Mutagenetix > Incidental Mutation

Incidental Mutation 'R9589:Slitrk3'

722922

Institutional Source

Beutler Lab

Gene Symbol

Slitrk3

Ensembl Gene

ENSMUSG00000048304

Gene Name

SLIT and NTRK-like family, member 3

Synonyms

ST3

MMRRC Submission

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.715) question?

Stock #

R9589 (G1)

Quality Score

225.009

Status

Not 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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

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: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrg3	A	G	8: 95,760,093 (GRCm39)	D104G	possibly damaging	Het
Ahnak2	G	T	12: 112,746,831 (GRCm39)	D1166E		Het
C2cd3	T	A	7: 100,081,756 (GRCm39)	S1133T		Het
Ccdc17	A	G	4: 116,454,791 (GRCm39)	Q168R	probably benign	Het
Fn1	A	T	1: 71,668,941 (GRCm39)	I668N	probably damaging	Het
Fyb2	C	A	4: 104,872,833 (GRCm39)	N735K	probably damaging	Het
Gad1	T	C	2: 70,416,284 (GRCm39)	S248P	possibly damaging	Het
Gcnt1	G	A	19: 17,307,422 (GRCm39)	A101V	probably benign	Het
Herc1	T	A	9: 66,372,840 (GRCm39)	M3132K	possibly damaging	Het
Htra3	T	C	5: 35,821,409 (GRCm39)	I323V	probably damaging	Het
Ighv11-2	A	T	12: 114,012,047 (GRCm39)	V56D	probably damaging	Het
Itga8	C	T	2: 12,237,701 (GRCm39)	G340R	probably damaging	Het
Kcnk15	C	T	2: 163,700,127 (GRCm39)	T122M	probably damaging	Het
Kif13a	G	T	13: 46,956,020 (GRCm39)	Q658K	probably benign	Het
Kif13b	T	C	14: 65,013,759 (GRCm39)	I1303T	possibly damaging	Het
Kifc3	A	T	8: 95,861,372 (GRCm39)	S94R	possibly damaging	Het
Lrrc63	A	T	14: 75,322,379 (GRCm39)	F575Y	possibly damaging	Het
Map1a	T	C	2: 121,136,398 (GRCm39)	S2405P	probably damaging	Het
Map2	A	G	1: 66,449,753 (GRCm39)	T159A	probably benign	Het
Mgam	A	T	6: 40,727,519 (GRCm39)	I1315F	probably damaging	Het
Or51a39	T	C	7: 102,363,372 (GRCm39)	T83A	probably damaging	Het
Pah	T	A	10: 87,403,197 (GRCm39)	F191I	probably damaging	Het
Plekhh2	G	A	17: 84,854,918 (GRCm39)	D51N	possibly damaging	Het
Ppp4r2	C	T	6: 100,838,409 (GRCm39)	T109M	probably damaging	Het
Rfx7	T	C	9: 72,525,122 (GRCm39)	S771P	possibly damaging	Het
Sec11a	T	C	7: 80,565,899 (GRCm39)	*171W	probably null	Het
Secisbp2l	C	A	2: 125,589,425 (GRCm39)	V708L	probably benign	Het
Secisbp2l	T	G	2: 125,589,430 (GRCm39)	D706A	probably damaging	Het
Shpk	C	T	11: 73,104,267 (GRCm39)	P139S	possibly damaging	Het
Slc6a18	A	G	13: 73,816,323 (GRCm39)	L352P	possibly damaging	Het
Smg9	T	G	7: 24,120,246 (GRCm39)	S407A	probably damaging	Het
Stmn4	A	G	14: 66,595,338 (GRCm39)	E121G	probably damaging	Het
Tmem237	G	A	1: 59,159,146 (GRCm39)	P10S	probably benign	Het
Vmn2r73	A	G	7: 85,519,659 (GRCm39)	I433T	probably benign	Het
Zfp28	T	A	7: 6,392,816 (GRCm39)	M164K	probably benign	Het
Zswim8	A	G	14: 20,763,171 (GRCm39)	M357V	probably 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
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
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'- AACGCATCTGGACCTTCGTG -3'

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

Posted On

2022-08-09