm39)	C33S	probably benign	Het
Timd5	T	A	11: 46,419,359 (GRCm39)	D58E	probably damaging	Het
Timm21	C	A	18: 84,967,539 (GRCm39)	V112L	possibly damaging	Het
Tmem240	T	A	4: 155,824,131 (GRCm39)	L92Q	probably damaging	Het
Tmem268	C	G	4: 63,486,777 (GRCm39)	S100C	probably damaging	Het
Tmod3	G	A	9: 75,418,488 (GRCm39)	P183S	probably damaging	Het
Trappc10	G	T	10: 78,052,994 (GRCm39)	F260L	possibly damaging	Het
Trim16	A	T	11: 62,727,638 (GRCm39)	Y233F	probably benign	Het
Trmt112	T	C	19: 6,888,121 (GRCm39)	V91A	probably benign	Het
Ttc3	A	G	16: 94,230,218 (GRCm39)	E450G	probably benign	Het
Ttk	A	G	9: 83,745,594 (GRCm39)	D647G	probably damaging	Het
Ubash3b	A	G	9: 40,948,755 (GRCm39)	C187R	possibly damaging	Het
Vmn1r29	T	A	6: 58,285,052 (GRCm39)	Y257*	probably null	Het
Vmn1r33	T	C	6: 66,589,089 (GRCm39)	N155S	probably benign	Het
Vmn2r28	T	A	7: 5,489,463 (GRCm39)	I459L	probably benign	Het
Vps16	A	G	2: 130,281,372 (GRCm39)	S235G	probably benign	Het
Vwde	T	C	6: 13,192,641 (GRCm39)	I421V	possibly damaging	Het
Xiap	T	C	X: 41,183,342 (GRCm39)	F23L	probably benign	Het
Xkr7	A	G	2: 152,896,300 (GRCm39)	T385A	probably benign	Het
Zbtb11	A	G	16: 55,826,428 (GRCm39)	Y819C	probably damaging	Het
Zfp112	A	G	7: 23,825,909 (GRCm39)	T624A	probably damaging	Het
Zfp592	A	G	7: 80,674,095 (GRCm39)	D353G	probably damaging	Het
Zfp62	T	A	11: 49,106,556 (GRCm39)	S216T	probably damaging	Het
Zfp677	A	T	17: 21,618,056 (GRCm39)	H371L	probably damaging	Het
Zfp780b	T	C	7: 27,662,873 (GRCm39)	K561E	possibly damaging	Het
Zfp936	G	A	7: 42,836,681 (GRCm39)	D31N	probably damaging	Het
Znfx1	T	C	2: 166,881,746 (GRCm39)	Y217C	probably damaging	Het
Zpbp	C	T	11: 11,365,248 (GRCm39)	E200K	probably benign	Het

Other mutations in Slitrk3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00465:Slitrk3	APN	3	72,958,436 (GRCm39)	missense	probably damaging	1.00
IGL00857:Slitrk3	APN	3	72,957,174 (GRCm39)	missense	probably damaging	1.00
IGL00990:Slitrk3	APN	3	72,957,414 (GRCm39)	missense	probably damaging	1.00
IGL01010:Slitrk3	APN	3	72,956,606 (GRCm39)	missense	probably benign	0.14
IGL01299:Slitrk3	APN	3	72,956,349 (GRCm39)	missense	probably benign	0.43
IGL01609:Slitrk3	APN	3	72,957,570 (GRCm39)	missense	probably damaging	1.00
IGL01881:Slitrk3	APN	3	72,956,639 (GRCm39)	missense	probably benign	0.00
IGL01941:Slitrk3	APN	3	72,958,404 (GRCm39)	missense	possibly damaging	0.72
IGL02183:Slitrk3	APN	3	72,957,312 (GRCm39)	missense	probably damaging	0.97
IGL02187:Slitrk3	APN	3	72,957,605 (GRCm39)	missense	probably damaging	1.00
IGL02478:Slitrk3	APN	3	72,958,046 (GRCm39)	missense	probably damaging	0.96
IGL02512:Slitrk3	APN	3	72,957,735 (GRCm39)	missense	probably benign	0.28
IGL02720:Slitrk3	APN	3	72,958,101 (GRCm39)	missense	probably damaging	1.00
IGL03113:Slitrk3	APN	3	72,957,723 (GRCm39)	missense	probably benign	0.00
IGL03224:Slitrk3	APN	3	72,957,263 (GRCm39)	missense	possibly damaging	0.72
wee	UTSW	3	72,958,118 (GRCm39)	missense	probably damaging	1.00
R0233:Slitrk3	UTSW	3	72,955,910 (GRCm39)	missense	probably benign	0.00
R0233:Slitrk3	UTSW	3	72,955,910 (GRCm39)	missense	probably benign	0.00
R0639:Slitrk3	UTSW	3	72,956,982 (GRCm39)	missense	probably benign	0.02
R1448:Slitrk3	UTSW	3	72,957,674 (GRCm39)	missense	probably damaging	0.99
R1656:Slitrk3	UTSW	3	72,957,672 (GRCm39)	missense	probably damaging	0.98
R1713:Slitrk3	UTSW	3	72,957,024 (GRCm39)	missense	probably benign	0.00
R1992:Slitrk3	UTSW	3	72,957,104 (GRCm39)	missense	possibly damaging	0.80
R1999:Slitrk3	UTSW	3	72,957,297 (GRCm39)	missense	probably benign	0.13
R2359:Slitrk3	UTSW	3	72,956,678 (GRCm39)	missense	possibly damaging	0.56
R3083:Slitrk3	UTSW	3	72,955,928 (GRCm39)	missense	probably benign	0.00
R3153:Slitrk3	UTSW	3	72,956,315 (GRCm39)	nonsense	probably null
R3821:Slitrk3	UTSW	3	72,956,549 (GRCm39)	missense	possibly damaging	0.94
R4208:Slitrk3	UTSW	3	72,958,490 (GRCm39)	missense	possibly damaging	0.67
R4323:Slitrk3	UTSW	3	72,958,118 (GRCm39)	missense	probably damaging	1.00
R4580:Slitrk3	UTSW	3	72,958,539 (GRCm39)	missense	probably damaging	0.96
R4730:Slitrk3	UTSW	3	72,956,852 (GRCm39)	missense	probably benign	0.08
R4742:Slitrk3	UTSW	3	72,955,898 (GRCm39)	missense	probably benign	0.00
R4979:Slitrk3	UTSW	3	72,957,129 (GRCm39)	missense	possibly damaging	0.95
R5018:Slitrk3	UTSW	3	72,957,845 (GRCm39)	missense	probably benign	0.31
R5057:Slitrk3	UTSW	3	72,957,981 (GRCm39)	missense	probably benign	0.24
R5156:Slitrk3	UTSW	3	72,956,592 (GRCm39)	missense	probably benign
R5500:Slitrk3	UTSW	3	72,957,680 (GRCm39)	missense	probably damaging	1.00
R5582:Slitrk3	UTSW	3	72,957,737 (GRCm39)	missense	probably benign	0.09
R5797:Slitrk3	UTSW	3	72,955,962 (GRCm39)	missense	probably damaging	0.99
R5963:Slitrk3	UTSW	3	72,958,046 (GRCm39)	missense	probably benign	0.30
R5985:Slitrk3	UTSW	3	72,958,233 (GRCm39)	missense	probably damaging	1.00
R6123:Slitrk3	UTSW	3	72,957,095 (GRCm39)	missense	probably damaging	1.00
R6393:Slitrk3	UTSW	3	72,957,247 (GRCm39)	missense	possibly damaging	0.79
R6529:Slitrk3	UTSW	3	72,958,551 (GRCm39)	missense	probably benign	0.02
R6584:Slitrk3	UTSW	3	72,956,558 (GRCm39)	missense	probably damaging	0.99
R6645:Slitrk3	UTSW	3	72,957,194 (GRCm39)	missense	probably benign	0.13
R7001:Slitrk3	UTSW	3	72,957,942 (GRCm39)	nonsense	probably null
R7282:Slitrk3	UTSW	3	72,957,798 (GRCm39)	missense	possibly damaging	0.70
R7534:Slitrk3	UTSW	3	72,957,440 (GRCm39)	missense	probably damaging	0.98
R7577:Slitrk3	UTSW	3	72,958,448 (GRCm39)	missense	probably damaging	0.99
R7757:Slitrk3	UTSW	3	72,958,172 (GRCm39)	missense	probably damaging	1.00
R8251:Slitrk3	UTSW	3	72,956,729 (GRCm39)	missense	possibly damaging	0.67
R8354:Slitrk3	UTSW	3	72,956,513 (GRCm39)	missense	probably benign	0.08
R8454:Slitrk3	UTSW	3	72,956,513 (GRCm39)	missense	probably benign	0.08
R8488:Slitrk3	UTSW	3	72,958,520 (GRCm39)	missense	probably benign	0.02
R8491:Slitrk3	UTSW	3	72,958,592 (GRCm39)	missense	possibly damaging	0.89
R8843:Slitrk3	UTSW	3	72,956,164 (GRCm39)	missense	probably benign	0.04
R9140:Slitrk3	UTSW	3	72,957,792 (GRCm39)	missense	probably benign	0.02
R9451:Slitrk3	UTSW	3	72,958,616 (GRCm39)	missense	possibly damaging	0.83
R9511:Slitrk3	UTSW	3	72,958,272 (GRCm39)	missense	possibly damaging	0.46
R9575:Slitrk3	UTSW	3	72,956,127 (GRCm39)	missense	probably benign	0.00
R9589:Slitrk3	UTSW	3	72,957,981 (GRCm39)	missense	probably benign	0.24
R9603:Slitrk3	UTSW	3	72,958,649 (GRCm39)	missense	probably benign	0.00
X0022:Slitrk3	UTSW	3	72,957,599 (GRCm39)	missense	probably damaging	1.00
Z1176:Slitrk3	UTSW	3	72,956,103 (GRCm39)	missense	probably benign	0.09
Z1177:Slitrk3	UTSW	3	72,956,475 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TAAAGCCTGGGATGTCGAAG -3'
(R):5'- ATCTGGACCTTCGTGGGAAC -3'

Sequencing Primer
(F):5'- CCTGGGATGTCGAAGGTGGTC -3'
(R):5'- ACAGGTTAAAGGTTCTCTTCTACCG -3'

Posted On

2016-06-06