Incidental Mutation 'R2899:Syngap1'
ID 261425
Institutional Source Beutler Lab
Gene Symbol Syngap1
Ensembl Gene ENSMUSG00000067629
Gene Name synaptic Ras GTPase activating protein 1 homolog (rat)
Synonyms Syngap
MMRRC Submission 040487-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2899 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 27160227-27191408 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 27178959 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 483 (E483G)
Ref Sequence ENSEMBL: ENSMUSP00000156340 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000081285] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000201702] [ENSMUST00000202939] [ENSMUST00000231853] [ENSMUST00000228963] [ENSMUST00000229490]
AlphaFold F6SEU4
Predicted Effect probably damaging
Transcript: ENSMUST00000081285
AA Change: E597G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: E597G

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 probably damaging
Transcript: ENSMUST00000177932
AA Change: E656G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: E656G

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: E640G
SMART Domains Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: E640G

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 damaging
Transcript: ENSMUST00000194598
AA Change: E656G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: E656G

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: ENSMUST00000200799
Predicted Effect probably benign
Transcript: ENSMUST00000201186
Predicted Effect unknown
Transcript: ENSMUST00000201349
AA Change: E655G
SMART Domains Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: E655G

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: E656G
SMART Domains Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: E656G

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 probably benign
Transcript: ENSMUST00000202939
SMART Domains Protein: ENSMUSP00000144403
Gene: ENSMUSG00000067629

DomainStartEndE-ValueType
Pfam:RasGAP 1 61 5.7e-7 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000202049
Predicted Effect probably benign
Transcript: ENSMUST00000202208
Predicted Effect probably damaging
Transcript: ENSMUST00000231853
AA Change: E483G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect probably damaging
Transcript: ENSMUST00000228963
AA Change: E597G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Predicted Effect probably damaging
Transcript: ENSMUST00000229490
AA Change: E656G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.4323 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.1%
Validation Efficiency 97% (30/31)
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: 29 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,771,443 (GRCm39) K211E probably benign Het
Amigo3 T C 9: 107,931,353 (GRCm39) S259P probably benign Het
Bahd1 C T 2: 118,746,887 (GRCm39) P169S probably damaging Het
Cd200r4 T C 16: 44,653,728 (GRCm39) I175T probably damaging Het
Cep131 T C 11: 119,962,854 (GRCm39) D425G probably benign Het
Clmp T C 9: 40,693,688 (GRCm39) S302P probably damaging Het
Dusp6 T C 10: 99,099,707 (GRCm39) S52P probably damaging Het
Epha5 T A 5: 84,381,667 (GRCm39) I395F probably damaging Het
F5 A G 1: 164,014,469 (GRCm39) E580G possibly damaging Het
Fbxo3 T A 2: 103,881,480 (GRCm39) Y271N probably damaging Het
Fuca1 G A 4: 135,650,323 (GRCm39) W131* probably null Het
Gdf7 C T 12: 8,348,470 (GRCm39) A276T unknown Het
Limk1 A T 5: 134,717,154 (GRCm39) probably null Het
Lrrc37a G A 11: 103,388,690 (GRCm39) T2245I unknown Het
Neb A G 2: 52,075,335 (GRCm39) I210T probably benign Het
Nf1 T G 11: 79,303,584 (GRCm39) N420K possibly damaging Het
Or5b101 T A 19: 13,005,058 (GRCm39) I212F probably damaging Het
Pask G T 1: 93,262,269 (GRCm39) T197K probably damaging Het
Potefam1 C A 2: 111,051,015 (GRCm39) probably benign Het
Pou4f3 T C 18: 42,528,588 (GRCm39) L177P probably benign Het
Rassf1 G A 9: 107,431,393 (GRCm39) G107R probably null Het
Rdx T C 9: 51,980,211 (GRCm39) probably benign Het
Saraf T C 8: 34,628,385 (GRCm39) L77P probably damaging Het
Tsku T C 7: 98,002,124 (GRCm39) N69S probably damaging Het
Usp36 G A 11: 118,167,582 (GRCm39) probably benign Het
Vmn2r129 G T 4: 156,686,692 (GRCm39) noncoding transcript Het
Zc3h6 T C 2: 128,844,152 (GRCm39) V232A probably benign Het
Zfp143 T A 7: 109,671,336 (GRCm39) S99R probably damaging Het
Zkscan3 A T 13: 21,578,143 (GRCm39) L219Q probably damaging Het
Other mutations in Syngap1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- CCAAGGTCATCCAGAACCTG -3'
(R):5'- TGACAAGAGTTCTGTGCAGAG -3'

Sequencing Primer
(F):5'- GGCCAACTTTTCCAAGTGAG -3'
(R):5'- GATAATCTCTCAGCCCAGGTG -3'
Posted On 2015-01-23