Mutagenetix > Incidental Mutation

Incidental Mutation 'R5018:Slitrk3'

389044

Institutional Source

Beutler Lab

Gene Symbol

Slitrk3

Ensembl Gene

ENSMUSG00000048304

Gene Name

SLIT and NTRK-like family, member 3

Synonyms

ST3

MMRRC Submission

042609-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.715) question?

Stock #

R5018 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

72954598-72965136 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 72957845 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 309 (T309I)

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: T309I

PolyPhen 2 Score 0.305 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000088561
Gene: ENSMUSG00000048304
AA Change: T309I

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: T309I

PolyPhen 2 Score 0.305 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000141236
Gene: ENSMUSG00000048304
AA Change: T309I

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

0.1508

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.8%

Validation Efficiency

98% (49/50)

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamdec1	A	T	14: 68,809,228 (GRCm39)	F245I	probably damaging	Het
Agbl5	G	A	5: 31,060,403 (GRCm39)	R141Q	probably damaging	Het
Alx4	G	T	2: 93,507,764 (GRCm39)	G353V	probably damaging	Het
Apol7b	A	G	15: 77,308,916 (GRCm39)	F61L	probably benign	Het
Aunip	T	A	4: 134,250,928 (GRCm39)		probably null	Het
Bfsp1	C	A	2: 143,704,802 (GRCm39)	R17L	possibly damaging	Het
Birc6	T	A	17: 74,947,054 (GRCm39)	D2926E	probably damaging	Het
Dmwd	A	G	7: 18,812,044 (GRCm39)	D166G	probably damaging	Het
Dnah10	T	C	5: 124,839,260 (GRCm39)	S1233P	possibly damaging	Het
Dnah11	G	T	12: 118,094,463 (GRCm39)	N868K	probably benign	Het
Eea1	T	C	10: 95,846,899 (GRCm39)	V393A	probably benign	Het
Fchsd1	C	T	18: 38,092,926 (GRCm39)		probably benign	Het
Flacc1	A	G	1: 58,730,109 (GRCm39)	V67A	probably benign	Het
Fyttd1	A	G	16: 32,722,787 (GRCm39)		probably null	Het
Hal	T	C	10: 93,343,413 (GRCm39)		probably null	Het
Hhat	A	T	1: 192,277,346 (GRCm39)	L371Q	probably damaging	Het
Hpse2	A	G	19: 43,373,263 (GRCm39)	F122S	possibly damaging	Het
Kif21b	A	G	1: 136,099,972 (GRCm39)	I1509V	probably benign	Het
Klhl20	T	C	1: 160,929,156 (GRCm39)	D334G	probably damaging	Het
Macf1	C	T	4: 123,279,392 (GRCm39)	D3870N	probably damaging	Het
Nlrc5	C	T	8: 95,252,080 (GRCm39)	A1867V	probably damaging	Het
Nr1h5	A	G	3: 102,855,111 (GRCm39)	L330P	probably damaging	Het
Or10g3b	A	C	14: 52,586,736 (GRCm39)	C256G	possibly damaging	Het
Pcdh15	T	G	10: 74,479,607 (GRCm39)	S573A	possibly damaging	Het
Polr1c	G	T	17: 46,558,635 (GRCm39)		probably benign	Het
Scd4	T	A	19: 44,326,048 (GRCm39)	M134K	probably benign	Het
Sh3gl2	A	G	4: 85,309,291 (GRCm39)		probably benign	Het
Sin3a	T	A	9: 57,018,175 (GRCm39)	S865T	probably benign	Het
Sspo	G	A	6: 48,432,634 (GRCm39)	E837K	probably damaging	Het
Stag1	A	G	9: 100,833,672 (GRCm39)	D1095G	probably benign	Het
Trat1	A	T	16: 48,555,168 (GRCm39)	L188*	probably null	Het
Ubn1	A	G	16: 4,881,589 (GRCm39)	D207G	probably damaging	Het
Ugp2	A	G	11: 21,281,052 (GRCm39)	Y219H	probably damaging	Het
Ugt2b1	G	T	5: 87,073,821 (GRCm39)	Y179*	probably null	Het
Vmn2r27	T	A	6: 124,201,141 (GRCm39)	D272V	probably benign	Het
Vmn2r3	T	C	3: 64,178,774 (GRCm39)	E497G	probably benign	Het
Vmn2r91	G	T	17: 18,356,700 (GRCm39)	C789F	probably damaging	Het
Zfp276	A	G	8: 123,991,716 (GRCm39)		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
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'- TTGCATGTACACCCAGTAGGAC -3'
(R):5'- CTGGAGCGAATACCTTACACAG -3'

Sequencing Primer
(F):5'- TGTACACCCAGTAGGACATATAATGG -3'
(R):5'- GAATACCTTACACAGCCCTGGTGG -3'

Posted On

2016-06-06