Incidental Mutation 'R3880:Syngap1'
| ID |
312799 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Syngap1
|
| Ensembl Gene |
ENSMUSG00000067629 |
| Gene Name |
synaptic Ras GTPase activating protein 1 homolog (rat) |
| Synonyms |
Syngap |
| MMRRC Submission |
040794-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R3880 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
17 |
| Chromosomal Location |
27160227-27191408 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 27172038 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Asparagine
at position 82
(I82N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000154838
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000081285]
[ENSMUST00000177932]
[ENSMUST00000194598]
[ENSMUST00000201702]
[ENSMUST00000202939]
[ENSMUST00000229490]
[ENSMUST00000228963]
[ENSMUST00000231853]
|
| AlphaFold |
F6SEU4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000081285
AA Change: I82N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: I82N
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
3.23e-8 |
SMART |
|
C2
|
263 |
362 |
7.4e-10 |
SMART |
|
RasGAP
|
392 |
729 |
3.33e-118 |
SMART |
|
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
|
low complexity region
|
938 |
973 |
N/A |
INTRINSIC |
|
low complexity region
|
1040 |
1068 |
N/A |
INTRINSIC |
|
low complexity region
|
1110 |
1125 |
N/A |
INTRINSIC |
|
coiled coil region
|
1186 |
1259 |
N/A |
INTRINSIC |
|
low complexity region
|
1308 |
1326 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175377
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000177932
AA Change: I141N
PolyPhen 2
Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: I141N
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
3.23e-8 |
SMART |
|
C2
|
263 |
362 |
7.4e-10 |
SMART |
|
RasGAP
|
392 |
729 |
3.33e-118 |
SMART |
|
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
|
low complexity region
|
938 |
973 |
N/A |
INTRINSIC |
|
low complexity region
|
1040 |
1068 |
N/A |
INTRINSIC |
|
low complexity region
|
1110 |
1125 |
N/A |
INTRINSIC |
|
coiled coil region
|
1186 |
1259 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000193200
AA Change: I125N
|
| SMART Domains |
Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: I125N
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
12 |
238 |
1.5e-10 |
SMART |
|
C2
|
248 |
347 |
4.8e-12 |
SMART |
|
RasGAP
|
377 |
714 |
2.1e-120 |
SMART |
|
low complexity region
|
772 |
788 |
N/A |
INTRINSIC |
|
low complexity region
|
923 |
958 |
N/A |
INTRINSIC |
|
low complexity region
|
1025 |
1053 |
N/A |
INTRINSIC |
|
low complexity region
|
1095 |
1110 |
N/A |
INTRINSIC |
|
coiled coil region
|
1171 |
1244 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000194598
AA Change: I141N
PolyPhen 2
Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: I141N
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
3.23e-8 |
SMART |
|
C2
|
263 |
362 |
7.4e-10 |
SMART |
|
RasGAP
|
392 |
729 |
3.33e-118 |
SMART |
|
low complexity region
|
787 |
803 |
N/A |
INTRINSIC |
|
low complexity region
|
938 |
973 |
N/A |
INTRINSIC |
|
low complexity region
|
1040 |
1068 |
N/A |
INTRINSIC |
|
low complexity region
|
1110 |
1125 |
N/A |
INTRINSIC |
|
coiled coil region
|
1186 |
1259 |
N/A |
INTRINSIC |
|
low complexity region
|
1308 |
1326 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000201349
AA Change: I140N
|
| SMART Domains |
Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: I140N
| Domain | Start | End | E-Value | Type |
|---|
|
RasGAP
|
9 |
346 |
2.2e-120 |
SMART |
|
low complexity region
|
404 |
420 |
N/A |
INTRINSIC |
|
low complexity region
|
555 |
590 |
N/A |
INTRINSIC |
|
low complexity region
|
657 |
685 |
N/A |
INTRINSIC |
|
low complexity region
|
727 |
742 |
N/A |
INTRINSIC |
|
Blast:RasGAP
|
761 |
876 |
3e-21 |
BLAST |
|
low complexity region
|
884 |
894 |
N/A |
INTRINSIC |
|
| Predicted Effect |
unknown
Transcript: ENSMUST00000201702
AA Change: I141N
|
| SMART Domains |
Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: I141N
| Domain | Start | End | E-Value | Type |
|---|
|
PH
|
27 |
253 |
1.5e-10 |
SMART |
|
C2
|
263 |
362 |
4.9e-12 |
SMART |
|
RasGAP
|
392 |
729 |
2.2e-120 |
SMART |
|
low complexity region
|
773 |
789 |
N/A |
INTRINSIC |
|
low complexity region
|
924 |
959 |
N/A |
INTRINSIC |
|
low complexity region
|
1026 |
1054 |
N/A |
INTRINSIC |
|
low complexity region
|
1096 |
1111 |
N/A |
INTRINSIC |
|
coiled coil region
|
1171 |
1243 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000202939
|
| SMART Domains |
Protein: ENSMUSP00000144403
Gene: ENSMUSG00000067629
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RasGAP
|
1 |
61 |
5.7e-7 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000229490
AA Change: I141N
PolyPhen 2
Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000228963
AA Change: I82N
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231853
|
| Meta Mutation Damage Score |
0.1451 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.5%
|
| Validation Efficiency |
92% (35/38) |
| MGI Phenotype |
FUNCTION: This gene encodes a Ras GTPase activating protein that is a member of the N-methyl-D-aspartate receptor complex. The N-terminal domain of the protein contains a Ras-GAP domain, a pleckstrin homology domain, and a C2 domain that may be involved in binding of calcium and phospholipids. The C-terminal domain consists of a ten histidine repeat region, serine and tyrosine phosphorylation sites, and a T/SXV motif required for postsynaptic scaffold protein interaction. The encoded protein negatively regulates Ras, Rap and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor trafficking to the postsynaptic membrane to regulate synaptic plasticity and neuronal homeostasis. Homozygous null mutations result in early post-embryonic lethality, while heterozygous mutant mice display a variety of phenotypes that include learning and memory defects, hyperactivity, and audiogenic seizures. [provided by RefSeq, Nov 2016]
PHENOTYPE: Homozygous mutant mice exhibit postnatal lethality, and by P3-P4, exhibit small body size and brain, reduced movement and do not feed. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 36 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc9 |
A |
G |
6: 142,584,959 (GRCm39) |
W872R |
probably damaging |
Het |
| Abcg3 |
T |
C |
5: 105,086,046 (GRCm39) |
|
probably benign |
Het |
| Adgrv1 |
T |
A |
13: 81,583,824 (GRCm39) |
Q4627L |
probably benign |
Het |
| Armc2 |
T |
C |
10: 41,839,721 (GRCm39) |
I415V |
possibly damaging |
Het |
| Atp1b1 |
C |
T |
1: 164,270,874 (GRCm39) |
R35H |
probably benign |
Het |
| Bcas3 |
A |
G |
11: 85,261,948 (GRCm39) |
M107V |
probably benign |
Het |
| Ccdc43 |
T |
C |
11: 102,583,029 (GRCm39) |
|
probably null |
Het |
| Dtx4 |
A |
C |
19: 12,463,820 (GRCm39) |
S321A |
probably benign |
Het |
| Enox1 |
A |
T |
14: 77,848,826 (GRCm39) |
H379L |
possibly damaging |
Het |
| Evx1 |
A |
T |
6: 52,290,846 (GRCm39) |
D6V |
probably damaging |
Het |
| Fubp1 |
T |
A |
3: 151,926,133 (GRCm39) |
V286E |
probably damaging |
Het |
| Itgav |
T |
C |
2: 83,598,645 (GRCm39) |
V234A |
probably damaging |
Het |
| Khdc3 |
T |
C |
9: 73,010,872 (GRCm39) |
S241P |
possibly damaging |
Het |
| Lipc |
T |
A |
9: 70,727,800 (GRCm39) |
I16F |
probably damaging |
Het |
| Mael |
T |
C |
1: 166,064,437 (GRCm39) |
|
probably benign |
Het |
| Myo7b |
T |
G |
18: 32,102,567 (GRCm39) |
E1487A |
probably damaging |
Het |
| Or52a33 |
T |
G |
7: 103,288,831 (GRCm39) |
K172T |
probably benign |
Het |
| Osgin1 |
A |
G |
8: 120,168,191 (GRCm39) |
H6R |
probably benign |
Het |
| Otog |
C |
T |
7: 45,937,445 (GRCm39) |
T1718I |
possibly damaging |
Het |
| Otogl |
T |
C |
10: 107,663,565 (GRCm39) |
E1002G |
probably damaging |
Het |
| Pkd1l1 |
T |
C |
11: 8,911,983 (GRCm39) |
N241S |
unknown |
Het |
| Psmd9 |
C |
T |
5: 123,372,653 (GRCm39) |
|
probably benign |
Het |
| Secisbp2l |
C |
T |
2: 125,582,657 (GRCm39) |
G933D |
possibly damaging |
Het |
| Slc6a2 |
C |
A |
8: 93,716,846 (GRCm39) |
N337K |
probably damaging |
Het |
| Snx19 |
A |
T |
9: 30,373,688 (GRCm39) |
Q917L |
probably damaging |
Het |
| Srsf3 |
T |
C |
17: 29,255,257 (GRCm39) |
V14A |
probably damaging |
Het |
| Sspo |
G |
A |
6: 48,471,874 (GRCm39) |
V4729I |
probably benign |
Het |
| Telo2 |
A |
T |
17: 25,325,807 (GRCm39) |
M407K |
probably damaging |
Het |
| Thsd7b |
G |
A |
1: 129,523,107 (GRCm39) |
G47D |
probably damaging |
Het |
| Tradd |
A |
T |
8: 105,987,287 (GRCm39) |
N6K |
possibly damaging |
Het |
| Trim30a |
C |
A |
7: 104,060,396 (GRCm39) |
C460F |
probably benign |
Het |
| Trip13 |
T |
C |
13: 74,066,597 (GRCm39) |
Y318C |
probably damaging |
Het |
| Ubfd1 |
T |
A |
7: 121,667,999 (GRCm39) |
|
probably benign |
Het |
| Uggt1 |
A |
G |
1: 36,215,885 (GRCm39) |
|
probably benign |
Het |
| Wdr7 |
T |
A |
18: 63,857,226 (GRCm39) |
C101S |
possibly damaging |
Het |
| Zfp345 |
T |
C |
2: 150,314,075 (GRCm39) |
I487M |
possibly damaging |
Het |
|
| Other mutations in Syngap1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
R0732:Syngap1
|
UTSW |
17 |
27,173,962 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R1178:Syngap1
|
UTSW |
17 |
27,176,779 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1680:Syngap1
|
UTSW |
17 |
27,171,553 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R1953:Syngap1
|
UTSW |
17 |
27,163,661 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R2213:Syngap1
|
UTSW |
17 |
27,172,043 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2696:Syngap1
|
UTSW |
17 |
27,176,385 (GRCm39) |
nonsense |
probably null |
|
|
R2899:Syngap1
|
UTSW |
17 |
27,178,959 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3237:Syngap1
|
UTSW |
17 |
27,176,067 (GRCm39) |
nonsense |
probably null |
|
|
R3705:Syngap1
|
UTSW |
17 |
27,178,994 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4019:Syngap1
|
UTSW |
17 |
27,171,315 (GRCm39) |
unclassified |
probably benign |
|
|
R4661:Syngap1
|
UTSW |
17 |
27,185,880 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4798:Syngap1
|
UTSW |
17 |
27,180,423 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5524:Syngap1
|
UTSW |
17 |
27,176,126 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5580:Syngap1
|
UTSW |
17 |
27,181,305 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R5610:Syngap1
|
UTSW |
17 |
27,178,754 (GRCm39) |
missense |
possibly damaging |
0.68 |
|
R5835:Syngap1
|
UTSW |
17 |
27,177,192 (GRCm39) |
missense |
probably benign |
0.09 |
|
R5974:Syngap1
|
UTSW |
17 |
27,182,012 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R6235:Syngap1
|
UTSW |
17 |
27,177,104 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6247:Syngap1
|
UTSW |
17 |
27,181,931 (GRCm39) |
nonsense |
probably null |
|
|
R6461:Syngap1
|
UTSW |
17 |
27,183,822 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6503:Syngap1
|
UTSW |
17 |
27,163,658 (GRCm39) |
missense |
probably benign |
0.40 |
|
R7134:Syngap1
|
UTSW |
17 |
27,178,985 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7248:Syngap1
|
UTSW |
17 |
27,176,741 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7298:Syngap1
|
UTSW |
17 |
27,181,961 (GRCm39) |
missense |
possibly damaging |
0.85 |
|
R7749:Syngap1
|
UTSW |
17 |
27,178,938 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7812:Syngap1
|
UTSW |
17 |
27,160,478 (GRCm39) |
missense |
probably benign |
|
|
R7864:Syngap1
|
UTSW |
17 |
27,189,502 (GRCm39) |
missense |
|
|
|
R7951:Syngap1
|
UTSW |
17 |
27,185,942 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R8024:Syngap1
|
UTSW |
17 |
27,160,426 (GRCm39) |
start codon destroyed |
probably benign |
0.01 |
|
R8132:Syngap1
|
UTSW |
17 |
27,177,154 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R8386:Syngap1
|
UTSW |
17 |
27,179,465 (GRCm39) |
missense |
possibly damaging |
0.60 |
|
R9127:Syngap1
|
UTSW |
17 |
27,181,095 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9185:Syngap1
|
UTSW |
17 |
27,182,057 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
R9189:Syngap1
|
UTSW |
17 |
27,183,948 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9461:Syngap1
|
UTSW |
17 |
27,173,962 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9505:Syngap1
|
UTSW |
17 |
27,180,579 (GRCm39) |
missense |
probably benign |
0.02 |
|
R9723:Syngap1
|
UTSW |
17 |
27,189,510 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
X0017:Syngap1
|
UTSW |
17 |
27,163,625 (GRCm39) |
missense |
probably benign |
0.11 |
|
Z1088:Syngap1
|
UTSW |
17 |
27,180,550 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- ACATCATACAGCACCCGTGG -3'
(R):5'- AGCAGGTCCTTCCTTGTCAC -3'
Sequencing Primer
(F):5'- CCCGTGGGAGCAAGGAAGAC -3'
(R):5'- TAGGCCAGCTCCTCTCAGATG -3'
|
| Posted On |
2015-04-30 |
Incidental Mutation