Incidental Mutation 'R3499:Slc6a9'
| ID |
273695 |
| 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 |
040662-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3499 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
4 |
| Chromosomal Location |
117692240-117726502 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 117714000 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 105
(I105V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000127289
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000030269]
[ENSMUST00000063857]
[ENSMUST00000123994]
[ENSMUST00000132043]
[ENSMUST00000149168]
[ENSMUST00000163288]
[ENSMUST00000169990]
[ENSMUST00000169885]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000030269
AA Change: I101V
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000030269
Gene: ENSMUSG00000028542
AA Change: I101V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SNF
|
27 |
562 |
5.1e-234 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000063857
AA Change: I101V
PolyPhen 2
Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
|
| SMART Domains |
Protein: ENSMUSP00000066102
Gene: ENSMUSG00000028542
AA Change: I101V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SNF
|
27 |
562 |
5.1e-234 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000123994
AA Change: I36V
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000127806
Gene: ENSMUSG00000028542
AA Change: I36V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SNF
|
1 |
114 |
1.5e-46 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000132043
AA Change: I106V
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000122676
Gene: ENSMUSG00000028542
AA Change: I106V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SNF
|
32 |
321 |
1.4e-132 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000135769
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136476
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000149168
AA Change: D73G
|
| SMART Domains |
Protein: ENSMUSP00000129359
Gene: ENSMUSG00000028542
AA Change: D73G
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
91 |
116 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000163288
AA Change: I105V
PolyPhen 2
Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000127289
Gene: ENSMUSG00000028542
AA Change: I105V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SNF
|
46 |
566 |
2.1e-212 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000169990
AA Change: I158V
PolyPhen 2
Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
|
| SMART Domains |
Protein: ENSMUSP00000127203
Gene: ENSMUSG00000028542
AA Change: I158V
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:SNF
|
84 |
373 |
2.3e-132 |
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 |
|
| Meta Mutation Damage Score |
0.2227 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.7%
- 20x: 96.3%
|
| Validation Efficiency |
100% (46/46) |
| 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: 46 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 6430571L13Rik |
A |
T |
9: 107,219,678 (GRCm39) |
T44S |
probably damaging |
Het |
| Cass4 |
C |
T |
2: 172,274,478 (GRCm39) |
P753L |
probably damaging |
Het |
| Cimip3 |
AC |
A |
17: 47,744,348 (GRCm39) |
|
probably benign |
Het |
| Ctif |
A |
T |
18: 75,744,828 (GRCm39) |
L92Q |
possibly damaging |
Het |
| Dnah11 |
C |
A |
12: 117,874,758 (GRCm39) |
D4036Y |
probably damaging |
Het |
| Dnah17 |
C |
T |
11: 117,971,675 (GRCm39) |
|
probably benign |
Het |
| Dnah6 |
G |
C |
6: 73,009,616 (GRCm39) |
A3725G |
probably benign |
Het |
| Ebag9 |
A |
G |
15: 44,493,528 (GRCm39) |
N117D |
probably benign |
Het |
| Elf4 |
C |
T |
X: 47,507,942 (GRCm39) |
E158K |
probably benign |
Het |
| Ephb6 |
C |
T |
6: 41,593,093 (GRCm39) |
R444* |
probably null |
Het |
| Fcgbpl1 |
T |
A |
7: 27,853,980 (GRCm39) |
I1648K |
probably benign |
Het |
| Fndc1 |
C |
T |
17: 7,972,416 (GRCm39) |
M1505I |
possibly damaging |
Het |
| Gpr35 |
A |
G |
1: 92,911,113 (GRCm39) |
Y275C |
probably damaging |
Het |
| Hmcn1 |
A |
T |
1: 150,480,853 (GRCm39) |
I4441N |
probably damaging |
Het |
| Kif13a |
T |
C |
13: 46,978,815 (GRCm39) |
D195G |
probably damaging |
Het |
| Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
| Ksr2 |
C |
A |
5: 117,827,640 (GRCm39) |
T473K |
probably damaging |
Het |
| Kxd1 |
T |
C |
8: 70,966,632 (GRCm39) |
|
probably null |
Het |
| Lyplal1 |
A |
G |
1: 185,820,857 (GRCm39) |
S197P |
possibly damaging |
Het |
| Macf1 |
A |
T |
4: 123,421,098 (GRCm39) |
L52* |
probably null |
Het |
| Mrgprb5 |
A |
G |
7: 47,818,661 (GRCm39) |
S25P |
probably benign |
Het |
| Nucb1 |
T |
C |
7: 45,148,300 (GRCm39) |
H171R |
probably benign |
Het |
| Or10d1c |
A |
G |
9: 38,893,761 (GRCm39) |
L193P |
probably damaging |
Het |
| Or4a15 |
A |
T |
2: 89,193,294 (GRCm39) |
F160I |
probably benign |
Het |
| Or56b35 |
G |
A |
7: 104,963,607 (GRCm39) |
C132Y |
probably damaging |
Het |
| Or8h8 |
A |
G |
2: 86,753,373 (GRCm39) |
F168L |
possibly damaging |
Het |
| Or8k18 |
A |
G |
2: 86,085,185 (GRCm39) |
M284T |
possibly damaging |
Het |
| Prkdc |
A |
T |
16: 15,585,889 (GRCm39) |
I2476F |
probably damaging |
Het |
| Ptprf |
A |
T |
4: 118,082,127 (GRCm39) |
I1037N |
probably damaging |
Het |
| Ralgapa1 |
T |
G |
12: 55,741,928 (GRCm39) |
|
probably benign |
Het |
| Ranbp17 |
GCCTGGATACTGACC |
GCC |
11: 33,169,203 (GRCm39) |
|
probably benign |
Het |
| Sla2 |
G |
A |
2: 156,717,862 (GRCm39) |
R137C |
probably damaging |
Het |
| Slc28a3 |
C |
T |
13: 58,721,253 (GRCm39) |
|
probably benign |
Het |
| Slc44a4 |
A |
G |
17: 35,140,656 (GRCm39) |
D283G |
probably benign |
Het |
| Smgc |
A |
G |
15: 91,726,206 (GRCm39) |
T51A |
possibly damaging |
Het |
| Smyd5 |
T |
A |
6: 85,415,172 (GRCm39) |
L60H |
probably damaging |
Het |
| Spred1 |
A |
T |
2: 117,005,867 (GRCm39) |
M210L |
probably benign |
Het |
| Syne2 |
G |
A |
12: 76,101,752 (GRCm39) |
|
probably null |
Het |
| Tab3 |
T |
C |
X: 84,658,727 (GRCm39) |
I418T |
probably benign |
Het |
| Tbc1d12 |
A |
T |
19: 38,884,478 (GRCm39) |
E343V |
possibly damaging |
Het |
| Tktl2 |
T |
A |
8: 66,965,897 (GRCm39) |
I485N |
probably damaging |
Het |
| Tmem181a |
T |
A |
17: 6,330,894 (GRCm39) |
Y51* |
probably null |
Het |
| Tmem229b-ps |
C |
T |
10: 53,351,223 (GRCm39) |
|
noncoding transcript |
Het |
| Trip11 |
A |
G |
12: 101,859,953 (GRCm39) |
I307T |
possibly damaging |
Het |
| Ttf1 |
T |
C |
2: 28,955,499 (GRCm39) |
S288P |
possibly damaging |
Het |
| Zfp395 |
G |
T |
14: 65,628,742 (GRCm39) |
R198L |
possibly 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 |
|
R2872:Slc6a9
|
UTSW |
4 |
117,706,578 (GRCm39) |
start codon destroyed |
probably null |
0.02 |
|
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'- AAGCACGAAGGTTTTACTGTGG -3'
(R):5'- CCTTGGCCATTGATGTTGC -3'
Sequencing Primer
(F):5'- CACGAAGGTTTTACTGTGGGTTTG -3'
(R):5'- GCCATTGATGTTGCGCTTG -3'
|
| Posted On |
2015-04-02 |
Incidental Mutation