Mutagenetix > Incidental Mutations

Incidental Mutation 'R0051:Slc6a9'

64278

Institutional Source

Beutler Lab

Gene Symbol

Slc6a9

Ensembl Gene

ENSMUSG00000028542

Gene Name

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

Synonyms

Glyt1, Glyt-1

MMRRC Submission

038345-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R0051 (G1)

Quality Score

119

Status

Validated

Chromosome

Chromosomal Location

117834506-117875198 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 117864859 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 440 (F440L)

Ref Sequence

ENSEMBL: ENSMUSP00000127289 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000030269
AA Change: F436L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: F436L

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000063857
AA Change: F436L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: F436L

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: 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

noncoding transcript
Transcript: ENSMUST00000154439

Predicted Effect

probably damaging
Transcript: ENSMUST00000163288
AA Change: F440L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: F440L

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163974

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164716

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: ENSMUST00000167287

SMART Domains

Protein: ENSMUSP00000126161
Gene: ENSMUSG00000078588

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000169885
AA Change: F324L

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: F324L

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

0.6496

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.1%
20x: 93.8%

Validation Efficiency

100% (64/64)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930432E11Rik	A	G	7: 29,579,101		noncoding transcript	Het
Abr	T	A	11: 76,472,502	Q163L	probably benign	Het
AI314180	A	G	4: 58,832,729	L877S	probably damaging	Het
Ankrd11	C	A	8: 122,889,742	C2457F	probably damaging	Het
Anks3	G	C	16: 4,947,749	T163S	probably benign	Het
Cacna1d	G	A	14: 30,111,095	P908S	probably damaging	Het
Ccdc146	C	A	5: 21,316,904	R374L	possibly damaging	Het
Cdc45	G	T	16: 18,794,774	A348E	probably damaging	Het
Cfap46	A	G	7: 139,676,035	C300R	probably damaging	Het
Coq2	T	C	5: 100,663,685	N146S	probably benign	Het
Dalrd3	T	C	9: 108,572,215	V120A	possibly damaging	Het
Dcp2	T	A	18: 44,405,374		probably benign	Het
Ddx39	A	G	8: 83,720,622	K137R	possibly damaging	Het
Diaph3	A	G	14: 87,037,454		probably null	Het
Dmbt1	G	T	7: 131,119,496	R1668L	possibly damaging	Het
Dnah7a	T	G	1: 53,521,086		probably benign	Het
Dpp7	A	G	2: 25,356,095	Y49H	possibly damaging	Het
Drd5	A	G	5: 38,320,614	S317G	probably benign	Het
Ecsit	C	T	9: 22,076,288	V152I	probably benign	Het
Emc1	T	A	4: 139,375,163	M923K	possibly damaging	Het
Fam102a	G	A	2: 32,558,053	R58Q	possibly damaging	Het
Fcrl6	A	T	1: 172,598,753	L159Q	probably benign	Het
Frrs1	T	C	3: 116,885,297		probably benign	Het
Hspd1	A	G	1: 55,082,046		probably benign	Het
Impg2	T	A	16: 56,258,048	S458T	probably damaging	Het
Klf17	T	C	4: 117,760,392	Y256C	probably damaging	Het
Lnx2	A	G	5: 147,029,353	F319L	probably damaging	Het
Mafg	G	T	11: 120,629,604	R57S	probably damaging	Het
Med13l	T	A	5: 118,742,655	W1271R	probably damaging	Het
Mrgprb1	A	G	7: 48,447,214	S24P	probably benign	Het
Mtrf1l	T	C	10: 5,813,384	E315G	probably damaging	Het
Naip1	T	C	13: 100,411,001	E1239G	probably damaging	Het
Ncaph2	T	C	15: 89,369,664	S320P	probably damaging	Het
Nek11	A	G	9: 105,218,539		probably benign	Het
Nlrp2	A	T	7: 5,322,334		probably benign	Het
Odf3	C	A	7: 140,850,221		probably benign	Het
Rbm26	A	C	14: 105,152,540	V216G	possibly damaging	Het
Rnf115	A	G	3: 96,785,022	D178G	probably damaging	Het
Rtel1	C	T	2: 181,350,656	Q424*	probably null	Het
Rwdd4a	A	G	8: 47,537,365		probably benign	Het
Ryr3	T	C	2: 112,869,075	D890G	probably damaging	Het
Scarb1	C	A	5: 125,281,100		probably null	Het
Serpina10	A	G	12: 103,626,897		probably benign	Het
Slc12a5	T	A	2: 164,986,663	W508R	probably damaging	Het
Slc43a2	T	C	11: 75,562,850	C225R	probably damaging	Het
Stac3	G	A	10: 127,508,148	R305H	probably damaging	Het
Stk32b	A	G	5: 37,459,596		probably benign	Het
Syna	A	T	5: 134,559,543	L184H	probably damaging	Het
Tmprss7	T	C	16: 45,673,939	N401S	probably damaging	Het
Yeats2	T	A	16: 20,193,724	Y557*	probably null	Het
Zcchc11	T	G	4: 108,527,004	S1089R	probably damaging	Het
Zfp352	T	C	4: 90,224,285	S221P	probably damaging	Het
Zfp575	A	G	7: 24,586,087	V43A	probably benign	Het
Zfp775	A	G	6: 48,620,772	T527A	probably benign	Het

Other mutations in Slc6a9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00904:Slc6a9	APN	4	117864617	missense	probably damaging	1.00
IGL01728:Slc6a9	APN	4	117864605	missense	probably damaging	1.00
IGL02111:Slc6a9	APN	4	117864013	missense	probably benign	0.19
R0051:Slc6a9	UTSW	4	117864859	missense	probably damaging	1.00
R1170:Slc6a9	UTSW	4	117864806	missense	possibly damaging	0.77
R2872:Slc6a9	UTSW	4	117849381	start codon destroyed	probably null	0.02
R2872:Slc6a9	UTSW	4	117849381	start codon destroyed	probably null	0.02
R3499:Slc6a9	UTSW	4	117856803	missense	probably benign	0.01
R4744:Slc6a9	UTSW	4	117867895	missense	probably benign	0.00
R4970:Slc6a9	UTSW	4	117856008	missense	probably damaging	1.00
R5055:Slc6a9	UTSW	4	117868150	splice site	probably null
R5103:Slc6a9	UTSW	4	117868155	missense	probably benign
R5726:Slc6a9	UTSW	4	117864013	missense	probably damaging	1.00
R6836:Slc6a9	UTSW	4	117867886	missense	possibly damaging	0.49
R7030:Slc6a9	UTSW	4	117857436	missense	possibly damaging	0.94
R7061:Slc6a9	UTSW	4	117868064	missense	probably benign	0.40
R7278:Slc6a9	UTSW	4	117868106	missense	probably benign	0.31
R7863:Slc6a9	UTSW	4	117864010	missense	probably damaging	1.00
R8036:Slc6a9	UTSW	4	117867886	missense	possibly damaging	0.49
R8722:Slc6a9	UTSW	4	117857255	missense	unknown
R9302:Slc6a9	UTSW	4	117849399	missense	possibly damaging	0.91
Z1176:Slc6a9	UTSW	4	117857366	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- GGAAGCAAGCTGGGTCTCCTAAAC -3'
(R):5'- TTGTCCATCAGCAGCAGCCAGTAG -3'

Sequencing Primer
(F):5'- ACTCAGGTATGGGgtgtgtg -3'
(R):5'- CAGTAGATGCCTGCCTGTG -3'

Posted On

2013-08-06