Mutagenetix > Incidental Mutation

Incidental Mutation 'R7278:Slc6a9'

571533

Institutional Source

Beutler Lab

Gene Symbol

Slc6a9

Ensembl Gene

ENSMUSG00000028542

Gene Name

solute carrier family 6 (neurotransmitter transporter, glycine), member 9

Synonyms

Glyt-1, Glyt1

MMRRC Submission

045360-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7278 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

117692240-117726502 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 117725303 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glutamine at position 589 (R589Q)

Ref Sequence

ENSEMBL: ENSMUSP00000066102 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030269] [ENSMUST00000063857] [ENSMUST00000084325] [ENSMUST00000106422] [ENSMUST00000131938] [ENSMUST00000132043] [ENSMUST00000149168] [ENSMUST00000163288] [ENSMUST00000164853] [ENSMUST00000166325] [ENSMUST00000167287] [ENSMUST00000167443] [ENSMUST00000169885] [ENSMUST00000169990] [ENSMUST00000171052]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000030269
AA Change: R589Q

PolyPhen 2 Score 0.308 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: R589Q

Domain	Start	End	E-Value	Type
Pfam:SNF	27	562	5.1e-234	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000063857
AA Change: R589Q

PolyPhen 2 Score 0.308 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: R589Q

Domain	Start	End	E-Value	Type
Pfam:SNF	27	562	5.1e-234	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000084325

SMART Domains

Protein: ENSMUSP00000081352
Gene: ENSMUSG00000028541

Domain	Start	End	E-Value	Type
transmembrane domain	13	35	N/A	INTRINSIC
Pfam:Glyco_transf_7N	94	230	1.9e-47	PFAM
Pfam:Glyco_transf_7C	232	310	2.6e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000106422

SMART Domains

Protein: ENSMUSP00000102030
Gene: ENSMUSG00000078588

Domain	Start	End	E-Value	Type
low complexity region	17	46	N/A	INTRINSIC
coiled coil region	133	158	N/A	INTRINSIC
low complexity region	254	266	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000131938

Predicted Effect

probably benign
Transcript: ENSMUST00000132043

SMART Domains

Protein: ENSMUSP00000122676
Gene: ENSMUSG00000028542

Domain	Start	End	E-Value	Type
Pfam:SNF	32	321	1.4e-132	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000149168

SMART Domains

Protein: ENSMUSP00000129359
Gene: ENSMUSG00000028542

Domain	Start	End	E-Value	Type
low complexity region	91	116	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000163288
AA Change: R593Q

PolyPhen 2 Score 0.205 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: R593Q

Domain	Start	End	E-Value	Type
Pfam:SNF	46	566	2.1e-212	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000164853

SMART Domains

Protein: ENSMUSP00000132114
Gene: ENSMUSG00000078588

Domain	Start	End	E-Value	Type
low complexity region	17	46	N/A	INTRINSIC
coiled coil region	133	158	N/A	INTRINSIC
low complexity region	254	266	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000166325

SMART Domains

Protein: ENSMUSP00000131493
Gene: ENSMUSG00000078588

Domain	Start	End	E-Value	Type
coiled coil region	33	57	N/A	INTRINSIC
low complexity region	61	90	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000167287

SMART Domains

Protein: ENSMUSP00000126161
Gene: ENSMUSG00000078588

Domain	Start	End	E-Value	Type
coiled coil region	13	38	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000167443

SMART Domains

Protein: ENSMUSP00000128771
Gene: ENSMUSG00000028541

Domain	Start	End	E-Value	Type
transmembrane domain	13	35	N/A	INTRINSIC
Pfam:Glyco_transf_7N	94	188	1.1e-24	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000169885
AA Change: R477Q

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: R477Q

Domain	Start	End	E-Value	Type
Pfam:SNF	1	450	1.2e-182	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000169990

SMART Domains

Protein: ENSMUSP00000127203
Gene: ENSMUSG00000028542

Domain	Start	End	E-Value	Type
Pfam:SNF	84	373	2.3e-132	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000171052

SMART Domains

Protein: ENSMUSP00000129502
Gene: ENSMUSG00000078588

Domain	Start	End	E-Value	Type
Pfam:CCDC24	21	201	3.9e-67	PFAM
low complexity region	282	294	N/A	INTRINSIC

Meta Mutation Damage Score

0.0852

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (78/79)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]
PHENOTYPE: Homozygous null mice die shortly after birth exhibiting breathing and movement deficiencies. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	T	C	3: 137,771,237 (GRCm39)	L142P	probably benign	Het
Abca13	A	T	11: 9,241,126 (GRCm39)	R996S	possibly damaging	Het
Abcb6	A	G	1: 75,151,017 (GRCm39)	F558L	possibly damaging	Het
Acp7	T	A	7: 28,330,307 (GRCm39)	D2V	unknown	Het
Acvr1c	T	C	2: 58,174,948 (GRCm39)	D280G	probably damaging	Het
Atp8a1	A	G	5: 67,781,380 (GRCm39)	S1124P		Het
B4galnt1	A	T	10: 127,003,657 (GRCm39)	T207S	probably benign	Het
C2cd4d	C	A	3: 94,271,445 (GRCm39)	T237N	probably benign	Het
C8b	T	C	4: 104,637,824 (GRCm39)	C99R	probably damaging	Het
Ccnk	C	A	12: 108,159,964 (GRCm39)	Q149K	possibly damaging	Het
Chfr	A	G	5: 110,288,226 (GRCm39)	D47G	probably benign	Het
Chid1	A	T	7: 141,109,401 (GRCm39)		probably null	Het
Cibar2	T	A	8: 120,895,342 (GRCm39)	T187S	possibly damaging	Het
Cmya5	T	A	13: 93,232,208 (GRCm39)	E960V	probably damaging	Het
Col18a1	A	G	10: 76,932,118 (GRCm39)	S112P	unknown	Het
Cps1	G	A	1: 67,210,080 (GRCm39)	V637I	probably damaging	Het
Crispld1	A	G	1: 17,823,102 (GRCm39)	T390A	probably benign	Het
Cyp2c54	A	T	19: 40,058,697 (GRCm39)	L245*	probably null	Het
Ddr2	G	T	1: 169,812,530 (GRCm39)	T654K	probably damaging	Het
Dnah10	T	C	5: 124,868,855 (GRCm39)		probably null	Het
Elavl4	C	T	4: 110,068,622 (GRCm39)		probably null	Het
Emilin1	T	C	5: 31,078,004 (GRCm39)	V921A	probably benign	Het
Evpl	T	A	11: 116,113,939 (GRCm39)	E1250D	probably damaging	Het
Fam228a	C	T	12: 4,782,790 (GRCm39)	G101E	probably benign	Het
Gemin4	T	C	11: 76,102,932 (GRCm39)	T610A	probably damaging	Het
Glis1	T	C	4: 107,292,880 (GRCm39)	M1T	probably null	Het
Gm14399	C	T	2: 174,972,252 (GRCm39)		probably benign	Het
Gorasp2	C	T	2: 70,509,849 (GRCm39)	T170I	probably damaging	Het
Gpr37	A	G	6: 25,669,341 (GRCm39)	V501A	possibly damaging	Het
Grik4	T	A	9: 42,533,356 (GRCm39)	Q388L	probably benign	Het
Hspg2	T	A	4: 137,278,436 (GRCm39)	D3035E	probably damaging	Het
Htr4	A	T	18: 62,545,247 (GRCm39)	N11Y	probably benign	Het
Itgb2l	A	G	16: 96,230,243 (GRCm39)	S356P	probably damaging	Het
Klk1b22	A	G	7: 43,764,173 (GRCm39)	N34D	probably benign	Het
Lmcd1	A	G	6: 112,287,500 (GRCm39)	D62G	possibly damaging	Het
Lrp2	C	T	2: 69,316,696 (GRCm39)	G2095E	probably damaging	Het
Macf1	T	A	4: 123,334,536 (GRCm39)	E4407V	possibly damaging	Het
Mcm5	T	C	8: 75,851,487 (GRCm39)	F631L	probably benign	Het
Mov10l1	A	G	15: 88,878,071 (GRCm39)	S170G	probably benign	Het
Muc5b	A	T	7: 141,411,239 (GRCm39)	D1395V	unknown	Het
Muc6	G	A	7: 141,226,842 (GRCm39)	T1395M	probably benign	Het
Myh15	A	G	16: 48,911,468 (GRCm39)	D300G	probably damaging	Het
Naa80	T	C	9: 107,460,498 (GRCm39)	L131P	probably damaging	Het
Ndst4	A	G	3: 125,231,952 (GRCm39)	T174A	probably benign	Het
Nek5	T	A	8: 22,580,500 (GRCm39)	N406I	probably benign	Het
Nr2c2	G	A	6: 92,136,359 (GRCm39)	V400I	probably damaging	Het
Or1l4	T	C	2: 37,092,092 (GRCm39)	Y280H	probably damaging	Het
Or1l4b	G	T	2: 37,037,021 (GRCm39)	V266L	probably benign	Het
Or51aa2	A	T	7: 103,187,935 (GRCm39)	Y169N	probably benign	Het
Or52m1	T	C	7: 102,290,190 (GRCm39)	S246P	probably damaging	Het
Or6b1	G	A	6: 42,811,330 (GRCm39)		probably null	Het
Or6c5c	T	A	10: 129,298,620 (GRCm39)	I25N	probably damaging	Het
Parn	T	C	16: 13,443,927 (GRCm39)		probably null	Het
Pfkl	T	C	10: 77,827,857 (GRCm39)	T468A	probably damaging	Het
Pi16	C	A	17: 29,538,208 (GRCm39)	P7Q	possibly damaging	Het
Plce1	T	C	19: 38,768,340 (GRCm39)	I2205T	possibly damaging	Het
Prss16	A	T	13: 22,187,317 (GRCm39)	N442K	probably damaging	Het
Pus7	A	G	5: 23,957,342 (GRCm39)	S370P	probably damaging	Het
Ripk3	G	T	14: 56,024,741 (GRCm39)	Y210*	probably null	Het
Rps6ka2	C	A	17: 7,539,034 (GRCm39)	F317L	probably damaging	Het
Slc13a3	G	A	2: 165,287,448 (GRCm39)	R169W	possibly damaging	Het
Slc6a21	T	A	7: 44,931,904 (GRCm39)	I256N	possibly damaging	Het
Slc8a2	T	C	7: 15,875,077 (GRCm39)	S442P	probably damaging	Het
Snupn	T	A	9: 56,890,028 (GRCm39)	M283K	probably damaging	Het
Steap3	A	T	1: 120,162,087 (GRCm39)	M395K	probably damaging	Het
Sv2b	G	A	7: 74,797,402 (GRCm39)	P331S	probably damaging	Het
Tlr1	A	G	5: 65,084,115 (GRCm39)	V154A	probably benign	Het
Tmem131	A	G	1: 36,835,382 (GRCm39)	S1580P	probably damaging	Het
Tmem51	TCCCC	TCCC	4: 141,764,996 (GRCm39)		probably null	Het
Trav14d-3-dv8	G	A	14: 53,316,218 (GRCm39)	R26H	probably benign	Het
Trp53	C	T	11: 69,482,081 (GRCm39)	L365F	probably benign	Het
Trp53bp1	A	T	2: 121,029,516 (GRCm39)	I1838N	probably damaging	Het
Ugt1a5	A	T	1: 88,094,608 (GRCm39)	K279*	probably null	Het
Unc80	A	G	1: 66,591,368 (GRCm39)	E1141G	possibly damaging	Het
Vti1b	T	C	12: 79,213,153 (GRCm39)	D49G	probably benign	Het
Wnt10a	A	T	1: 74,832,641 (GRCm39)	H78L	possibly damaging	Het
Zfp869	G	A	8: 70,159,128 (GRCm39)	H482Y	probably damaging	Het
Zfyve1	A	G	12: 83,598,314 (GRCm39)	V638A	probably damaging	Het

Other mutations in Slc6a9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00904:Slc6a9	APN	4	117,721,814 (GRCm39)	missense	probably damaging	1.00
IGL01728:Slc6a9	APN	4	117,721,802 (GRCm39)	missense	probably damaging	1.00
IGL02111:Slc6a9	APN	4	117,721,210 (GRCm39)	missense	probably benign	0.19
R0051:Slc6a9	UTSW	4	117,722,056 (GRCm39)	missense	probably damaging	1.00
R0051:Slc6a9	UTSW	4	117,722,056 (GRCm39)	missense	probably damaging	1.00
R1170:Slc6a9	UTSW	4	117,722,003 (GRCm39)	missense	possibly damaging	0.77
R2872:Slc6a9	UTSW	4	117,706,578 (GRCm39)	start codon destroyed	probably null	0.02
R2872:Slc6a9	UTSW	4	117,706,578 (GRCm39)	start codon destroyed	probably null	0.02
R3499:Slc6a9	UTSW	4	117,714,000 (GRCm39)	missense	probably benign	0.01
R4744:Slc6a9	UTSW	4	117,725,092 (GRCm39)	missense	probably benign	0.00
R4970:Slc6a9	UTSW	4	117,713,205 (GRCm39)	missense	probably damaging	1.00
R5055:Slc6a9	UTSW	4	117,725,347 (GRCm39)	splice site	probably null
R5103:Slc6a9	UTSW	4	117,725,352 (GRCm39)	missense	probably benign
R5726:Slc6a9	UTSW	4	117,721,210 (GRCm39)	missense	probably damaging	1.00
R6836:Slc6a9	UTSW	4	117,725,083 (GRCm39)	missense	possibly damaging	0.49
R7030:Slc6a9	UTSW	4	117,714,633 (GRCm39)	missense	possibly damaging	0.94
R7061:Slc6a9	UTSW	4	117,725,261 (GRCm39)	missense	probably benign	0.40
R7863:Slc6a9	UTSW	4	117,721,207 (GRCm39)	missense	probably damaging	1.00
R8036:Slc6a9	UTSW	4	117,725,083 (GRCm39)	missense	possibly damaging	0.49
R8722:Slc6a9	UTSW	4	117,714,452 (GRCm39)	missense	unknown
R9302:Slc6a9	UTSW	4	117,706,596 (GRCm39)	missense	possibly damaging	0.91
R9575:Slc6a9	UTSW	4	117,714,603 (GRCm39)	missense	probably benign
R9627:Slc6a9	UTSW	4	117,721,210 (GRCm39)	missense	probably damaging	1.00
R9749:Slc6a9	UTSW	4	117,721,198 (GRCm39)	missense	probably damaging	0.98
Z1176:Slc6a9	UTSW	4	117,714,563 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- CTTCTTCAGGTGAGGAGTGAAGATG -3'
(R):5'- TCAAGGTGACAGCAGCCATC -3'

Sequencing Primer
(F):5'- GATGGACTGAACGGGGAC -3'
(R):5'- TCCGTGGTGGGAGCAAG -3'

Posted On

2019-09-13