Mutagenetix > Incidental Mutation

Incidental Mutation 'R9723:Syngap1'

730958

Institutional Source

Beutler Lab

Gene Symbol

Syngap1

Ensembl Gene

ENSMUSG00000067629

Gene Name

synaptic Ras GTPase activating protein 1 homolog (rat)

Synonyms

Syngap

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9723 (G1)

Quality Score

139.008

Status

Not validated

Chromosome

Chromosomal Location

27160227-27191408 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 27189510 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 1305 (R1305H)

Ref Sequence

ENSEMBL: ENSMUSP00000141686 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000081285] [ENSMUST00000120016] [ENSMUST00000133257] [ENSMUST00000177932] [ENSMUST00000194598] [ENSMUST00000201702] [ENSMUST00000228963] [ENSMUST00000229490] [ENSMUST00000231853]

AlphaFold

F6SEU4

Predicted Effect

possibly damaging
Transcript: ENSMUST00000081285
AA Change: R1246H

PolyPhen 2 Score 0.951 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: R1246H

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: ENSMUST00000120016

SMART Domains

Protein: ENSMUSP00000112778
Gene: ENSMUSG00000079605

Domain	Start	End	E-Value	Type
low complexity region	3	14	N/A	INTRINSIC
BTB	48	142	4.08e-21	SMART
low complexity region	144	164	N/A	INTRINSIC
low complexity region	315	328	N/A	INTRINSIC
ZnF_C2H2	397	419	1.36e-2	SMART
ZnF_C2H2	424	444	4.99e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000133257

SMART Domains

Protein: ENSMUSP00000115777
Gene: ENSMUSG00000048731

Domain	Start	End	E-Value	Type
low complexity region	144	157	N/A	INTRINSIC
internal_repeat_1	264	280	1.14e-6	PROSPERO
Pfam:Ubiquitin_3	281	368	1.5e-47	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000177932
AA Change: V1308M

SMART Domains

Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: V1308M

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

probably benign
Transcript: ENSMUST00000193200

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629

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

possibly damaging
Transcript: ENSMUST00000194598
AA Change: R1305H

PolyPhen 2 Score 0.951 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: R1305H

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

probably benign
Transcript: ENSMUST00000201349

SMART Domains

Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629

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: V1289M

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

unknown
Transcript: ENSMUST00000228963
AA Change: V1246M

Predicted Effect

probably benign
Transcript: ENSMUST00000229490
AA Change: V1305M

PolyPhen 2 Score 0.333 (Sensitivity: 0.90; Specificity: 0.89)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231853
AA Change: R1132H

PolyPhen 2 Score 0.951 (Sensitivity: 0.79; Specificity: 0.95)

Coding Region Coverage

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

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb6	G	A	1: 75,156,366 (GRCm39)	R133W	probably benign	Het
Abcc3	T	A	11: 94,250,725 (GRCm39)	T877S	probably benign	Het
Alb	A	T	5: 90,611,962 (GRCm39)	K130N	probably damaging	Het
Alkbh8	G	A	9: 3,385,283 (GRCm39)	S560N	probably benign	Het
Angel2	T	G	1: 190,671,342 (GRCm39)	L234R	probably damaging	Het
Catip	C	T	1: 74,403,745 (GRCm39)	T154I	probably benign	Het
Ccdc163	C	T	4: 116,569,595 (GRCm39)	Q102*	probably null	Het
Cep250	A	G	2: 155,823,337 (GRCm39)	E997G	probably benign	Het
Ces2f	T	C	8: 105,677,463 (GRCm39)	I183T	possibly damaging	Het
Commd8	A	G	5: 72,318,309 (GRCm39)	V158A	possibly damaging	Het
Cyp2b9	C	T	7: 25,909,596 (GRCm39)	Q455*	probably null	Het
D5Ertd579e	G	T	5: 36,772,284 (GRCm39)	H704N	probably damaging	Het
Dnah1	T	C	14: 30,987,946 (GRCm39)	T3491A	probably damaging	Het
Dnai1	T	G	4: 41,603,302 (GRCm39)	F195C	possibly damaging	Het
Dock7	A	G	4: 98,908,270 (GRCm39)	V620A		Het
Dock7	A	T	4: 98,960,660 (GRCm39)	D289E		Het
Dpys	T	A	15: 39,691,509 (GRCm39)	E271V	probably damaging	Het
Elovl3	T	C	19: 46,123,155 (GRCm39)	Y244H	probably damaging	Het
Enam	G	A	5: 88,652,241 (GRCm39)	G1250E	probably damaging	Het
Espl1	C	T	15: 102,229,170 (GRCm39)	T1774M	probably benign	Het
Fasl	T	C	1: 161,615,535 (GRCm39)	K107R	probably benign	Het
Fbn1	A	T	2: 125,202,119 (GRCm39)	C1251*	probably null	Het
Fn1	G	T	1: 71,663,369 (GRCm39)	Q1040K	possibly damaging	Het
Frem3	C	T	8: 81,341,352 (GRCm39)	S1215L	probably benign	Het
G3bp2	A	T	5: 92,214,388 (GRCm39)	D135E	possibly damaging	Het
Gabpb1	C	T	2: 126,488,648 (GRCm39)	V240I	probably benign	Het
Galnt12	C	G	4: 47,119,541 (GRCm39)	Y452*	probably null	Het
Ggta1	G	T	2: 35,303,418 (GRCm39)	D91E	probably benign	Het
Gm12258	C	T	11: 58,750,448 (GRCm39)	P541L	unknown	Het
Gm12789	T	A	4: 101,846,083 (GRCm39)	W115R	possibly damaging	Het
Gm8126	T	C	14: 43,119,141 (GRCm39)		probably null	Het
Gpr179	A	T	11: 97,225,546 (GRCm39)	L2203H	possibly damaging	Het
H1f6	A	G	13: 23,879,906 (GRCm39)	K20E	probably damaging	Het
Hapln3	A	T	7: 78,771,736 (GRCm39)	V51E	possibly damaging	Het
Ifit1	A	G	19: 34,626,257 (GRCm39)	*464W	probably null	Het
Il1r1	A	C	1: 40,332,721 (GRCm39)	I137L	probably benign	Het
Il1rap	T	A	16: 26,442,907 (GRCm39)	M1K	probably null	Het
Lgi2	A	G	5: 52,695,843 (GRCm39)	L372P	probably damaging	Het
Lrrc46	A	G	11: 96,925,773 (GRCm39)	S230P	possibly damaging	Het
Ltbr	G	A	6: 125,284,348 (GRCm39)	R365W	probably damaging	Het
Mapk8ip3	C	A	17: 25,132,585 (GRCm39)	W339L	possibly damaging	Het
Msln	A	T	17: 25,969,008 (GRCm39)	M459K	possibly damaging	Het
Msr1	A	G	8: 40,042,357 (GRCm39)	V406A	possibly damaging	Het
Ndst2	G	T	14: 20,775,512 (GRCm39)	D659E	probably benign	Het
Npat	T	A	9: 53,473,746 (GRCm39)	S513T	probably benign	Het
Npat	T	G	9: 53,481,861 (GRCm39)	L1190V	probably damaging	Het
Npc1	A	G	18: 12,343,649 (GRCm39)	I448T	probably benign	Het
Omd	T	C	13: 49,743,838 (GRCm39)	F296S	probably damaging	Het
Oprm1	A	G	10: 6,788,514 (GRCm39)	N423S	possibly damaging	Het
Oxtr	G	A	6: 112,466,304 (GRCm39)	T152I	probably benign	Het
Pak2	A	T	16: 31,852,650 (GRCm39)	V297E	probably damaging	Het
Pcnx4	T	C	12: 72,603,039 (GRCm39)	Y434H	probably damaging	Het
Pet100	G	A	8: 3,672,374 (GRCm39)	M20I	probably damaging	Het
Pfpl	G	C	19: 12,406,297 (GRCm39)	E183Q	probably damaging	Het
Plekhn1	A	G	4: 156,306,875 (GRCm39)	S505P	probably benign	Het
Plin5	G	A	17: 56,423,290 (GRCm39)	A90V	probably damaging	Het
Poc5	A	G	13: 96,551,026 (GRCm39)	T526A	probably benign	Het
Potefam1	T	C	2: 111,058,700 (GRCm39)	H84R	probably damaging	Het
Pramel7	C	T	2: 87,320,019 (GRCm39)	V425I	possibly damaging	Het
Rad51d	A	T	11: 82,781,162 (GRCm39)		probably null	Het
Rbp3	T	C	14: 33,677,474 (GRCm39)	M474T	possibly damaging	Het
Rcan3	A	G	4: 135,152,680 (GRCm39)	S14P	probably benign	Het
Rps6ka4	A	T	19: 6,816,663 (GRCm39)	V140E	probably damaging	Het
Rsbn1l	G	A	5: 21,101,464 (GRCm39)	S692L	possibly damaging	Het
Sgk1	A	T	10: 21,872,239 (GRCm39)	I272F	probably damaging	Het
Skor1	A	G	9: 63,053,714 (GRCm39)	V85A	probably damaging	Het
Slc12a1	A	T	2: 125,059,827 (GRCm39)	D909V	probably damaging	Het
Slc25a18	C	A	6: 120,770,489 (GRCm39)	A283E	probably benign	Het
Slc41a1	T	C	1: 131,772,103 (GRCm39)	L411P	possibly damaging	Het
Spata13	T	C	14: 60,928,498 (GRCm39)	S19P	probably damaging	Het
Stab1	T	A	14: 30,885,848 (GRCm39)	H42L	probably benign	Het
Stag3	T	A	5: 138,298,103 (GRCm39)	D698E	probably benign	Het
Tek	T	G	4: 94,692,539 (GRCm39)	W216G	possibly damaging	Het
Trappc9	A	G	15: 72,461,963 (GRCm39)	Y1101H	possibly damaging	Het
Ttn	A	G	2: 76,601,929 (GRCm39)	Y10251H	probably damaging	Het
Uhrf1	A	G	17: 56,625,061 (GRCm39)	K535E	probably damaging	Het
Usp14	G	T	18: 10,009,993 (GRCm39)	Q185K	probably damaging	Het
Usp32	A	T	11: 84,935,536 (GRCm39)	Y413*	probably null	Het
Uvssa	G	A	5: 33,547,382 (GRCm39)		probably null	Het
Vmn1r177	A	T	7: 23,565,774 (GRCm39)	L34Q	probably damaging	Het
Wdr41	T	C	13: 95,151,671 (GRCm39)	L277P	probably damaging	Het
Zc2hc1b	T	A	10: 13,044,497 (GRCm39)	L55F	probably damaging	Het
Zfp345	A	C	2: 150,314,189 (GRCm39)	Y449*	probably null	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
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
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'- GGTTTCCTGGAGGTGAGAAAC -3'
(R):5'- TGCCCCAAGGAGGCATTAAG -3'

Sequencing Primer
(F):5'- TTTCCTGGAGGTGAGAAACAAACAG -3'
(R):5'- GGAGACAATCCCGCTGTC -3'

Posted On

2022-10-06