Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00904:Slc6a9'

27208

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Slc6a9

Ensembl Gene

ENSMUSG00000028542

Gene Name

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

Synonyms

Glyt-1, Glyt1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL00904

Quality Score

Status

Chromosome

Chromosomal Location

117692240-117726502 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 117721814 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 280 (L280P)

Ref Sequence

ENSEMBL: ENSMUSP00000127093 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000030269
AA Change: L392P

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

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: L392P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000063857
AA Change: L392P

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

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: L392P

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: 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: L396P

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

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: L396P

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000169885
AA Change: L280P

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

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: L280P

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163974

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164716

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: 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

Coding Region Coverage

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: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aak1	G	T	6: 86,923,135 (GRCm39)	G236C	probably damaging	Het
Abi1	C	T	2: 22,831,942 (GRCm39)	R404Q	possibly damaging	Het
Atp8b3	C	T	10: 80,364,598 (GRCm39)	G532R	probably damaging	Het
Bysl	C	T	17: 47,912,796 (GRCm39)	M331I	probably benign	Het
Ccdc121rt3	G	A	5: 112,502,994 (GRCm39)	R237*	probably null	Het
Cndp1	A	G	18: 84,629,790 (GRCm39)	S468P	probably benign	Het
Esd	A	G	14: 74,987,128 (GRCm39)	*266W	probably null	Het
F5	T	C	1: 164,021,578 (GRCm39)	V1351A	probably benign	Het
Fchsd2	A	G	7: 100,920,829 (GRCm39)	D454G	probably benign	Het
Fndc1	T	A	17: 7,975,195 (GRCm39)	M1415L	probably benign	Het
Ghr	T	A	15: 3,357,602 (GRCm39)	Y222F	probably benign	Het
Gtf3c2	C	T	5: 31,330,202 (GRCm39)	S299N	probably damaging	Het
Ice1	C	T	13: 70,750,408 (GRCm39)	D93N	probably damaging	Het
Ints7	T	A	1: 191,328,276 (GRCm39)		probably null	Het
Kif18a	A	G	2: 109,122,471 (GRCm39)	D182G	probably damaging	Het
Mcm9	A	T	10: 53,499,017 (GRCm39)	H308Q	possibly damaging	Het
Mesp2	A	G	7: 79,462,401 (GRCm39)	D319G	probably benign	Het
Mrpl55	T	A	11: 59,096,499 (GRCm39)	S84T	probably benign	Het
Mybpc3	T	C	2: 90,950,374 (GRCm39)	V123A	probably benign	Het
Myom1	T	C	17: 71,406,944 (GRCm39)		probably benign	Het
Nfia	C	T	4: 97,953,623 (GRCm39)	P325S	probably damaging	Het
Notch4	T	C	17: 34,794,535 (GRCm39)		probably null	Het
Npepps	A	C	11: 97,149,132 (GRCm39)	V130G	probably damaging	Het
Or7c70	A	T	10: 78,683,597 (GRCm39)	S51T	probably damaging	Het
Pja2	G	T	17: 64,590,526 (GRCm39)	T669K	probably damaging	Het
Rnf112	G	T	11: 61,343,610 (GRCm39)	D98E	probably damaging	Het
Rsl1d1	G	A	16: 11,017,558 (GRCm39)	T136I	probably damaging	Het
Samsn1	A	T	16: 75,706,008 (GRCm39)		probably benign	Het
Svep1	T	C	4: 58,097,398 (GRCm39)	N1382D	probably benign	Het
Vmn2r100	T	G	17: 19,746,262 (GRCm39)	C474G	probably damaging	Het
Vmn2r74	C	T	7: 85,606,788 (GRCm39)	R186H	probably benign	Het
Wdr7	T	C	18: 63,929,302 (GRCm39)	I1046T	probably benign	Het

Other mutations in Slc6a9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
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

Posted On

2013-04-17