Mutagenetix > Incidental Mutation

Incidental Mutation 'R5055:Slc6a9'

390760

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

042645-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5055 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

117692240-117726502 bp(+) (GRCm39)

Type of Mutation

splice site (4146 bp from exon)

DNA Base Change (assembly)

G to A at 117725347 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000127203 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030266] [ENSMUST00000030269] [ENSMUST00000063857] [ENSMUST00000084325] [ENSMUST00000106422] [ENSMUST00000131938] [ENSMUST00000163288] [ENSMUST00000169885] [ENSMUST00000149168] [ENSMUST00000164853] [ENSMUST00000132043] [ENSMUST00000166325] [ENSMUST00000171052] [ENSMUST00000169990] [ENSMUST00000167443] [ENSMUST00000167287]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000030266

SMART Domains

Protein: ENSMUSP00000030266
Gene: ENSMUSG00000028541

Domain	Start	End	E-Value	Type
transmembrane domain	13	35	N/A	INTRINSIC
Pfam:Glyco_transf_7N	94	228	4.2e-59	PFAM
Pfam:Glyco_transf_7C	232	310	2.1e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000030269
AA Change: G604R

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: G604R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000063857
AA Change: G604R

PolyPhen 2 Score 0.201 (Sensitivity: 0.92; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: G604R

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

noncoding transcript
Transcript: ENSMUST00000130758

Predicted Effect

probably benign
Transcript: ENSMUST00000131938

Predicted Effect

probably benign
Transcript: ENSMUST00000163288
AA Change: G608R

PolyPhen 2 Score 0.229 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: G608R

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

Predicted Effect

probably benign
Transcript: ENSMUST00000169885
AA Change: G492R

PolyPhen 2 Score 0.175 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: G492R

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164716

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000154439

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163974

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: 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 null
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: 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: 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

Predicted Effect

probably null
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: 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: ENSMUST00000167287

SMART Domains

Protein: ENSMUSP00000126161
Gene: ENSMUSG00000078588

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

Meta Mutation Damage Score

0.5977

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.5%
20x: 92.9%

Validation Efficiency

98% (84/86)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam19	G	A	11: 46,013,996 (GRCm39)	V329I	probably damaging	Het
Adgrl3	C	A	5: 81,794,398 (GRCm39)	A541E	possibly damaging	Het
Agbl1	A	T	7: 76,063,325 (GRCm39)	I263F	probably damaging	Het
Ash1l	T	C	3: 88,930,519 (GRCm39)		probably null	Het
Bccip	A	G	7: 133,316,652 (GRCm39)	T91A	probably benign	Het
Bnc1	A	T	7: 81,624,163 (GRCm39)	F355I	probably damaging	Het
Bpifa2	A	T	2: 153,855,630 (GRCm39)	D185V	probably damaging	Het
Capn8	T	A	1: 182,399,526 (GRCm39)	V89D	probably damaging	Het
Cfap46	A	T	7: 139,241,106 (GRCm39)	M421K	probably damaging	Het
Chd2	A	T	7: 73,130,256 (GRCm39)	L800M	probably damaging	Het
Chd4	A	G	6: 125,077,949 (GRCm39)	D137G	possibly damaging	Het
Crtap	A	G	9: 114,219,208 (GRCm39)	Y154H	probably benign	Het
Ctdp1	T	A	18: 80,499,303 (GRCm39)	Q213L	probably damaging	Het
Cts6	T	C	13: 61,344,164 (GRCm39)	Y296C	probably damaging	Het
Daxx	G	T	17: 34,131,134 (GRCm39)	V354F	probably benign	Het
Dnah2	A	G	11: 69,411,599 (GRCm39)	I341T	possibly damaging	Het
Epha2	A	G	4: 141,036,380 (GRCm39)	D272G	probably benign	Het
Etfa	A	G	9: 55,407,417 (GRCm39)	V24A	probably damaging	Het
Fbxl7	C	A	15: 26,553,022 (GRCm39)	G82W	probably damaging	Het
Fcamr	G	A	1: 130,739,174 (GRCm39)	C158Y	probably damaging	Het
Fyb1	A	C	15: 6,614,630 (GRCm39)		probably benign	Het
Gars1	G	A	6: 55,045,077 (GRCm39)	R454H	probably damaging	Het
Ghsr	T	C	3: 27,426,421 (GRCm39)	V159A	probably benign	Het
Glp1r	A	T	17: 31,137,861 (GRCm39)	Q97H	probably benign	Het
Gm27047	T	C	6: 130,606,909 (GRCm39)		noncoding transcript	Het
Igkv3-3	A	C	6: 70,664,223 (GRCm39)	I22L	probably benign	Het
Inpp5b	G	T	4: 124,636,824 (GRCm39)		probably null	Het
Ipo9	C	A	1: 135,330,097 (GRCm39)	E448*	probably null	Het
Itgb2l	A	T	16: 96,229,003 (GRCm39)	I400N	probably damaging	Het
Kat6b	T	A	14: 21,567,062 (GRCm39)	H40Q	probably damaging	Het
Kcna7	G	A	7: 45,056,015 (GRCm39)	R77H	probably damaging	Het
Kcnq2	G	T	2: 180,728,554 (GRCm39)		probably benign	Het
Klf7	T	C	1: 64,118,439 (GRCm39)	T53A	probably benign	Het
Kmt2a	A	G	9: 44,729,649 (GRCm39)		probably benign	Het
Lrp10	C	T	14: 54,705,802 (GRCm39)	R331C	probably benign	Het
Map4k5	A	T	12: 69,878,332 (GRCm39)	D289E	probably benign	Het
Mfsd4b2	A	T	10: 39,799,773 (GRCm39)	M43K	possibly damaging	Het
Msr1	T	G	8: 40,076,997 (GRCm39)	R138S	possibly damaging	Het
Myh7b	G	C	2: 155,474,293 (GRCm39)	R1669S	possibly damaging	Het
Myh9	G	A	15: 77,648,723 (GRCm39)	A1711V	probably benign	Het
Myo18b	A	G	5: 113,023,083 (GRCm39)		probably benign	Het
Nampt	A	T	12: 32,883,120 (GRCm39)	N102Y	possibly damaging	Het
Nell2	T	C	15: 95,371,460 (GRCm39)	I92V	probably benign	Het
Nes	A	G	3: 87,884,521 (GRCm39)	N883D	probably benign	Het
Neurl3	T	A	1: 36,312,463 (GRCm39)		probably benign	Het
Ocln	T	A	13: 100,675,930 (GRCm39)	T188S	probably benign	Het
Or2ag20	T	A	7: 106,464,937 (GRCm39)	M250K	probably damaging	Het
Or5m10	T	C	2: 85,717,585 (GRCm39)	F147S	probably benign	Het
Parp14	T	A	16: 35,664,733 (GRCm39)	Q1305L	probably benign	Het
Pde3a	C	T	6: 141,433,682 (GRCm39)	Q855*	probably null	Het
Pde4b	T	C	4: 102,052,311 (GRCm39)		probably benign	Het
Pdk2	T	C	11: 94,930,242 (GRCm39)	M65V	probably benign	Het
Phf21a	T	C	2: 92,182,201 (GRCm39)	S377P	probably damaging	Het
Plcb2	T	A	2: 118,548,703 (GRCm39)	T408S	probably benign	Het
Ppp1r12b	G	T	1: 134,883,471 (GRCm39)	A17E	probably benign	Het
Ppp6r2	A	G	15: 89,167,152 (GRCm39)	D789G	probably benign	Het
Prdm16	T	C	4: 154,419,719 (GRCm39)	M897V	possibly damaging	Het
Prss57	A	G	10: 79,620,178 (GRCm39)		probably null	Het
Psd	G	T	19: 46,310,907 (GRCm39)	L381I	probably benign	Het
Ptprq	A	T	10: 107,370,540 (GRCm39)	D2050E	probably benign	Het
Rfc1	G	T	5: 65,423,505 (GRCm39)	N1034K	probably damaging	Het
Ryr3	C	T	2: 112,661,504 (GRCm39)	G1829S	probably benign	Het
Scaper	T	C	9: 55,767,003 (GRCm39)		probably null	Het
Scn5a	A	G	9: 119,351,632 (GRCm39)	I783T	probably damaging	Het
Slc28a1	A	G	7: 80,818,796 (GRCm39)	N583S	possibly damaging	Het
Slc35e3	C	T	10: 117,580,884 (GRCm39)	G140D	probably damaging	Het
Sptlc1	A	G	13: 53,496,218 (GRCm39)	S376P	probably benign	Het
Sspo	G	A	6: 48,441,729 (GRCm39)	C1913Y	probably damaging	Het
Taar7b	A	T	10: 23,876,845 (GRCm39)	I337F	possibly damaging	Het
Tdpoz2	T	A	3: 93,559,235 (GRCm39)	I246F	probably damaging	Het
Trpa1	C	T	1: 14,946,183 (GRCm39)	V983M	probably damaging	Het
Trpm5	A	T	7: 142,626,521 (GRCm39)	M1112K	probably benign	Het
Tsbp1	G	A	17: 34,667,770 (GRCm39)	C154Y	possibly damaging	Het
Uso1	A	T	5: 92,340,594 (GRCm39)	K670I	probably benign	Het
Washc4	A	G	10: 83,392,771 (GRCm39)	D257G	probably damaging	Het
Wdr41	T	A	13: 95,151,725 (GRCm39)		probably null	Het
Zbtb17	A	G	4: 141,193,860 (GRCm39)	Q668R	possibly 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
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
R7278:Slc6a9	UTSW	4	117,725,303 (GRCm39)	missense	probably benign	0.31
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'- CTTCTTCAGGTGAGGAGTGAAG -3'
(R):5'- TCAAGGTGACAGCAGCCATC -3'

Sequencing Primer
(F):5'- CTTCAGGTGAGGAGTGAAGATGGAC -3'
(R):5'- TGTGATGGGGCAGGCCTC -3'

Posted On

2016-06-06