Mutagenetix > Incidental Mutation

Incidental Mutation 'R0233:Slitrk3'

58869

Institutional Source

Beutler Lab

Gene Symbol

Slitrk3

Ensembl Gene

ENSMUSG00000048304

Gene Name

SLIT and NTRK-like family, member 3

Synonyms

ST3

MMRRC Submission

038474-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.715) question?

Stock #

R0233 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

72954598-72965136 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 72955910 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Asparagine at position 954 (S954N)

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: S954N

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000088561
Gene: ENSMUSG00000048304
AA Change: S954N

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

noncoding transcript
Transcript: ENSMUST00000192141

Predicted Effect

probably benign
Transcript: ENSMUST00000192477
AA Change: S954N

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000141236
Gene: ENSMUSG00000048304
AA Change: S954N

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

0.0706

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.6%
20x: 95.4%

Validation Efficiency

99% (93/94)

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3425401B19Rik	A	G	14: 32,385,330 (GRCm39)	S212P	probably benign	Het
A730018C14Rik	A	C	12: 112,381,864 (GRCm39)		noncoding transcript	Het
Acsf3	A	G	8: 123,507,031 (GRCm39)	Y108C	probably damaging	Het
Acsl1	A	G	8: 46,966,606 (GRCm39)		probably benign	Het
Adad1	T	A	3: 37,139,097 (GRCm39)	I389N	possibly damaging	Het
Ankrd27	T	C	7: 35,300,985 (GRCm39)	L95P	probably damaging	Het
Ano5	T	C	7: 51,185,218 (GRCm39)	F46S	possibly damaging	Het
Ap2a1	T	C	7: 44,565,397 (GRCm39)	N114S	probably damaging	Het
Arap1	C	T	7: 101,049,448 (GRCm39)	S970L	possibly damaging	Het
Atad3a	A	T	4: 155,830,524 (GRCm39)	S525T	probably damaging	Het
B4galnt1	T	C	10: 127,006,780 (GRCm39)		probably benign	Het
Bltp1	T	A	3: 37,002,712 (GRCm39)	C1552*	probably null	Het
Cacna2d2	A	T	9: 107,391,869 (GRCm39)	I463F	probably damaging	Het
Casp6	T	A	3: 129,699,624 (GRCm39)	N34K	probably damaging	Het
Ccdc175	A	T	12: 72,152,650 (GRCm39)	F752I	probably benign	Het
Cdhr4	A	G	9: 107,874,133 (GRCm39)	I76V	probably benign	Het
Copa	T	C	1: 171,915,234 (GRCm39)		probably null	Het
Cox11	C	T	11: 90,535,326 (GRCm39)	T259I	probably damaging	Het
Cuzd1	C	A	7: 130,913,545 (GRCm39)	K357N	possibly damaging	Het
Dnah5	T	A	15: 28,333,216 (GRCm39)	F2206I	probably damaging	Het
Dnase2b	T	A	3: 146,288,305 (GRCm39)	K263N	probably benign	Het
Dync1h1	T	A	12: 110,607,414 (GRCm39)	D2668E	probably benign	Het
Eno1b	T	C	18: 48,180,806 (GRCm39)	I328T	probably benign	Het
Fam124b	T	C	1: 80,190,703 (GRCm39)	S227G	probably damaging	Het
Fam13b	T	A	18: 34,581,137 (GRCm39)	Y675F	probably damaging	Het
Fgf21	T	A	7: 45,264,721 (GRCm39)	M4L	probably benign	Het
Flg2	T	A	3: 93,109,104 (GRCm39)	C377*	probably null	Het
Foxp2	T	C	6: 15,409,752 (GRCm39)	S451P	probably damaging	Het
Gli2	A	T	1: 118,763,655 (GRCm39)	S1499T	probably damaging	Het
Gm9920	A	T	15: 54,975,857 (GRCm39)		probably benign	Het
Gpx5	T	A	13: 21,471,573 (GRCm39)	D210V	probably damaging	Het
H2-T5	A	G	17: 36,478,361 (GRCm39)	Y224H	probably benign	Het
Hoxb5	T	A	11: 96,195,853 (GRCm39)	S234T	probably benign	Het
Irf9	C	A	14: 55,843,551 (GRCm39)	N140K	probably benign	Het
Isg20	C	A	7: 78,566,334 (GRCm39)	D94E	probably damaging	Het
Isg20	C	T	7: 78,564,243 (GRCm39)	T50M	probably damaging	Het
Izumo1	T	C	7: 45,273,592 (GRCm39)	L115P	probably damaging	Het
Kdm3b	G	A	18: 34,942,473 (GRCm39)	E655K	probably damaging	Het
Kdm5b	T	G	1: 134,532,372 (GRCm39)		probably benign	Het
Kifc3	A	G	8: 95,828,100 (GRCm39)		probably null	Het
Kpna2	T	C	11: 106,883,457 (GRCm39)	S111G	probably benign	Het
Krt73	A	T	15: 101,710,451 (GRCm39)	N94K	probably benign	Het
Lgmn	G	T	12: 102,366,248 (GRCm39)	D247E	probably damaging	Het
Lilra6	C	T	7: 3,917,935 (GRCm39)	V70I	possibly damaging	Het
Lrig3	G	A	10: 125,849,395 (GRCm39)		probably null	Het
Lrrc4	T	C	6: 28,829,734 (GRCm39)	H627R	probably benign	Het
Macf1	G	A	4: 123,343,920 (GRCm39)		probably benign	Het
Nat9	C	A	11: 115,074,234 (GRCm39)		probably null	Het
Nutm2	A	G	13: 50,621,441 (GRCm39)	D2G	probably benign	Het
Or10j3b	A	T	1: 173,043,868 (GRCm39)	I217F	probably benign	Het
Or5h23	A	T	16: 58,906,038 (GRCm39)	D269E	probably benign	Het
Or5w8	A	G	2: 87,688,096 (GRCm39)	I192M	probably benign	Het
Parl	G	A	16: 20,106,657 (GRCm39)	P184L	probably damaging	Het
Pdzd8	A	T	19: 59,288,811 (GRCm39)	M863K	probably damaging	Het
Phlda3	T	C	1: 135,694,559 (GRCm39)	S125P	probably damaging	Het
Pkd1l3	A	T	8: 110,377,412 (GRCm39)	R217*	probably null	Het
Plekhg5	T	C	4: 152,196,676 (GRCm39)	C695R	probably damaging	Het
Pramel24	A	T	4: 143,452,633 (GRCm39)	E21D	possibly damaging	Het
Prg4	T	C	1: 150,329,298 (GRCm39)		probably benign	Het
Prkab1	A	G	5: 116,159,711 (GRCm39)		probably benign	Het
Pyroxd1	A	G	6: 142,300,356 (GRCm39)	E162G	possibly damaging	Het
R3hcc1l	G	A	19: 42,571,360 (GRCm39)		probably null	Het
Rgs12	T	A	5: 35,187,842 (GRCm39)	S500T	probably damaging	Het
Ripor3	T	C	2: 167,834,518 (GRCm39)	D299G	probably damaging	Het
Robo4	T	C	9: 37,313,977 (GRCm39)	L76P	probably damaging	Het
Sbno1	T	C	5: 124,514,289 (GRCm39)	Y1302C	probably damaging	Het
Sec63	A	G	10: 42,699,904 (GRCm39)	I655V	possibly damaging	Het
Serpina11	T	A	12: 103,946,729 (GRCm39)	M389L	probably benign	Het
Sfswap	C	A	5: 129,631,607 (GRCm39)	P745Q	possibly damaging	Het
Slc17a3	C	T	13: 24,039,841 (GRCm39)	S293F	probably damaging	Het
Sorbs2	A	G	8: 46,222,866 (GRCm39)	T190A	probably damaging	Het
Sos2	A	T	12: 69,664,104 (GRCm39)	I460N	probably benign	Het
Spink7	T	A	18: 62,727,423 (GRCm39)	I34L	probably benign	Het
Srbd1	A	G	17: 86,365,173 (GRCm39)	S628P	probably damaging	Het
Srm	G	A	4: 148,677,829 (GRCm39)	G156S	probably damaging	Het
Sulf2	T	C	2: 165,927,589 (GRCm39)		probably benign	Het
Tmc4	T	A	7: 3,669,866 (GRCm39)	Y6F	probably benign	Het
Tmcc2	A	G	1: 132,288,389 (GRCm39)	F433L	probably damaging	Het
Tmprss13	T	G	9: 45,248,398 (GRCm39)		probably benign	Het
Tnxb	T	C	17: 34,918,007 (GRCm39)	F2307L	probably benign	Het
Tsr3	A	G	17: 25,461,484 (GRCm39)	E274G	probably benign	Het
Ttn	T	C	2: 76,725,488 (GRCm39)		probably benign	Het
Tub	T	C	7: 108,628,548 (GRCm39)	V352A	possibly damaging	Het
Tubb2a	A	G	13: 34,259,325 (GRCm39)	I155T	possibly damaging	Het
Ugt2a2	T	C	5: 87,622,860 (GRCm39)	N36S	probably damaging	Het
Usp13	T	A	3: 32,969,813 (GRCm39)		probably null	Het
Vmn1r52	T	G	6: 90,156,593 (GRCm39)	L120R	possibly damaging	Het
Vmn2r11	A	T	5: 109,201,968 (GRCm39)	S179T	probably benign	Het
Vwf	A	T	6: 125,663,473 (GRCm39)	R2805W	possibly damaging	Het
Wdr7	A	G	18: 64,037,172 (GRCm39)	T1199A	probably benign	Het
Zfp286	T	C	11: 62,671,219 (GRCm39)	T285A	possibly damaging	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
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
R5023:Slitrk3	UTSW	3	72,957,981 (GRCm39)	missense	probably benign	0.24
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'- TGGCAAAAGTCTGCGAAGGCAC -3'
(R):5'- GGTTCCGCCACCATGAGAAGAATG -3'

Sequencing Primer
(F):5'- CTGCGAAGGCACTTCATTG -3'
(R):5'- TCTGCTACTAGACCGTGAGAG -3'

Posted On

2013-07-11