Incidental Mutation 'R5835:Syngap1'
ID 449567
Institutional Source Beutler Lab
Gene Symbol Syngap1
Ensembl Gene ENSMUSG00000067629
Gene Name synaptic Ras GTPase activating protein 1 homolog (rat)
Synonyms Syngap
MMRRC Submission 044056-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5835 (G1)
Quality Score 160
Status Not validated
Chromosome 17
Chromosomal Location 27160227-27191408 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 27177192 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Leucine at position 65 (H65L)
Ref Sequence ENSEMBL: ENSMUSP00000144403 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000081285] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000202939] [ENSMUST00000201702] [ENSMUST00000228963] [ENSMUST00000231853] [ENSMUST00000229490]
AlphaFold F6SEU4
Predicted Effect probably benign
Transcript: ENSMUST00000081285
AA Change: H499L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: H499L

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: ENSMUST00000177932
AA Change: H558L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: H558L

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: H542L
SMART Domains Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: H542L

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: H558L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: H558L

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 probably benign
Transcript: ENSMUST00000202939
AA Change: H65L

PolyPhen 2 Score 0.086 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000144403
Gene: ENSMUSG00000067629
AA Change: H65L

DomainStartEndE-ValueType
Pfam:RasGAP 1 61 5.7e-7 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000201349
AA Change: H557L
SMART Domains Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: H557L

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: H558L
SMART Domains Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: H558L

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: ENSMUST00000202049
Predicted Effect probably benign
Transcript: ENSMUST00000202208
Predicted Effect probably benign
Transcript: ENSMUST00000228963
AA Change: H499L

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
Predicted Effect probably benign
Transcript: ENSMUST00000231853
AA Change: H385L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
Predicted Effect probably benign
Transcript: ENSMUST00000229490
AA Change: H558L

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.1%
  • 20x: 94.5%
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930505A04Rik C T 11: 30,376,349 (GRCm39) V173M probably damaging Het
A2m A G 6: 121,616,295 (GRCm39) K141R probably damaging Het
Ablim3 T C 18: 61,956,993 (GRCm39) E278G probably damaging Het
Adam28 A G 14: 68,893,130 (GRCm39) W4R possibly damaging Het
Ahnak2 T C 12: 112,742,230 (GRCm39) N614S possibly damaging Het
Arfgef1 A G 1: 10,230,964 (GRCm39) S1182P probably damaging Het
Asb8 A T 15: 98,034,263 (GRCm39) D97E probably damaging Het
AU041133 T A 10: 81,987,046 (GRCm39) L232H probably damaging Het
Bmp2k T G 5: 97,204,841 (GRCm39) V392G possibly damaging Het
Capn12 C A 7: 28,581,383 (GRCm39) H79N probably benign Het
Casp2 C A 6: 42,244,520 (GRCm39) S54R possibly damaging Het
Ccdc18 T C 5: 108,288,740 (GRCm39) S163P possibly damaging Het
Ccdc92b A G 11: 74,528,838 (GRCm39) E114G probably benign Het
Cd209c C A 8: 3,995,699 (GRCm39) M34I probably benign Het
Ceacam18 A T 7: 43,286,382 (GRCm39) H85L probably benign Het
Cndp1 C A 18: 84,630,958 (GRCm39) A434S probably benign Het
Crybg1 T A 10: 43,851,129 (GRCm39) T1581S probably benign Het
Cyb5d2 A T 11: 72,680,036 (GRCm39) D86E probably damaging Het
Duox1 T G 2: 122,158,341 (GRCm39) V608G probably benign Het
Exosc10 A G 4: 148,649,844 (GRCm39) R425G probably damaging Het
Fat3 A T 9: 16,287,129 (GRCm39) I798N probably damaging Het
Habp2 T A 19: 56,295,218 (GRCm39) D36E probably benign Het
Herpud1 T C 8: 95,118,867 (GRCm39) V207A probably damaging Het
Htt A G 5: 34,970,534 (GRCm39) I561V probably benign Het
Hyls1 G A 9: 35,472,480 (GRCm39) S312F probably benign Het
Igkv18-36 A G 6: 69,969,512 (GRCm39) I93T probably damaging Het
Kalrn T G 16: 33,807,461 (GRCm39) E2636A probably benign Het
Kif27 A G 13: 58,460,960 (GRCm39) probably null Het
Mep1a G A 17: 43,789,055 (GRCm39) H574Y probably benign Het
Myh6 T C 14: 55,187,864 (GRCm39) K1197E probably damaging Het
Obscn T C 11: 58,892,907 (GRCm39) T6780A probably benign Het
Obscn C T 11: 58,932,953 (GRCm39) V4808M probably damaging Het
Or6c210 A G 10: 129,495,803 (GRCm39) I43V probably benign Het
Pkhd1 T C 1: 20,271,307 (GRCm39) D3082G probably benign Het
Plch1 T C 3: 63,604,943 (GRCm39) M1645V probably benign Het
Ppip5k1 A G 2: 121,168,380 (GRCm39) V674A probably benign Het
Prrc2b T A 2: 32,096,485 (GRCm39) S619T probably benign Het
Rab44 A T 17: 29,367,212 (GRCm39) H714L probably benign Het
Rybp A G 6: 100,210,151 (GRCm39) Y70H possibly damaging Het
Sfrp1 A G 8: 23,936,260 (GRCm39) K234R possibly damaging Het
Slc1a2 A G 2: 102,607,795 (GRCm39) N481S probably damaging Het
Slc44a3 T G 3: 121,320,849 (GRCm39) I51L probably benign Het
Slitrk1 A G 14: 109,149,004 (GRCm39) F569S possibly damaging Het
Smurf2 A T 11: 106,726,974 (GRCm39) N451K probably damaging Het
Sptbn2 T A 19: 4,788,247 (GRCm39) D1075E probably damaging Het
Tdrd12 T C 7: 35,228,689 (GRCm39) D11G probably damaging Het
Tex2 C T 11: 106,410,739 (GRCm39) A926T unknown Het
Tm7sf2 A G 19: 6,113,914 (GRCm39) F209S probably damaging Het
Trbv12-2 G A 6: 41,095,774 (GRCm39) probably benign Het
Virma T A 4: 11,514,036 (GRCm39) L630H probably damaging Het
Vmn1r68 A G 7: 10,261,747 (GRCm39) I117T possibly damaging Het
Zan C A 5: 137,454,917 (GRCm39) R1373L unknown 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
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'- CTTGGAAAGTGTGACCGCTC -3'
(R):5'- ACATCATAATGGCTCTGTGGC -3'

Sequencing Primer
(F):5'- AAGTGTGACCGCTCCCTGTTG -3'
(R):5'- GCTCACTTTGGTTAGAGGCCATC -3'
Posted On 2016-12-20