Incidental Mutation 'R8024:Syngap1'
ID 617614
Institutional Source Beutler Lab
Gene Symbol Syngap1
Ensembl Gene ENSMUSG00000067629
Gene Name synaptic Ras GTPase activating protein 1 homolog (rat)
Synonyms Syngap
MMRRC Submission 067463-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8024 (G1)
Quality Score 225.009
Status Validated
Chromosome 17
Chromosomal Location 27160227-27191408 bp(+) (GRCm39)
Type of Mutation start codon destroyed
DNA Base Change (assembly) A to T at 27160426 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Leucine at position 1 (M1L)
Ref Sequence ENSEMBL: ENSMUSP00000141686 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025027] [ENSMUST00000073724] [ENSMUST00000114935] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000201702] [ENSMUST00000229490]
AlphaFold F6SEU4
Predicted Effect probably benign
Transcript: ENSMUST00000025027
SMART Domains Protein: ENSMUSP00000025027
Gene: ENSMUSG00000024194

DomainStartEndE-ValueType
transmembrane domain 7 29 N/A INTRINSIC
low complexity region 45 60 N/A INTRINSIC
Pfam:CutA1 67 165 6.9e-44 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000073724
SMART Domains Protein: ENSMUSP00000073402
Gene: ENSMUSG00000024193

DomainStartEndE-ValueType
TUDOR 29 86 5.61e-11 SMART
PHD 89 140 2.81e-8 SMART
PHD 188 238 2.42e0 SMART
low complexity region 410 416 N/A INTRINSIC
low complexity region 481 495 N/A INTRINSIC
Pfam:Mtf2_C 523 557 7.7e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000114935
SMART Domains Protein: ENSMUSP00000110585
Gene: ENSMUSG00000024194

DomainStartEndE-ValueType
signal peptide 1 24 N/A INTRINSIC
Pfam:CutA1 43 144 1.7e-44 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000177932
AA Change: M1L

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: M1L

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 probably benign
Transcript: ENSMUST00000193200
SMART Domains Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629

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: M1L

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: M1L

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 benign
Transcript: ENSMUST00000201349
SMART Domains Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629

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
SMART Domains Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: M1L

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: ENSMUST00000229490
AA Change: M1L

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 100% (74/74)
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2210408I21Rik A T 13: 77,760,713 (GRCm39) N1257Y probably benign Het
2310057J18Rik A T 10: 28,858,591 (GRCm39) Y133* probably null Het
2310057J18Rik A C 10: 28,862,213 (GRCm39) S26A possibly damaging Het
9930012K11Rik G T 14: 70,394,116 (GRCm39) P220T probably damaging Het
Adam1b A C 5: 121,638,986 (GRCm39) S686R probably benign Het
Adam8 T C 7: 139,567,489 (GRCm39) D418G probably damaging Het
Adcy8 A G 15: 64,792,095 (GRCm39) L287P probably damaging Het
Adhfe1 T A 1: 9,634,080 (GRCm39) M373K probably benign Het
Alpk2 T C 18: 65,438,106 (GRCm39) S1096G probably benign Het
Ankmy1 A G 1: 92,812,716 (GRCm39) V531A probably benign Het
Ano3 C T 2: 110,498,128 (GRCm39) E738K probably damaging Het
Ano4 T A 10: 88,807,194 (GRCm39) I796F probably damaging Het
Apeh T C 9: 107,969,790 (GRCm39) E190G probably benign Het
Atpsckmt T C 15: 31,608,317 (GRCm39) Y123H probably damaging Het
Cadm3 A G 1: 173,165,622 (GRCm39) L346P probably damaging Het
Ccdc9b A G 2: 118,591,005 (GRCm39) probably null Het
Clec2e G A 6: 129,071,388 (GRCm39) H150Y possibly damaging Het
Cnga4 A T 7: 105,056,042 (GRCm39) N318Y probably damaging Het
Cnr2 T A 4: 135,644,196 (GRCm39) F91L probably damaging Het
Diaph3 T A 14: 86,893,835 (GRCm39) E1147V probably damaging Het
Elmo2 T C 2: 165,133,775 (GRCm39) T738A unknown Het
Exoc4 T A 6: 33,324,866 (GRCm39) W387R probably damaging Het
Focad T C 4: 88,315,237 (GRCm39) V1379A unknown Het
Frmd4a T C 2: 4,608,513 (GRCm39) S794P probably damaging Het
Ftl1-ps1 A G 13: 74,555,170 (GRCm39) T150A probably benign Het
Gm43517 A T 12: 49,436,409 (GRCm39) probably benign Het
Gm5773 C T 3: 93,680,475 (GRCm39) A49V probably benign Het
Helz T A 11: 107,577,247 (GRCm39) L1867Q unknown Het
Il22ra1 A G 4: 135,461,589 (GRCm39) H118R probably benign Het
Inf2 C T 12: 112,575,336 (GRCm39) P856S unknown Het
Ints5 T A 19: 8,873,504 (GRCm39) L488I probably damaging Het
Iqca1l A G 5: 24,755,634 (GRCm39) M296T possibly damaging Het
Kifc1 G A 17: 34,102,177 (GRCm39) R479C probably damaging Het
Lrba T A 3: 86,202,708 (GRCm39) C289* probably null Het
Mael A G 1: 166,054,196 (GRCm39) L196S probably damaging Het
Med23 T A 10: 24,755,581 (GRCm39) S229R possibly damaging Het
Mroh9 T C 1: 162,866,802 (GRCm39) N645D probably benign Het
Myom3 G A 4: 135,529,059 (GRCm39) V1132I probably benign Het
Naalad2 T G 9: 18,308,769 (GRCm39) probably benign Het
Ndufa13 A T 8: 70,347,187 (GRCm39) L71H probably damaging Het
Nepro A T 16: 44,551,778 (GRCm39) H212L probably benign Het
Nmd3 T A 3: 69,637,298 (GRCm39) probably benign Het
Nox4 T A 7: 86,954,118 (GRCm39) L141Q probably damaging Het
Or4a81 T C 2: 89,619,390 (GRCm39) E102G probably benign Het
Or5p53 T C 7: 107,533,645 (GRCm39) V306A probably benign Het
Or5p58 T A 7: 107,694,496 (GRCm39) T94S probably benign Het
Or6c215 T G 10: 129,637,812 (GRCm39) E194A probably damaging Het
Or8s2 T A 15: 98,276,878 (GRCm39) M38L probably benign Het
Pfpl A G 19: 12,407,570 (GRCm39) D607G possibly damaging Het
Pkd1l2 A T 8: 117,802,921 (GRCm39) F233L possibly damaging Het
Prl6a1 A G 13: 27,502,678 (GRCm39) probably benign Het
Ptprz1 A T 6: 23,042,750 (GRCm39) E2058V probably damaging Het
Rag1 A T 2: 101,472,852 (GRCm39) N763K probably damaging Het
Rhbg A C 3: 88,155,760 (GRCm39) D63E probably damaging Het
Rrm1 T A 7: 102,106,472 (GRCm39) F330L probably benign Het
Scaf8 A T 17: 3,209,568 (GRCm39) Q97L unknown Het
Sdr9c7 G A 10: 127,734,751 (GRCm39) V80I probably benign Het
Slc18a1 A G 8: 69,527,799 (GRCm39) V4A probably benign Het
Slco3a1 T A 7: 74,204,218 (GRCm39) I41F probably benign Het
Slirp T C 12: 87,494,370 (GRCm39) V45A probably damaging Het
Spata31 A T 13: 65,070,618 (GRCm39) Q922L probably benign Het
Spg11 A G 2: 121,927,802 (GRCm39) S661P possibly damaging Het
Stab2 G T 10: 86,681,916 (GRCm39) T2495K probably benign Het
Supt16 A G 14: 52,408,332 (GRCm39) I871T probably damaging Het
Sval2 A G 6: 41,837,298 (GRCm39) Q9R probably damaging Het
Tfpi A T 2: 84,284,266 (GRCm39) M62K possibly damaging Het
Tm4sf1 A T 3: 57,195,186 (GRCm39) Y200* probably null Het
Tmc1 A T 19: 20,878,181 (GRCm39) W105R probably damaging Het
Tmtc2 T C 10: 105,025,987 (GRCm39) E827G probably benign Het
Tollip T C 7: 141,446,563 (GRCm39) I33V probably benign Het
Unc80 T A 1: 66,645,803 (GRCm39) V1493D possibly damaging Het
Vmn2r6 G A 3: 64,467,245 (GRCm39) R85W probably benign Het
Vwa5a C A 9: 38,647,316 (GRCm39) S565* probably null Het
Xbp1 T A 11: 5,471,910 (GRCm39) V12D probably benign 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
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
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'- TGTATGAGTCAGGGGTCCCTC -3'
(R):5'- CTTGAAAAGGCCCGTGTCCC -3'

Sequencing Primer
(F):5'- AGTCAGGGGTCCCTCGTTCTC -3'
(R):5'- GTGTCCCAGCCCCTCTATC -3'
Posted On 2020-01-23