Mutagenetix > Incidental Mutation

Incidental Mutation 'R7134:Syngap1'

552952

Institutional Source

Beutler Lab

Gene Symbol

Syngap1

Ensembl Gene

ENSMUSG00000067629

Gene Name

synaptic Ras GTPase activating protein 1 homolog (rat)

Synonyms

Syngap

MMRRC Submission

045219-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7134 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

27160227-27191408 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27178985 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 665 (Y665H)

Ref Sequence

ENSEMBL: ENSMUSP00000141686 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000081285] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000201702] [ENSMUST00000202939] [ENSMUST00000228963] [ENSMUST00000229490] [ENSMUST00000231853]

AlphaFold

F6SEU4

Predicted Effect

probably damaging
Transcript: ENSMUST00000081285
AA Change: Y606H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: Y606H

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

probably damaging
Transcript: ENSMUST00000177932
AA Change: Y665H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: Y665H

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

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: Y649H

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 damaging
Transcript: ENSMUST00000194598
AA Change: Y665H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: Y665H

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

probably benign
Transcript: ENSMUST00000201186

Predicted Effect

SMART Domains

Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: Y664H

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

SMART Domains

Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: Y665H

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: ENSMUST00000202049

Predicted Effect

probably benign
Transcript: ENSMUST00000202208

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

probably damaging
Transcript: ENSMUST00000228963
AA Change: Y606H

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000229490
AA Change: Y665H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000231853
AA Change: Y492H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

99% (84/85)

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf1	A	G	17: 36,270,144 (GRCm39)	F638S	possibly damaging	Het
Actl6b	T	A	5: 137,562,762 (GRCm39)	N159K	probably damaging	Het
Adam6a	T	G	12: 113,508,655 (GRCm39)	S343A	probably benign	Het
Ankrd17	G	A	5: 90,380,173 (GRCm39)	T2505I	probably damaging	Het
Ankrd17	T	C	5: 90,433,382 (GRCm39)	T728A	probably benign	Het
Asap2	G	T	12: 21,315,964 (GRCm39)	E919*	probably null	Het
Atp10b	A	T	11: 43,136,291 (GRCm39)	I1140F	probably damaging	Het
Cep126	A	T	9: 8,103,383 (GRCm39)	V209E	probably damaging	Het
Cfap65	C	T	1: 74,965,792 (GRCm39)	R406Q	probably benign	Het
Cldn1	T	C	16: 26,190,376 (GRCm39)	M1V	probably null	Het
Cryl1	C	T	14: 57,512,956 (GRCm39)	D304N	probably benign	Het
D3Ertd751e	T	C	3: 41,708,212 (GRCm39)		probably null	Het
D630044L22Rik	A	T	17: 26,181,090 (GRCm39)	M156L	probably benign	Het
Ddx21	T	C	10: 62,427,634 (GRCm39)	D423G	possibly damaging	Het
Dock2	T	A	11: 34,260,363 (GRCm39)	M993L	probably benign	Het
Dusp29	A	T	14: 21,727,129 (GRCm39)	I173N	probably damaging	Het
Eif4g1	C	T	16: 20,500,252 (GRCm39)	A675V	probably damaging	Het
Eml1	C	T	12: 108,472,810 (GRCm39)	S206L	probably benign	Het
Farp2	A	C	1: 93,531,181 (GRCm39)	I560L	probably benign	Het
Fbn1	A	T	2: 125,223,969 (GRCm39)	D593E	probably benign	Het
Fetub	A	G	16: 22,748,007 (GRCm39)	D61G	possibly damaging	Het
Fpgs	T	C	2: 32,576,641 (GRCm39)	K329E	probably benign	Het
Fpgt	T	C	3: 154,797,120 (GRCm39)	Y45C	probably damaging	Het
Gas2l1	A	T	11: 5,011,106 (GRCm39)	C574*	probably null	Het
Gm9747	G	T	1: 82,211,837 (GRCm39)	C12F	unknown	Het
H2-T23	T	C	17: 36,342,709 (GRCm39)	Y143C	probably damaging	Het
Hhip	A	T	8: 80,719,142 (GRCm39)	S462T	probably benign	Het
Hnf1a	C	T	5: 115,091,446 (GRCm39)	G416R	probably damaging	Het
Hoxa5	C	T	6: 52,181,023 (GRCm39)	C103Y	probably damaging	Het
Kansl3	G	T	1: 36,390,848 (GRCm39)	D395E	possibly damaging	Het
Marchf10	A	G	11: 105,299,502 (GRCm39)	S116P	probably benign	Het
Med12l	C	T	3: 59,001,180 (GRCm39)	Q748*	probably null	Het
Mroh7	T	A	4: 106,577,791 (GRCm39)	N296Y	probably damaging	Het
Mtbp	T	G	15: 55,421,961 (GRCm39)	D61E	probably benign	Het
Muc5b	A	T	7: 141,411,391 (GRCm39)	I1446L	unknown	Het
Myh15	T	C	16: 48,901,705 (GRCm39)	V266A	possibly damaging	Het
Nap1l1	G	A	10: 111,330,655 (GRCm39)		probably null	Het
Napsa	A	G	7: 44,235,159 (GRCm39)	T315A	probably benign	Het
Nlrc5	A	T	8: 95,206,350 (GRCm39)	I734F	probably damaging	Het
Nnt	A	G	13: 119,531,198 (GRCm39)	V183A	probably damaging	Het
Nploc4	A	T	11: 120,276,614 (GRCm39)	D477E	probably benign	Het
Nrip3	A	G	7: 109,364,695 (GRCm39)	S144P	probably damaging	Het
Ntng1	A	T	3: 109,842,445 (GRCm39)	F109L	probably benign	Het
Or5p61	A	G	7: 107,758,883 (GRCm39)	Y66H	probably damaging	Het
Or5v1	T	A	17: 37,809,776 (GRCm39)	V78D	probably damaging	Het
Or6aa1	G	A	7: 86,044,752 (GRCm39)		probably benign	Het
Or8b36	A	G	9: 37,937,795 (GRCm39)	E231G	probably benign	Het
Pacsin1	G	A	17: 27,921,707 (GRCm39)	D30N	probably damaging	Het
Pbld2	A	T	10: 62,860,368 (GRCm39)		probably benign	Het
Pcnx4	C	T	12: 72,613,750 (GRCm39)	T565I	probably damaging	Het
Pdzk1	A	T	3: 96,763,246 (GRCm39)	T225S	probably benign	Het
Phyhip	T	G	14: 70,704,639 (GRCm39)	I286S	probably benign	Het
Pkd1	T	A	17: 24,813,086 (GRCm39)	Y3903N	probably damaging	Het
Plcb3	A	T	19: 6,942,698 (GRCm39)	L222Q	probably damaging	Het
Plcd4	T	A	1: 74,593,662 (GRCm39)	H262Q	probably benign	Het
Plekhh1	C	T	12: 79,109,390 (GRCm39)	A474V	probably benign	Het
Plppr3	T	C	10: 79,701,537 (GRCm39)	E435G	probably damaging	Het
Poln	T	A	5: 34,276,340 (GRCm39)	N305I	possibly damaging	Het
Pou3f2	T	C	4: 22,486,874 (GRCm39)	T420A	probably benign	Het
Ppdpf	T	C	2: 180,829,523 (GRCm39)	Y17H	probably damaging	Het
Prrx2	C	A	2: 30,768,485 (GRCm39)	T104K	probably damaging	Het
Ptprj	A	T	2: 90,294,822 (GRCm39)	L462H	probably benign	Het
Radil	T	C	5: 142,471,304 (GRCm39)	T991A	probably damaging	Het
Rbsn	T	C	6: 92,178,608 (GRCm39)	E147G	probably damaging	Het
Ror2	C	T	13: 53,300,742 (GRCm39)	V35M	probably benign	Het
Rps6ka1	T	C	4: 133,599,373 (GRCm39)	Q18R	probably benign	Het
Setbp1	T	A	18: 78,902,734 (GRCm39)	D311V	possibly damaging	Het
Setd2	C	T	9: 110,377,865 (GRCm39)	S560L	possibly damaging	Het
Slc12a5	A	T	2: 164,816,878 (GRCm39)	I134F	probably damaging	Het
Speer1h	C	T	5: 11,647,706 (GRCm39)	T148I	possibly damaging	Het
Svil	A	G	18: 5,116,080 (GRCm39)	D2035G	probably damaging	Het
Tbc1d9b	T	C	11: 50,043,519 (GRCm39)	Y547H	possibly damaging	Het
Tgm2	A	G	2: 157,980,812 (GRCm39)	V83A	probably benign	Het
Tmem233	T	C	5: 116,189,429 (GRCm39)	I117V	probably benign	Het
Tsen34	A	G	7: 3,703,640 (GRCm39)	T293A	probably damaging	Het
Ttn	A	G	2: 76,709,023 (GRCm39)	V8752A	unknown	Het
Ubac1	A	G	2: 25,904,974 (GRCm39)	V88A	probably benign	Het
Uchl4	T	C	9: 64,142,621 (GRCm39)	V34A	probably damaging	Het
Ugt2a2	C	T	5: 87,608,435 (GRCm39)	R468H	probably benign	Het
Vmn2r102	A	T	17: 19,897,749 (GRCm39)	T255S	probably benign	Het
Wdr6	T	A	9: 108,450,564 (GRCm39)	N988I	probably damaging	Het
Wnk1	A	T	6: 119,903,389 (GRCm39)	I2359N	unknown	Het
Ybey	A	G	10: 76,304,025 (GRCm39)	V59A	probably benign	Het
Zfp268	T	A	4: 145,349,375 (GRCm39)	C271S	possibly damaging	Het
Zfp397	A	G	18: 24,090,122 (GRCm39)	N142S	probably benign	Het
Zfy1	A	T	Y: 725,788 (GRCm39)	V659E	probably damaging	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
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
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'- CAGAACCTGGCCAACTTTTCC -3'
(R):5'- AGGTGACAAGAGTTCTGTGC -3'

Sequencing Primer
(F):5'- GCCAACTTTTCCAAGTGAGG -3'
(R):5'- GATAATCTCTCAGCCCAGGTG -3'

Posted On

2019-05-15