Incidental Mutation 'R2213:Syngap1'
| ID |
239556 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Syngap1
|
| Ensembl Gene |
ENSMUSG00000067629 |
| Gene Name |
synaptic Ras GTPase activating protein 1 homolog (rat) |
| Synonyms |
Syngap |
| MMRRC Submission |
040215-MU
|
| Accession Numbers |
|
| Essential gene? |
Essential
(E-score: 1.000)
|
| Stock # |
R2213 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
17 |
| Chromosomal Location |
27160227-27191408 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 27172043 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Serine
at position 84
(R84S)
|
| 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: R84S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: R84S
| 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 |
possibly damaging
Transcript: ENSMUST00000177932
AA Change: R143S
PolyPhen 2
Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: R143S
| 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: R127S
|
| SMART Domains |
Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: R127S
| 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 benign
Transcript: ENSMUST00000194598
AA Change: R143S
PolyPhen 2
Score 0.359 (Sensitivity: 0.90; Specificity: 0.89)
|
| SMART Domains |
Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: R143S
| 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: R142S
|
| SMART Domains |
Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: R142S
| 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: R143S
|
| SMART Domains |
Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: R143S
| 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 |
possibly damaging
Transcript: ENSMUST00000229490
AA Change: R143S
PolyPhen 2
Score 0.658 (Sensitivity: 0.87; Specificity: 0.91)
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000228963
AA Change: R84S
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000231853
|
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.1%
|
| Validation Efficiency |
|
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akr1c12 |
T |
C |
13: 4,326,247 (GRCm39) |
D78G |
probably damaging |
Het |
| Anxa1 |
C |
T |
19: 20,360,239 (GRCm39) |
R124H |
probably damaging |
Het |
| Arhgef4 |
G |
A |
1: 34,846,230 (GRCm39) |
|
probably null |
Het |
| C87436 |
G |
A |
6: 86,422,455 (GRCm39) |
V10I |
probably benign |
Het |
| Ces1a |
G |
T |
8: 93,751,853 (GRCm39) |
P427Q |
probably damaging |
Het |
| Cpm |
T |
C |
10: 117,495,744 (GRCm39) |
Y78H |
probably damaging |
Het |
| Csmd3 |
G |
A |
15: 47,683,843 (GRCm39) |
T1663I |
possibly damaging |
Het |
| Cul7 |
T |
C |
17: 46,962,398 (GRCm39) |
F10L |
probably damaging |
Het |
| Cyp2j5 |
T |
C |
4: 96,547,852 (GRCm39) |
N130S |
probably benign |
Het |
| Dclk1 |
G |
A |
3: 55,387,854 (GRCm39) |
C100Y |
probably damaging |
Het |
| Ddb1 |
T |
C |
19: 10,585,691 (GRCm39) |
L135P |
probably damaging |
Het |
| Dixdc1 |
A |
G |
9: 50,613,245 (GRCm39) |
S211P |
probably benign |
Het |
| Dnah12 |
G |
T |
14: 26,460,485 (GRCm39) |
K970N |
probably benign |
Het |
| Eps15 |
A |
G |
4: 109,218,417 (GRCm39) |
K391E |
probably damaging |
Het |
| Fabp9 |
A |
G |
3: 10,259,860 (GRCm39) |
V51A |
probably damaging |
Het |
| Flg |
T |
C |
3: 93,200,335 (GRCm39) |
|
probably benign |
Het |
| Flnb |
AAGGAG |
AAG |
14: 7,881,652 (GRCm38) |
|
probably benign |
Het |
| Fscb |
A |
T |
12: 64,520,890 (GRCm39) |
I192N |
possibly damaging |
Het |
| Galntl5 |
A |
G |
5: 25,422,527 (GRCm39) |
I333V |
probably benign |
Het |
| Gcnt3 |
A |
T |
9: 69,941,989 (GRCm39) |
V193E |
probably benign |
Het |
| Gle1 |
T |
C |
2: 29,839,313 (GRCm39) |
F535S |
probably damaging |
Het |
| Gpr87 |
A |
T |
3: 59,086,465 (GRCm39) |
S347T |
probably damaging |
Het |
| Gstm2 |
C |
T |
3: 107,893,409 (GRCm39) |
R18H |
probably damaging |
Het |
| H1f7 |
T |
A |
15: 98,154,219 (GRCm39) |
Q310L |
unknown |
Het |
| Haus6 |
C |
T |
4: 86,500,229 (GRCm39) |
E927K |
possibly damaging |
Het |
| Hunk |
A |
G |
16: 90,229,505 (GRCm39) |
N122S |
probably damaging |
Het |
| Itih4 |
T |
A |
14: 30,612,670 (GRCm39) |
V232E |
probably damaging |
Het |
| Jag1 |
G |
T |
2: 136,931,812 (GRCm39) |
D586E |
probably benign |
Het |
| Klk1b1 |
T |
C |
7: 43,619,905 (GRCm39) |
S155P |
probably damaging |
Het |
| Lama1 |
G |
T |
17: 68,084,029 (GRCm39) |
G1424* |
probably null |
Het |
| Lrp1 |
T |
A |
10: 127,376,571 (GRCm39) |
N4279I |
probably damaging |
Het |
| Lrrc43 |
G |
A |
5: 123,641,640 (GRCm39) |
V525I |
possibly damaging |
Het |
| Lrrc4c |
G |
A |
2: 97,460,816 (GRCm39) |
V481M |
probably benign |
Het |
| Mecr |
T |
A |
4: 131,581,126 (GRCm39) |
|
probably null |
Het |
| Megf10 |
T |
A |
18: 57,421,081 (GRCm39) |
Y906* |
probably null |
Het |
| Mpdz |
A |
G |
4: 81,228,409 (GRCm39) |
F1319L |
probably damaging |
Het |
| Mtf2 |
A |
G |
5: 108,248,780 (GRCm39) |
E364G |
possibly damaging |
Het |
| Nelfe |
T |
A |
17: 35,072,859 (GRCm39) |
D160E |
probably benign |
Het |
| Nin |
A |
G |
12: 70,092,128 (GRCm39) |
L727P |
probably damaging |
Het |
| Npat |
A |
G |
9: 53,463,681 (GRCm39) |
T155A |
probably benign |
Het |
| Nup58 |
T |
C |
14: 60,476,945 (GRCm39) |
D242G |
probably benign |
Het |
| Or4a78 |
A |
T |
2: 89,497,891 (GRCm39) |
L113Q |
probably damaging |
Het |
| Pnlip |
T |
C |
19: 58,662,202 (GRCm39) |
V116A |
probably benign |
Het |
| Prl7a2 |
T |
A |
13: 27,849,051 (GRCm39) |
L79F |
probably benign |
Het |
| Rbm25 |
A |
T |
12: 83,722,856 (GRCm39) |
I760L |
probably benign |
Het |
| Rbms3 |
A |
T |
9: 116,788,534 (GRCm39) |
|
probably null |
Het |
| Rif1 |
GCCACCA |
GCCA |
2: 52,000,336 (GRCm39) |
|
probably benign |
Het |
| Rps10 |
C |
A |
17: 27,849,473 (GRCm39) |
|
probably benign |
Het |
| Slc35e4 |
T |
C |
11: 3,863,159 (GRCm39) |
E10G |
possibly damaging |
Het |
| Smad2 |
A |
T |
18: 76,437,697 (GRCm39) |
T434S |
probably damaging |
Het |
| Sox30 |
C |
T |
11: 45,875,679 (GRCm39) |
S477F |
probably damaging |
Het |
| Speer4a3 |
G |
T |
5: 26,158,175 (GRCm39) |
T59K |
probably benign |
Het |
| Stat4 |
A |
T |
1: 52,053,014 (GRCm39) |
D65V |
probably damaging |
Het |
| Strip2 |
A |
G |
6: 29,931,147 (GRCm39) |
D366G |
probably damaging |
Het |
| Synpo2l |
A |
G |
14: 20,710,734 (GRCm39) |
Y629H |
probably damaging |
Het |
| Taf4 |
A |
T |
2: 179,577,683 (GRCm39) |
|
probably null |
Het |
| Ttc21a |
A |
G |
9: 119,769,527 (GRCm39) |
H68R |
probably benign |
Het |
| Txndc8 |
T |
A |
4: 57,984,199 (GRCm39) |
Q144L |
probably benign |
Het |
| Tyr |
T |
G |
7: 87,142,086 (GRCm39) |
Q158P |
probably damaging |
Het |
| Uchl3 |
T |
A |
14: 101,904,106 (GRCm39) |
|
probably null |
Het |
| Vwa5b1 |
T |
C |
4: 138,332,123 (GRCm39) |
K298R |
probably benign |
Het |
| Wrn |
T |
C |
8: 33,747,043 (GRCm39) |
N891S |
probably benign |
Het |
| Ylpm1 |
A |
G |
12: 85,116,492 (GRCm39) |
S2125G |
probably benign |
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 |
|
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 |
|
R3880:Syngap1
|
UTSW |
17 |
27,172,038 (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'- TTAGGCCAGCTCCTCTCAGATG -3'
Sequencing Primer
(F):5'- CCCGTGGGAGCAAGGAAGAC -3'
(R):5'- AGATGTCTCTTGCACCCCGAC -3'
|
| Posted On |
2014-10-15 |
Incidental Mutation