Mutagenetix > Incidental Mutations

Incidental Mutation 'R1680:Syngap1'

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

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1680 (G1)

Quality Score

225

Status

Not validated

Chromosome

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

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

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

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

unknown
Transcript: ENSMUST00000193200
AA Change: S89P

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: S89P

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 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

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

unknown
Transcript: ENSMUST00000201349
AA Change: S104P

SMART Domains

Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: S104P

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

unknown
Transcript: ENSMUST00000201702
AA Change: S105P

SMART Domains

Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: S105P

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

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017N19Rik	C	G	10: 100,603,528	P187R	probably damaging	Het
Ahnak	T	A	19: 9,009,963	H2870Q	probably benign	Het
Arhgef33	C	T	17: 80,347,651	S95F	probably damaging	Het
Atp1a2	T	A	1: 172,278,954	D827V	probably damaging	Het
Bcat1	T	G	6: 145,039,628	D96A	probably damaging	Het
Birc6	A	T	17: 74,548,746	I184L	probably benign	Het
Ccdc129	C	T	6: 55,968,766	T824I	probably damaging	Het
Clca3b	A	T	3: 144,837,824	L415M	probably damaging	Het
Clstn1	T	C	4: 149,643,726	V617A	probably benign	Het
Col22a1	G	A	15: 71,799,361	A1050V	unknown	Het
Col5a3	C	T	9: 20,784,668		probably null	Het
Csmd3	G	A	15: 47,741,170	T1059I	probably damaging	Het
Dclk2	C	T	3: 86,805,639	R503Q	possibly damaging	Het
Dnm3	A	G	1: 162,010,976	V272A	probably benign	Het
Dnmt3a	A	G	12: 3,873,361	Q187R	probably damaging	Het
Dpp9	A	G	17: 56,190,103	Y710H	probably benign	Het
Eef1a2	A	T	2: 181,152,941	M155K	possibly damaging	Het
Entpd8	G	A	2: 25,084,024	C331Y	probably damaging	Het
Erc1	A	C	6: 119,575,761	L1072R	probably damaging	Het
Fam160b2	T	C	14: 70,586,851	Y482C	probably damaging	Het
Gtf3c2	A	G	5: 31,173,868	S155P	probably damaging	Het
Gucy2c	A	G	6: 136,722,493	S617P	probably damaging	Het
Ice1	T	C	13: 70,605,448	R840G	probably benign	Het
Il1rl2	T	C	1: 40,351,793	Y299H	possibly damaging	Het
Ints7	T	G	1: 191,621,162		probably null	Het
Ireb2	C	T	9: 54,881,518	T92I	probably damaging	Het
Kcnj8	A	T	6: 142,570,189	L64*	probably null	Het
Mapk8ip3	A	G	17: 24,901,011	V983A	probably damaging	Het
Mertk	A	G	2: 128,801,636	D985G	probably benign	Het
Mical3	A	T	6: 120,959,643	S1307R	probably benign	Het
Ncaph2	A	G	15: 89,364,622	D222G	probably benign	Het
Nf1	C	A	11: 79,550,998	S295*	probably null	Het
Nlrp12	T	A	7: 3,241,174	D236V	probably damaging	Het
Npnt	A	G	3: 132,906,802	V74A	probably benign	Het
Oasl1	A	G	5: 114,935,944	D304G	probably damaging	Het
Olfr1098	C	T	2: 86,923,161	V124I	probably benign	Het
Olfr556	A	G	7: 102,670,733	D271G	possibly damaging	Het
Olfr834	A	G	9: 18,988,516	H176R	possibly damaging	Het
Olfr936	T	C	9: 39,047,000	I140V	probably benign	Het
Patz1	A	G	11: 3,307,812	K604E	probably damaging	Het
Pcsk6	T	A	7: 66,035,250	V793E	probably benign	Het
Pla2g4d	C	T	2: 120,277,750		probably null	Het
Plxnc1	A	C	10: 94,841,551	L938R	probably benign	Het
Pou4f2	G	T	8: 78,434,831	A381D	probably damaging	Het
Prdm4	A	G	10: 85,899,223	L685P	possibly damaging	Het
Pxn	T	A	5: 115,552,147	V383E	probably damaging	Het
Rbl1	A	G	2: 157,174,783	L632P	probably damaging	Het
Rnf135	T	A	11: 80,196,881	S219T	possibly damaging	Het
Sdk2	T	C	11: 113,791,436	D2039G	possibly damaging	Het
Sdk2	C	T	11: 113,838,646		silent	Het
Slc5a6	A	G	5: 31,042,644	Y131H	probably damaging	Het
Slc9a1	T	C	4: 133,418,080	I492T	probably damaging	Het
Soga3	A	T	10: 29,196,839	Q709L	probably damaging	Het
Spag5	A	G	11: 78,320,616	K993E	probably damaging	Het
Sptbn1	T	G	11: 30,159,371	I75L	possibly damaging	Het
Tfcp2l1	T	A	1: 118,675,605	F458I	probably damaging	Het
Tmem67	A	G	4: 12,087,840	V102A	probably benign	Het
Tomm70a	T	C	16: 57,121,961	S34P	unknown	Het
Txlnb	G	T	10: 17,843,233	G604V	probably benign	Het
Ube2q1	A	G	3: 89,776,176	T143A	probably benign	Het
Unc80	C	T	1: 66,503,669	R361*	probably null	Het
Vcan	T	C	13: 89,703,547	D1098G	probably benign	Het
Vmn1r176	T	A	7: 23,835,381	T116S	probably damaging	Het
Wdr81	C	T	11: 75,454,423	R6K	probably benign	Het
Zan	T	A	5: 137,403,050	T4136S	unknown	Het
Zbtb14	C	A	17: 69,388,502	F398L	probably damaging	Het
Zfp606	A	T	7: 12,493,971	H615L	probably damaging	Het
Zp3r	A	T	1: 130,582,880	N433K	probably benign	Het

Other mutations in Syngap1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0732:Syngap1	UTSW	17	26954988	missense	possibly damaging	0.94
R1178:Syngap1	UTSW	17	26957805	missense	probably damaging	0.99
R1953:Syngap1	UTSW	17	26944687	missense	possibly damaging	0.94
R2213:Syngap1	UTSW	17	26953069	missense	probably damaging	1.00
R2696:Syngap1	UTSW	17	26957411	nonsense	probably null
R2899:Syngap1	UTSW	17	26959985	missense	probably damaging	1.00
R3237:Syngap1	UTSW	17	26957093	nonsense	probably null
R3705:Syngap1	UTSW	17	26960020	missense	probably damaging	1.00
R3880:Syngap1	UTSW	17	26953064	missense	probably damaging	1.00
R4019:Syngap1	UTSW	17	26952341	unclassified	probably benign
R4661:Syngap1	UTSW	17	26966906	missense	probably damaging	1.00
R4798:Syngap1	UTSW	17	26961449	missense	probably benign	0.00
R5524:Syngap1	UTSW	17	26957152	missense	probably damaging	1.00
R5580:Syngap1	UTSW	17	26962331	missense	probably damaging	0.97
R5610:Syngap1	UTSW	17	26959780	missense	possibly damaging	0.68
R5835:Syngap1	UTSW	17	26958218	missense	probably benign	0.09
R5974:Syngap1	UTSW	17	26963038	missense	probably damaging	0.98
R6235:Syngap1	UTSW	17	26958130	missense	probably benign	0.00
R6247:Syngap1	UTSW	17	26962957	nonsense	probably null
R6461:Syngap1	UTSW	17	26964848	missense	probably damaging	1.00
R6503:Syngap1	UTSW	17	26944684	missense	probably benign	0.40
R7134:Syngap1	UTSW	17	26960011	missense	probably damaging	1.00
R7248:Syngap1	UTSW	17	26957767	missense	probably damaging	1.00
R7298:Syngap1	UTSW	17	26962987	missense	possibly damaging	0.85
R7749:Syngap1	UTSW	17	26959964	missense	probably damaging	0.99
R7812:Syngap1	UTSW	17	26941504	missense	probably benign
R7864:Syngap1	UTSW	17	26970528	missense
R7951:Syngap1	UTSW	17	26966968	missense	possibly damaging	0.46
R8024:Syngap1	UTSW	17	26941452	start codon destroyed	probably benign	0.01
R8132:Syngap1	UTSW	17	26958180	missense	probably damaging	0.98
R8386:Syngap1	UTSW	17	26960491	missense	possibly damaging	0.60
R9127:Syngap1	UTSW	17	26962121	missense	probably damaging	1.00
R9185:Syngap1	UTSW	17	26963083	missense	possibly damaging	0.69
R9189:Syngap1	UTSW	17	26964974	missense	probably damaging	1.00
X0017:Syngap1	UTSW	17	26944651	missense	probably benign	0.11
Z1088:Syngap1	UTSW	17	26961576	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