Mutagenetix > Incidental Mutation

Incidental Mutation 'R6836:Slc6a9'

534555

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6836 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

117834506-117875198 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 117867886 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 559 (A559V)

Ref Sequence

ENSEMBL: ENSMUSP00000127289 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000030269
AA Change: A555V

PolyPhen 2 Score 0.430 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: A555V

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

Predicted Effect

probably benign
Transcript: ENSMUST00000063857
AA Change: A555V

PolyPhen 2 Score 0.430 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: A555V

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: ENSMUST00000131938

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

possibly damaging
Transcript: ENSMUST00000163288
AA Change: A559V

PolyPhen 2 Score 0.485 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: A559V

Domain	Start	End	E-Value	Type
Pfam:SNF	46	566	2.1e-212	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: 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: ENSMUST00000167287

SMART Domains

Protein: ENSMUSP00000126161
Gene: ENSMUSG00000078588

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

Predicted Effect

probably benign
Transcript: ENSMUST00000169885
AA Change: A443V

PolyPhen 2 Score 0.350 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000127093
Gene: ENSMUSG00000028542
AA Change: A443V

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

0.2221

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 97.9%

Validation Efficiency

100% (62/62)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5430419D17Rik	A	T	7: 131,196,504	I81F	possibly damaging	Het
Adamtsl2	T	C	2: 27,081,706	M1T	probably null	Het
Aim2	C	G	1: 173,463,980	T317R	probably damaging	Het
Alox8	T	C	11: 69,186,505	Y473C	probably damaging	Het
Alox8	T	C	11: 69,189,889	R209G	possibly damaging	Het
Asb5	A	G	8: 54,585,071	M210V	probably benign	Het
Atp2c2	T	A	8: 119,734,415	L249Q	probably damaging	Het
AU018091	T	G	7: 3,164,156	D77A	probably damaging	Het
Bahcc1	A	T	11: 120,271,757	K294*	probably null	Het
Baz2b	C	T	2: 59,917,425	R1298Q	probably damaging	Het
Bivm	T	A	1: 44,143,136	N501K	possibly damaging	Het
Bpifb5	T	A	2: 154,228,065	I145N	probably benign	Het
Casq2	A	T	3: 102,086,760	N41I	probably damaging	Het
Ccdc18	T	C	5: 108,197,967	L993P	probably damaging	Het
Cfap44	A	G	16: 44,404,079	D50G	probably damaging	Het
Clca3a2	T	A	3: 144,806,383	I91F	probably damaging	Het
Crebbp	T	A	16: 4,180,022	H66L	possibly damaging	Het
Cyfip2	T	C	11: 46,272,640	T321A	probably benign	Het
Dido1	A	G	2: 180,662,307	V1268A	probably benign	Het
E030030I06Rik	A	C	10: 22,148,492	V174G	probably damaging	Het
Gm20730	G	T	6: 43,081,833		probably null	Het
Gm36176	T	C	10: 77,847,142		probably benign	Het
Gper1	T	A	5: 139,426,680	M260K	probably damaging	Het
Igfbp2	T	C	1: 72,849,658	L89P	probably damaging	Het
Katnal1	T	C	5: 148,894,164	N200S	probably damaging	Het
Kcnk13	G	T	12: 100,061,689	R341L	probably damaging	Het
Klhl20	T	A	1: 161,105,406	E277D	probably benign	Het
Lingo1	T	C	9: 56,619,772	Y517C	probably damaging	Het
Lrrk1	C	T	7: 66,342,779	E82K	probably benign	Het
Mtor	T	A	4: 148,489,498	V1275D	possibly damaging	Het
Ncan	C	T	8: 70,100,315	S1089N	possibly damaging	Het
Notch4	C	T	17: 34,586,100	T1643I	probably damaging	Het
Olfr1258	T	C	2: 89,930,339	C177R	probably damaging	Het
Olfr1357	A	G	10: 78,612,590	L17P	probably damaging	Het
Olfr1387	A	T	11: 49,460,077	T133S	possibly damaging	Het
Olfr539	A	C	7: 140,668,180	I298L	possibly damaging	Het
Pcdhgb6	T	C	18: 37,742,962	V241A	probably benign	Het
Phf11b	T	A	14: 59,328,123	T102S	possibly damaging	Het
Pkd1	T	A	17: 24,581,259	V2998E	probably damaging	Het
Ppp1r13b	T	C	12: 111,835,195	S352G	probably benign	Het
Ptprh	C	T	7: 4,551,135	V778M	probably damaging	Het
Ptprz1	C	T	6: 23,030,665	Q1008*	probably null	Het
Ralgapa1	A	T	12: 55,604,273		probably null	Het
Rbm20	G	A	19: 53,814,069	G336E	probably damaging	Het
Sdsl	T	C	5: 120,462,102	I77V	probably benign	Het
Serpina3b	G	A	12: 104,134,082	E308K	probably benign	Het
Sfrp5	G	A	19: 42,201,710	T101I	probably damaging	Het
Slc2a13	C	T	15: 91,321,632	V451I	probably benign	Het
Spg11	C	T	2: 122,059,535	A2109T	probably damaging	Het
Stard9	C	T	2: 120,699,843	R2194C	probably benign	Het
Tfeb	T	C	17: 47,786,198		probably null	Het
Tiam2	T	A	17: 3,414,380	I128N	probably benign	Het
Tmem161b	C	A	13: 84,222,418		probably benign	Het
Tpr	T	G	1: 150,436,673		probably null	Het
Traf3ip1	T	C	1: 91,521,000	I456T	probably benign	Het
Ttll4	T	A	1: 74,689,413	D892E	probably damaging	Het
Ubr1	T	A	2: 120,896,675		probably null	Het
Vmn2r74	T	A	7: 85,957,422	I239F	probably benign	Het
Wdfy3	C	T	5: 101,952,999	V251M	probably damaging	Het
Xylb	T	A	9: 119,391,754	L531H	probably damaging	Het
Zfp960	T	A	17: 17,088,172	C383S	probably damaging	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
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
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
R9575:Slc6a9	UTSW	4	117857406	missense	probably benign
R9627:Slc6a9	UTSW	4	117864013	missense	probably damaging	1.00
R9749:Slc6a9	UTSW	4	117864001	missense	probably damaging	0.98
Z1176:Slc6a9	UTSW	4	117857366	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- GTTGACAGTTGCCTATGCCC -3'
(R):5'- TTTCAAACGCTGCAGGCAG -3'

Sequencing Primer
(F):5'- CACCTTTTGCTGACCTAGGAGGAG -3'
(R):5'- GGGGGCGCAGTGAAAAGC -3'

Posted On

2018-09-12