Mutagenetix > Incidental Mutation

Incidental Mutation 'R4661:Syngap1'

352891

Institutional Source

Beutler Lab

Gene Symbol

Syngap1

Ensembl Gene

ENSMUSG00000067629

Gene Name

synaptic Ras GTPase activating protein 1 homolog (rat)

Synonyms

Syngap

MMRRC Submission

041600-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4661 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

27160227-27191408 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 27185880 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 1270 (L1270P)

Ref Sequence

ENSEMBL: ENSMUSP00000137587 (fasta)

Gene Model

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

AlphaFold

F6SEU4

Predicted Effect

probably damaging
Transcript: ENSMUST00000081285
AA Change: L1211P

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: L1211P

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: L1270P

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

SMART Domains

Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: L1270P

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: L1254P

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: L1254P

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: L1270P

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: L1270P

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

silent
Transcript: ENSMUST00000201186

Predicted Effect

silent
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

unknown
Transcript: ENSMUST00000201702
AA Change: L1254P

SMART Domains

Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: L1254P

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

unknown
Transcript: ENSMUST00000202208
AA Change: L97P

Predicted Effect

silent
Transcript: ENSMUST00000202049

Predicted Effect

probably damaging
Transcript: ENSMUST00000231853
AA Change: L1097P

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

Predicted Effect

probably damaging
Transcript: ENSMUST00000229490
AA Change: L1270P

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

Predicted Effect

probably damaging
Transcript: ENSMUST00000228963
AA Change: L1211P

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcg4	T	C	9: 44,198,627 (GRCm39)	N42D	probably damaging	Het
Adamdec1	G	A	14: 68,807,562 (GRCm39)	T366I	probably damaging	Het
Adamts7	C	A	9: 90,075,383 (GRCm39)	H1038Q	probably benign	Het
Aff3	T	C	1: 38,666,209 (GRCm39)	D5G	possibly damaging	Het
Amhr2	A	T	15: 102,362,688 (GRCm39)	D485V	probably damaging	Het
Arhgap35	A	T	7: 16,298,663 (GRCm39)	F134Y	probably damaging	Het
Asxl3	A	G	18: 22,649,534 (GRCm39)	T508A	probably benign	Het
Atp10a	TGGCGGCGGC	TGGCGGC	7: 58,308,248 (GRCm39)		probably benign	Het
Atp4a	G	A	7: 30,419,650 (GRCm39)	R671Q	probably benign	Het
Atp9a	A	G	2: 168,479,592 (GRCm39)	F928L	possibly damaging	Het
BC034090	A	T	1: 155,108,221 (GRCm39)	D13E	probably damaging	Het
Bco1	A	G	8: 117,855,980 (GRCm39)	E425G	probably benign	Het
Brsk1	T	C	7: 4,710,298 (GRCm39)	S436P	possibly damaging	Het
C1s1	T	C	6: 124,513,449 (GRCm39)	I193V	probably benign	Het
Calb2	A	G	8: 110,894,709 (GRCm39)	F21L	probably benign	Het
Catsperz	T	G	19: 6,902,171 (GRCm39)	T108P	probably benign	Het
Cep57l1	T	A	10: 41,595,767 (GRCm39)	D329V	possibly damaging	Het
Cfdp1	A	G	8: 112,557,577 (GRCm39)	F188S	probably benign	Het
Chrna2	G	A	14: 66,386,292 (GRCm39)	G146D	probably damaging	Het
Col6a1	A	C	10: 76,550,506 (GRCm39)	F520V	unknown	Het
Cyb5d2	C	A	11: 72,669,771 (GRCm39)	V43L	probably damaging	Het
Cyp2c40	T	C	19: 39,775,290 (GRCm39)	T321A	probably benign	Het
Dnajc16	A	C	4: 141,490,859 (GRCm39)	Y764D	probably damaging	Het
Dsg1a	G	A	18: 20,473,590 (GRCm39)	V888M	probably damaging	Het
F5	A	C	1: 164,012,489 (GRCm39)	T468P	probably damaging	Het
Faap24	A	G	7: 35,094,509 (GRCm39)	M97T	probably benign	Het
Fam227b	A	T	2: 125,849,230 (GRCm39)	I334N	probably damaging	Het
Frem2	G	T	3: 53,562,864 (GRCm39)	P548T	probably damaging	Het
Gfm1	A	G	3: 67,340,731 (GRCm39)	E94G	probably damaging	Het
Gm17606	A	T	14: 54,885,696 (GRCm39)		probably benign	Het
Gnb2	A	T	5: 137,528,515 (GRCm39)	M1K	probably null	Het
Gys1	G	A	7: 45,104,258 (GRCm39)	A544T	probably damaging	Het
Hdac5	T	C	11: 102,096,675 (GRCm39)	Y230C	probably damaging	Het
Hunk	A	T	16: 90,244,196 (GRCm39)		probably null	Het
Ifnl2	A	G	7: 28,209,635 (GRCm39)	F51L	probably damaging	Het
Itpr1	T	C	6: 108,387,892 (GRCm39)		probably null	Het
Kcnj1	A	G	9: 32,307,918 (GRCm39)	Y114C	probably benign	Het
Kdm4b	T	A	17: 56,706,459 (GRCm39)	S322T	probably damaging	Het
Kif27	T	C	13: 58,471,730 (GRCm39)	E786G	probably damaging	Het
Kif6	T	C	17: 50,060,909 (GRCm39)	V414A	probably benign	Het
L1td1	A	G	4: 98,621,861 (GRCm39)	K141R	possibly damaging	Het
Loxhd1	A	G	18: 77,490,581 (GRCm39)	I1394V	possibly damaging	Het
Lrfn5	A	T	12: 61,886,433 (GRCm39)	M74L	probably damaging	Het
Lrp6	C	T	6: 134,488,230 (GRCm39)	D289N	probably benign	Het
Mroh7	A	G	4: 106,548,710 (GRCm39)		probably null	Het
Muc4	A	C	16: 32,589,651 (GRCm39)	E2885A	possibly damaging	Het
Myo18b	G	T	5: 113,023,041 (GRCm39)		probably benign	Het
Ncln	G	A	10: 81,328,902 (GRCm39)	A172V	probably damaging	Het
Nek9	G	A	12: 85,367,666 (GRCm39)	T335M	possibly damaging	Het
Notch2	A	G	3: 98,042,829 (GRCm39)	Y1398C	probably damaging	Het
Or10g6	A	T	9: 39,933,823 (GRCm39)	I45F	probably damaging	Het
Or2d4	T	A	7: 106,544,074 (GRCm39)	I45F	probably damaging	Het
Or5p52	A	T	7: 107,502,188 (GRCm39)	H88L	probably benign	Het
Pax2	G	A	19: 44,749,376 (GRCm39)	V40M	probably damaging	Het
Pde6c	A	G	19: 38,157,887 (GRCm39)	Y637C	probably damaging	Het
Plppr5	A	G	3: 117,414,618 (GRCm39)	I80V	probably damaging	Het
Pold1	G	T	7: 44,182,233 (GRCm39)	P1100T	probably damaging	Het
Prune2	T	C	19: 16,977,387 (GRCm39)	Y41H	probably damaging	Het
Rgl2	C	T	17: 34,152,200 (GRCm39)	A329V	possibly damaging	Het
Rilp	T	A	11: 75,402,250 (GRCm39)	Y250N	probably damaging	Het
Rilpl1	A	G	5: 124,652,751 (GRCm39)	V19A	probably benign	Het
Rtp3	T	C	9: 110,815,519 (GRCm39)		probably null	Het
Rufy4	A	G	1: 74,172,266 (GRCm39)	K246E	probably damaging	Het
Saraf	C	A	8: 34,635,616 (GRCm39)	A306E	probably damaging	Het
Slc26a8	A	T	17: 28,857,658 (GRCm39)	N828K	probably benign	Het
Src	C	T	2: 157,311,852 (GRCm39)	P527S	probably damaging	Het
Susd3	C	T	13: 49,384,778 (GRCm39)		probably null	Het
Taf1c	G	A	8: 120,325,589 (GRCm39)	P758S	probably damaging	Het
Tenm2	A	T	11: 35,915,275 (GRCm39)	N2087K	probably damaging	Het
Tfrc	A	T	16: 32,448,969 (GRCm39)	I703F	probably damaging	Het
Thap1	C	G	8: 26,650,874 (GRCm39)	T48S	probably benign	Het
Tspear	T	C	10: 77,702,163 (GRCm39)	F199L	probably benign	Het
Usp17lc	A	T	7: 103,067,797 (GRCm39)	H364L	probably benign	Het
Usp9x	A	G	X: 12,989,747 (GRCm39)	R776G	possibly damaging	Homo
Vmn1r1	T	C	1: 181,984,789 (GRCm39)	E292G	possibly damaging	Het
Vmn1r125	T	G	7: 21,006,552 (GRCm39)	V150G	probably damaging	Het
Vmn1r167	A	T	7: 23,204,117 (GRCm39)	L300I	probably damaging	Het
Vmn2r106	A	C	17: 20,487,885 (GRCm39)	I838S	probably benign	Het
Wdr64	A	T	1: 175,554,060 (GRCm39)	S197C	probably damaging	Het
Zfp248	A	T	6: 118,410,268 (GRCm39)	V47E	possibly 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
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
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'- ACAGGCATCTTTTAGGTAATGGG -3'
(R):5'- CAGGAGTAAGGCTGGCTCTG -3'

Sequencing Primer
(F):5'- CATCTTTTAGGTAATGGGGGAAGAAG -3'
(R):5'- TCTGCCAGGAGTGACGGAG -3'

Posted On

2015-10-08