Mutagenetix > Incidental Mutation

Incidental Mutation 'R2872:Slc6a9'

253868

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

040460-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2872 (G1)

Quality Score

213

Status

Not validated

Chromosome

Chromosomal Location

117692240-117726502 bp(+) (GRCm39)

Type of Mutation

start codon destroyed

DNA Base Change (assembly)

T to A at 117706578 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 1 (M1K)

Ref Sequence

ENSEMBL: ENSMUSP00000127289 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030269] [ENSMUST00000063857] [ENSMUST00000132043] [ENSMUST00000149168] [ENSMUST00000163288] [ENSMUST00000169885] [ENSMUST00000169990]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000030269

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542

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

Predicted Effect

probably benign
Transcript: ENSMUST00000063857

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542

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

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

noncoding transcript
Transcript: ENSMUST00000136476

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 null
Transcript: ENSMUST00000163288
AA Change: M1K

PolyPhen 2 Score 0.024 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: M1K

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164716

Predicted Effect

probably benign
Transcript: ENSMUST00000169885

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542

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

Meta Mutation Damage Score

0.9664

Coding Region Coverage

1x: 99.6%
3x: 98.6%
10x: 94.5%
20x: 80.3%

Validation Efficiency

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	A	G	11: 109,846,002 (GRCm39)	C811R	possibly damaging	Het
Ak8	T	C	2: 28,632,732 (GRCm39)	I317T	possibly damaging	Het
Als2	A	G	1: 59,250,296 (GRCm39)	S483P	probably damaging	Het
Arhgef10	T	C	8: 15,025,093 (GRCm39)		probably null	Het
Arhgef10	A	G	8: 15,025,666 (GRCm39)	I459V	probably benign	Het
Armc2	C	T	10: 41,842,696 (GRCm39)		probably null	Het
Atp12a	A	G	14: 56,624,407 (GRCm39)	R952G	possibly damaging	Het
Atp6v1g1	A	G	4: 63,468,258 (GRCm39)	Y87C	probably benign	Het
Cilk1	A	T	9: 78,047,382 (GRCm39)		probably null	Het
Col12a1	A	T	9: 79,606,831 (GRCm39)	F531I	probably damaging	Het
Csmd2	T	C	4: 128,451,511 (GRCm39)	F113S	unknown	Het
Ctnnd1	C	T	2: 84,451,232 (GRCm39)	V123I	possibly damaging	Het
Cyp4a14	C	A	4: 115,344,498 (GRCm39)	G456W	probably damaging	Het
Cyp4a30b	A	G	4: 115,315,559 (GRCm39)	H260R	possibly damaging	Het
Eef2	GCCC	GCCCC	10: 81,014,601 (GRCm39)		probably null	Het
Frmpd4	A	T	X: 166,260,243 (GRCm39)	D1166E	probably benign	Het
Gpr156	T	A	16: 37,812,585 (GRCm39)	V307D	probably damaging	Het
Gpr35	G	A	1: 92,910,848 (GRCm39)	V187I	probably benign	Het
Gria2	G	A	3: 80,609,799 (GRCm39)	T670I	probably damaging	Het
Hdac10	G	T	15: 89,010,059 (GRCm39)	Q300K	possibly damaging	Het
Hdhd2	T	C	18: 77,042,702 (GRCm39)	F44L	probably damaging	Het
Hjurp	GT	GTT	1: 88,194,246 (GRCm39)		probably null	Het
Hmcn1	A	T	1: 150,614,467 (GRCm39)	V1313D	possibly damaging	Het
Ift172	C	T	5: 31,415,205 (GRCm39)	V1335I	probably benign	Het
Igsf9b	A	G	9: 27,233,519 (GRCm39)	I340V	probably benign	Het
Kif1c	A	G	11: 70,614,907 (GRCm39)	E567G	probably damaging	Het
Klf8	A	T	X: 152,165,678 (GRCm39)	E82D	probably damaging	Het
Matr3	T	A	18: 35,705,349 (GRCm39)	S91R	probably benign	Het
Mideas	C	T	12: 84,203,245 (GRCm39)	G886S	probably benign	Het
Mroh2a	GCCC	GC	1: 88,159,979 (GRCm39)		probably null	Het
Mtor	T	A	4: 148,624,487 (GRCm39)	M2089K	probably benign	Het
Myo9b	T	C	8: 71,743,610 (GRCm39)	Y224H	probably benign	Het
Nlrc3	T	C	16: 3,775,190 (GRCm39)	D774G	possibly damaging	Het
Notum	A	G	11: 120,551,022 (GRCm39)	V48A	probably benign	Het
Nox3	T	C	17: 3,733,191 (GRCm39)	H240R	probably damaging	Het
Nsun2	A	G	13: 69,777,801 (GRCm39)	T425A	probably damaging	Het
Or10g1	T	G	14: 52,648,318 (GRCm39)	T4P	probably benign	Het
Or10z1	T	C	1: 174,078,092 (GRCm39)	S134G	probably benign	Het
Or1o4	A	G	17: 37,590,867 (GRCm39)	V148A	possibly damaging	Het
Or52u1	T	C	7: 104,237,700 (GRCm39)	S230P	possibly damaging	Het
Ostc	T	C	3: 130,497,157 (GRCm39)	N80S	probably damaging	Het
Otud4	T	A	8: 80,387,702 (GRCm39)	N300K	possibly damaging	Het
Palmd	T	C	3: 116,717,400 (GRCm39)	R366G	possibly damaging	Het
Paqr5	A	T	9: 61,876,061 (GRCm39)		probably null	Het
Parp1	A	G	1: 180,401,230 (GRCm39)	D45G	probably damaging	Het
Pcdhga9	T	A	18: 37,870,524 (GRCm39)	Y118N	possibly damaging	Het
Pkd1l2	C	T	8: 117,764,903 (GRCm39)	V1332I	probably benign	Het
Plcl1	A	T	1: 55,736,309 (GRCm39)	D550V	probably benign	Het
Plekhg1	T	G	10: 3,913,982 (GRCm39)	S1235A	probably benign	Het
Plekhg5	T	A	4: 152,191,960 (GRCm39)	C433S	probably benign	Het
Plin2	A	G	4: 86,586,915 (GRCm39)	M1T	probably null	Het
Polg2	A	G	11: 106,666,251 (GRCm39)		probably null	Het
Ppp1r7	T	A	1: 93,285,585 (GRCm39)		probably null	Het
Prdx4	A	G	X: 154,123,460 (GRCm39)	V15A	probably benign	Het
Rapgef6	T	A	11: 54,552,001 (GRCm39)	F956L	probably damaging	Het
Rasl12	A	G	9: 65,315,605 (GRCm39)	N83S	probably benign	Het
Rel	T	C	11: 23,711,129 (GRCm39)	I13V	probably benign	Het
Reln	C	T	5: 22,254,789 (GRCm39)	V527I	possibly damaging	Het
Sel1l3	C	T	5: 53,295,225 (GRCm39)	W792*	probably null	Het
Shoc1	A	C	4: 59,093,850 (GRCm39)	L226R	probably damaging	Het
Slc39a8	T	A	3: 135,592,554 (GRCm39)		probably null	Het
Smpdl3a	T	A	10: 57,678,626 (GRCm39)	F143Y	possibly damaging	Het
Spsb4	G	T	9: 96,878,071 (GRCm39)	T84K	probably damaging	Het
Tbc1d8	A	G	1: 39,444,398 (GRCm39)	F187S	probably damaging	Het
Tdpoz3	T	A	3: 93,733,735 (GRCm39)	F137I	probably benign	Het
Tgm7	G	A	2: 120,940,174 (GRCm39)		probably benign	Het
Tnni3k	C	T	3: 154,644,387 (GRCm39)		probably null	Het
Tpd52	A	T	3: 9,068,466 (GRCm39)	Y16*	probably null	Het
Trpa1	A	G	1: 14,957,844 (GRCm39)	C705R	probably damaging	Het
Ttn	A	G	2: 76,581,195 (GRCm39)	S23233P	probably damaging	Het
Uevld	T	C	7: 46,597,693 (GRCm39)	D154G	probably null	Het
Ugt1a1	AT	A	1: 88,140,093 (GRCm39)		probably null	Het
Zfp292	G	A	4: 34,808,595 (GRCm39)	T1483M	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
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
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'- CTTGCTGAAAACAAGGGAACAC -3'
(R):5'- CAGACCACTTAGTCCCTTGC -3'

Sequencing Primer
(F):5'- TCGTTCTCCAGCTCCGGAG -3'
(R):5'- AGTCCCTTGCCCCACCAC -3'

Posted On

2014-12-04