Mutagenetix > Incidental Mutation

Incidental Mutation 'R5726:Slc6a9'

452479

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

043344-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5726 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

117692240-117726502 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 117721210 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 208 (Y208C)

Ref Sequence

ENSEMBL: ENSMUSP00000127093 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000030269
AA Change: Y320C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: Y320C

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000063857
AA Change: Y320C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: Y320C

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

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: Y324C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: Y324C

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000163974

Predicted Effect

probably damaging
Transcript: ENSMUST00000169885
AA Change: Y208C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: Y208C

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

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

Meta Mutation Damage Score

0.2311

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.6%
20x: 93.3%

Validation Efficiency

100% (72/72)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9130023H24Rik	T	C	7: 127,835,832 (GRCm39)	K254E	probably damaging	Het
Aak1	C	T	6: 86,902,106 (GRCm39)	Q92*	probably null	Het
Acss3	T	C	10: 106,959,183 (GRCm39)	T88A	possibly damaging	Het
Adcy4	A	T	14: 56,021,118 (GRCm39)	S6R	probably damaging	Het
Aldh1l2	T	C	10: 83,348,170 (GRCm39)	E311G	possibly damaging	Het
Arhgap25	C	T	6: 87,440,441 (GRCm39)	S402N	probably benign	Het
Btn1a1	T	A	13: 23,643,522 (GRCm39)	D309V	probably damaging	Het
Cdh23	C	T	10: 60,243,259 (GRCm39)	V1037M	probably damaging	Het
Clcn2	T	C	16: 20,529,285 (GRCm39)		probably benign	Het
Cln3	T	C	7: 126,174,673 (GRCm39)	T276A	probably null	Het
CN725425	A	G	15: 91,144,706 (GRCm39)	E523G	possibly damaging	Het
Crppa	T	C	12: 36,597,829 (GRCm39)	V320A	probably damaging	Het
Cspg4	A	T	9: 56,793,188 (GRCm39)	T308S	probably damaging	Het
Dgkh	G	T	14: 78,862,342 (GRCm39)	F208L	probably benign	Het
Eif2ak4	A	G	2: 118,273,613 (GRCm39)	D846G	probably damaging	Het
Fmo4	A	G	1: 162,635,828 (GRCm39)		probably null	Het
Foxp4	A	G	17: 48,180,033 (GRCm39)	Y623H	unknown	Het
Fxr2	T	C	11: 69,524,172 (GRCm39)	V10A	probably benign	Het
Gm10271	T	C	10: 116,792,792 (GRCm39)		probably null	Het
Gsk3b	T	C	16: 38,028,498 (GRCm39)		probably benign	Het
Ift43	T	A	12: 86,208,957 (GRCm39)	D169E	probably damaging	Het
Ift57	T	A	16: 49,519,861 (GRCm39)	L54H	probably damaging	Het
Ighv1-37	T	C	12: 114,860,294 (GRCm39)		probably benign	Het
Kl	A	G	5: 150,915,003 (GRCm39)	N910S	possibly damaging	Het
Lrp2	T	C	2: 69,339,491 (GRCm39)	D1140G	probably damaging	Het
Map1a	G	A	2: 121,135,546 (GRCm39)	A1883T	probably damaging	Het
Map4k2	G	T	19: 6,401,362 (GRCm39)	G611C	probably damaging	Het
Mical1	A	G	10: 41,359,692 (GRCm39)		probably benign	Het
Myh14	A	G	7: 44,292,886 (GRCm39)		probably null	Het
Myh8	T	A	11: 67,185,392 (GRCm39)	V881D	possibly damaging	Het
Myo1g	G	T	11: 6,459,420 (GRCm39)	Q817K	probably benign	Het
Nin	A	C	12: 70,124,953 (GRCm39)	V123G	probably damaging	Het
Nup160	A	G	2: 90,548,195 (GRCm39)	D976G	probably damaging	Het
Nup210l	A	T	3: 90,036,514 (GRCm39)		probably null	Het
Or5an1c	A	G	19: 12,218,644 (GRCm39)	I127T	probably damaging	Het
Phf14	T	C	6: 11,933,537 (GRCm39)		probably benign	Het
Podxl2	T	C	6: 88,825,721 (GRCm39)	D400G	probably damaging	Het
Pygl	C	T	12: 70,237,916 (GRCm39)	W707*	probably null	Het
Rnf19b	T	C	4: 128,965,685 (GRCm39)	V261A	possibly damaging	Het
Rnf213	A	G	11: 119,307,284 (GRCm39)	Y648C	probably damaging	Het
Scn5a	C	T	9: 119,362,913 (GRCm39)	R569H	probably damaging	Het
Sdk2	A	G	11: 113,742,626 (GRCm39)	L761P	probably damaging	Het
Shroom3	C	T	5: 93,090,864 (GRCm39)	P1124S	probably benign	Het
Sirt4	A	G	5: 115,617,705 (GRCm39)	V317A	probably benign	Het
Skic3	T	C	13: 76,266,466 (GRCm39)	Y238H	probably damaging	Het
Slc12a2	G	T	18: 58,029,426 (GRCm39)	A271S	probably benign	Het
Snap23	T	A	2: 120,414,752 (GRCm39)		probably benign	Het
Sra1	C	T	18: 36,803,226 (GRCm39)		probably benign	Het
Srbd1	C	T	17: 86,428,157 (GRCm39)	D359N	possibly damaging	Het
Srp19	A	G	18: 34,464,826 (GRCm39)	Y22C	probably damaging	Het
Sstr4	T	C	2: 148,238,003 (GRCm39)	S205P	probably damaging	Het
Sv2b	T	C	7: 74,773,962 (GRCm39)	D503G	possibly damaging	Het
Tbc1d30	C	T	10: 121,103,479 (GRCm39)	V518M	probably damaging	Het
Tlr4	A	G	4: 66,758,652 (GRCm39)	K482E	probably benign	Het
Tpm1	G	A	9: 66,930,694 (GRCm39)	L310F	probably damaging	Het
Trpm6	A	G	19: 18,830,981 (GRCm39)	Y1282C	probably damaging	Het
Tsc22d1	T	A	14: 76,742,757 (GRCm39)	L65*	probably null	Het
Ttc39c	C	A	18: 12,830,992 (GRCm39)	A284D	probably damaging	Het
Txndc16	G	A	14: 45,403,221 (GRCm39)	H297Y	probably benign	Het
Utrn	A	T	10: 12,545,550 (GRCm39)	D1698E	probably benign	Het
Vmn1r232	C	T	17: 21,133,601 (GRCm39)	R333H	probably benign	Het
Vmn2r14	A	T	5: 109,365,486 (GRCm39)	D529E	possibly damaging	Het
Vmn2r70	C	T	7: 85,208,315 (GRCm39)	V721I	probably damaging	Het
Zbtb18	A	G	1: 177,276,119 (GRCm39)	H484R	probably damaging	Het
Zc3h13	T	A	14: 75,568,269 (GRCm39)	S1187R	possibly damaging	Het
Zfhx4	T	A	3: 5,468,381 (GRCm39)	D2846E	probably benign	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
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'- TGTACTACCTGACCCCACAATG -3'
(R):5'- GCCTTCTACTTTCACACTGGAG -3'

Sequencing Primer
(F):5'- ATCCTGGAGGCCAAGGTG -3'
(R):5'- TGGAGATACAAGATCCTCAAGACTTC -3'

Posted On

2017-01-03