Incidental Mutation 'R1680:Syngap1'
ID 188454
Institutional Source Beutler Lab
Gene Symbol Syngap1
Ensembl Gene ENSMUSG00000067629
Gene Name synaptic Ras GTPase activating protein 1 homolog (rat)
Synonyms Syngap
MMRRC Submission 039716-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1680 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 26941253-26972434 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 26952579 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 46 (S46P)
Ref Sequence ENSEMBL: ENSMUSP00000154838 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000081285] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000201702] [ENSMUST00000228963] [ENSMUST00000229490] [ENSMUST00000231853]
AlphaFold F6SEU4
Predicted Effect possibly damaging
Transcript: ENSMUST00000081285
AA Change: S46P

PolyPhen 2 Score 0.465 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: S46P

DomainStartEndE-ValueType
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 benign
Transcript: ENSMUST00000177932
AA Change: S105P

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: S105P

DomainStartEndE-ValueType
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: S89P
SMART Domains Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: S89P

DomainStartEndE-ValueType
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: S105P

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: S105P

DomainStartEndE-ValueType
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: S104P
SMART Domains Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: S104P

DomainStartEndE-ValueType
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: S105P
SMART Domains Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: S105P

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000228963
AA Change: S46P

PolyPhen 2 Score 0.600 (Sensitivity: 0.87; Specificity: 0.91)
Predicted Effect probably benign
Transcript: ENSMUST00000229490
AA Change: S105P

PolyPhen 2 Score 0.151 (Sensitivity: 0.92; Specificity: 0.87)
Predicted Effect probably benign
Transcript: ENSMUST00000231853
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.4%
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: 68 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017N19Rik C G 10: 100,603,528 (GRCm38) P187R probably damaging Het
Ahnak T A 19: 9,009,963 (GRCm38) H2870Q probably benign Het
Arhgef33 C T 17: 80,347,651 (GRCm38) S95F probably damaging Het
Atp1a2 T A 1: 172,278,954 (GRCm38) D827V probably damaging Het
Bcat1 T G 6: 145,039,628 (GRCm38) D96A probably damaging Het
Birc6 A T 17: 74,548,746 (GRCm38) I184L probably benign Het
Ccdc129 C T 6: 55,968,766 (GRCm38) T824I probably damaging Het
Clca3b A T 3: 144,837,824 (GRCm38) L415M probably damaging Het
Clstn1 T C 4: 149,643,726 (GRCm38) V617A probably benign Het
Col22a1 G A 15: 71,799,361 (GRCm38) A1050V unknown Het
Col5a3 C T 9: 20,784,668 (GRCm38) probably null Het
Csmd3 G A 15: 47,741,170 (GRCm38) T1059I probably damaging Het
Dclk2 C T 3: 86,805,639 (GRCm38) R503Q possibly damaging Het
Dnm3 A G 1: 162,010,976 (GRCm38) V272A probably benign Het
Dnmt3a A G 12: 3,873,361 (GRCm38) Q187R probably damaging Het
Dpp9 A G 17: 56,190,103 (GRCm38) Y710H probably benign Het
Eef1a2 A T 2: 181,152,941 (GRCm38) M155K possibly damaging Het
Entpd8 G A 2: 25,084,024 (GRCm38) C331Y probably damaging Het
Erc1 A C 6: 119,575,761 (GRCm38) L1072R probably damaging Het
Fam160b2 T C 14: 70,586,851 (GRCm38) Y482C probably damaging Het
Gtf3c2 A G 5: 31,173,868 (GRCm38) S155P probably damaging Het
Gucy2c A G 6: 136,722,493 (GRCm38) S617P probably damaging Het
Ice1 T C 13: 70,605,448 (GRCm38) R840G probably benign Het
Il1rl2 T C 1: 40,351,793 (GRCm38) Y299H possibly damaging Het
Ints7 T G 1: 191,621,162 (GRCm38) probably null Het
Ireb2 C T 9: 54,881,518 (GRCm38) T92I probably damaging Het
Kcnj8 A T 6: 142,570,189 (GRCm38) L64* probably null Het
Mapk8ip3 A G 17: 24,901,011 (GRCm38) V983A probably damaging Het
Mertk A G 2: 128,801,636 (GRCm38) D985G probably benign Het
Mical3 A T 6: 120,959,643 (GRCm38) S1307R probably benign Het
Ncaph2 A G 15: 89,364,622 (GRCm38) D222G probably benign Het
Nf1 C A 11: 79,550,998 (GRCm38) S295* probably null Het
Nlrp12 T A 7: 3,241,174 (GRCm38) D236V probably damaging Het
Npnt A G 3: 132,906,802 (GRCm38) V74A probably benign Het
Oasl1 A G 5: 114,935,944 (GRCm38) D304G probably damaging Het
Olfr1098 C T 2: 86,923,161 (GRCm38) V124I probably benign Het
Olfr556 A G 7: 102,670,733 (GRCm38) D271G possibly damaging Het
Olfr834 A G 9: 18,988,516 (GRCm38) H176R possibly damaging Het
Olfr936 T C 9: 39,047,000 (GRCm38) I140V probably benign Het
Patz1 A G 11: 3,307,812 (GRCm38) K604E probably damaging Het
Pcsk6 T A 7: 66,035,250 (GRCm38) V793E probably benign Het
Pla2g4d C T 2: 120,277,750 (GRCm38) probably null Het
Plxnc1 A C 10: 94,841,551 (GRCm38) L938R probably benign Het
Pou4f2 G T 8: 78,434,831 (GRCm38) A381D probably damaging Het
Prdm4 A G 10: 85,899,223 (GRCm38) L685P possibly damaging Het
Pxn T A 5: 115,552,147 (GRCm38) V383E probably damaging Het
Rbl1 A G 2: 157,174,783 (GRCm38) L632P probably damaging Het
Rnf135 T A 11: 80,196,881 (GRCm38) S219T possibly damaging Het
Sdk2 C T 11: 113,838,646 (GRCm38) silent Het
Sdk2 T C 11: 113,791,436 (GRCm38) D2039G possibly damaging Het
Slc5a6 A G 5: 31,042,644 (GRCm38) Y131H probably damaging Het
Slc9a1 T C 4: 133,418,080 (GRCm38) I492T probably damaging Het
Soga3 A T 10: 29,196,839 (GRCm38) Q709L probably damaging Het
Spag5 A G 11: 78,320,616 (GRCm38) K993E probably damaging Het
Sptbn1 T G 11: 30,159,371 (GRCm38) I75L possibly damaging Het
Tfcp2l1 T A 1: 118,675,605 (GRCm38) F458I probably damaging Het
Tmem67 A G 4: 12,087,840 (GRCm38) V102A probably benign Het
Tomm70a T C 16: 57,121,961 (GRCm38) S34P unknown Het
Txlnb G T 10: 17,843,233 (GRCm38) G604V probably benign Het
Ube2q1 A G 3: 89,776,176 (GRCm38) T143A probably benign Het
Unc80 C T 1: 66,503,669 (GRCm38) R361* probably null Het
Vcan T C 13: 89,703,547 (GRCm38) D1098G probably benign Het
Vmn1r176 T A 7: 23,835,381 (GRCm38) T116S probably damaging Het
Wdr81 C T 11: 75,454,423 (GRCm38) R6K probably benign Het
Zan T A 5: 137,403,050 (GRCm38) T4136S unknown Het
Zbtb14 C A 17: 69,388,502 (GRCm38) F398L probably damaging Het
Zfp606 A T 7: 12,493,971 (GRCm38) H615L probably damaging Het
Zp3r A T 1: 130,582,880 (GRCm38) N433K probably benign Het
Other mutations in Syngap1
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0732:Syngap1 UTSW 17 26,954,988 (GRCm38) missense possibly damaging 0.94
R1178:Syngap1 UTSW 17 26,957,805 (GRCm38) missense probably damaging 0.99
R1953:Syngap1 UTSW 17 26,944,687 (GRCm38) missense possibly damaging 0.94
R2213:Syngap1 UTSW 17 26,953,069 (GRCm38) missense probably damaging 1.00
R2696:Syngap1 UTSW 17 26,957,411 (GRCm38) nonsense probably null
R2899:Syngap1 UTSW 17 26,959,985 (GRCm38) missense probably damaging 1.00
R3237:Syngap1 UTSW 17 26,957,093 (GRCm38) nonsense probably null
R3705:Syngap1 UTSW 17 26,960,020 (GRCm38) missense probably damaging 1.00
R3880:Syngap1 UTSW 17 26,953,064 (GRCm38) missense probably damaging 1.00
R4019:Syngap1 UTSW 17 26,952,341 (GRCm38) unclassified probably benign
R4661:Syngap1 UTSW 17 26,966,906 (GRCm38) missense probably damaging 1.00
R4798:Syngap1 UTSW 17 26,961,449 (GRCm38) missense probably benign 0.00
R5524:Syngap1 UTSW 17 26,957,152 (GRCm38) missense probably damaging 1.00
R5580:Syngap1 UTSW 17 26,962,331 (GRCm38) missense probably damaging 0.97
R5610:Syngap1 UTSW 17 26,959,780 (GRCm38) missense possibly damaging 0.68
R5835:Syngap1 UTSW 17 26,958,218 (GRCm38) missense probably benign 0.09
R5974:Syngap1 UTSW 17 26,963,038 (GRCm38) missense probably damaging 0.98
R6235:Syngap1 UTSW 17 26,958,130 (GRCm38) missense probably benign 0.00
R6247:Syngap1 UTSW 17 26,962,957 (GRCm38) nonsense probably null
R6461:Syngap1 UTSW 17 26,964,848 (GRCm38) missense probably damaging 1.00
R6503:Syngap1 UTSW 17 26,944,684 (GRCm38) missense probably benign 0.40
R7134:Syngap1 UTSW 17 26,960,011 (GRCm38) missense probably damaging 1.00
R7248:Syngap1 UTSW 17 26,957,767 (GRCm38) missense probably damaging 1.00
R7298:Syngap1 UTSW 17 26,962,987 (GRCm38) missense possibly damaging 0.85
R7749:Syngap1 UTSW 17 26,959,964 (GRCm38) missense probably damaging 0.99
R7812:Syngap1 UTSW 17 26,941,504 (GRCm38) missense probably benign
R7864:Syngap1 UTSW 17 26,970,528 (GRCm38) missense
R7951:Syngap1 UTSW 17 26,966,968 (GRCm38) missense possibly damaging 0.46
R8024:Syngap1 UTSW 17 26,941,452 (GRCm38) start codon destroyed probably benign 0.01
R8132:Syngap1 UTSW 17 26,958,180 (GRCm38) missense probably damaging 0.98
R8386:Syngap1 UTSW 17 26,960,491 (GRCm38) missense possibly damaging 0.60
R9127:Syngap1 UTSW 17 26,962,121 (GRCm38) missense probably damaging 1.00
R9185:Syngap1 UTSW 17 26,963,083 (GRCm38) missense possibly damaging 0.69
R9189:Syngap1 UTSW 17 26,964,974 (GRCm38) missense probably damaging 1.00
R9461:Syngap1 UTSW 17 26,954,988 (GRCm38) missense possibly damaging 0.94
R9505:Syngap1 UTSW 17 26,961,605 (GRCm38) missense probably benign 0.02
R9723:Syngap1 UTSW 17 26,970,536 (GRCm38) missense possibly damaging 0.95
X0017:Syngap1 UTSW 17 26,944,651 (GRCm38) missense probably benign 0.11
Z1088:Syngap1 UTSW 17 26,961,576 (GRCm38) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTGCTGACTGACTGCCTATCCAAG -3'
(R):5'- GAGCCCTGACACCAGTTTGTCTTC -3'

Sequencing Primer
(F):5'- CCTATCCAAGTCATGGGCTTAAGG -3'
(R):5'- CTGTATGATGTGAGCAGATACAC -3'
Posted On 2014-05-09