Mutagenetix > Incidental Mutation

Incidental Mutation 'R6247:Syngap1'

505736

Institutional Source

Beutler Lab

Gene Symbol

Syngap1

Ensembl Gene

ENSMUSG00000067629

Gene Name

synaptic Ras GTPase activating protein 1 homolog (rat)

Synonyms

Syngap

MMRRC Submission

044366-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6247 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

27160227-27191408 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to A at 27181931 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Stop codon at position 975 (S975*)

Ref Sequence

ENSEMBL: ENSMUSP00000156340 (fasta)

Gene Model

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

AlphaFold

F6SEU4

Predicted Effect

probably null
Transcript: ENSMUST00000081285
AA Change: S1089*

SMART Domains

Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: S1089*

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 null
Transcript: ENSMUST00000177932
AA Change: S1148*

SMART Domains

Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: S1148*

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 null
Transcript: ENSMUST00000193200
AA Change: S1132*

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: S1132*

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 null
Transcript: ENSMUST00000194598
AA Change: S1148*

SMART Domains

Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: S1148*

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: ENSMUST00000200799

Predicted Effect

probably null
Transcript: ENSMUST00000201186
AA Change: S79*

Predicted Effect

probably null
Transcript: ENSMUST00000201349
AA Change: S1147*

SMART Domains

Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: S1147*

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

probably null
Transcript: ENSMUST00000201702
AA Change: S1134*

SMART Domains

Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: S1134*

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: 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 null
Transcript: ENSMUST00000228963
AA Change: S1089*

Predicted Effect

probably benign
Transcript: ENSMUST00000202049

Predicted Effect

probably null
Transcript: ENSMUST00000231853
AA Change: S975*

Predicted Effect

probably null
Transcript: ENSMUST00000229490
AA Change: S1148*

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.4%

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	T	C	11: 72,049,768 (GRCm39)	D871G	probably benign	Het
A4galt	G	T	15: 83,112,020 (GRCm39)	H254Q	probably damaging	Het
AA986860	C	A	1: 130,670,780 (GRCm39)	T334K	possibly damaging	Het
Abca13	T	C	11: 9,353,874 (GRCm39)	I3732T	probably benign	Het
Abcf1	C	T	17: 36,271,956 (GRCm39)	D353N	probably damaging	Het
Adss1	A	G	12: 112,594,790 (GRCm39)	H83R	probably damaging	Het
Amer2	C	A	14: 60,616,321 (GRCm39)	A172E	probably damaging	Het
Ankhd1	A	G	18: 36,787,199 (GRCm39)	T2300A	probably benign	Het
Ano5	G	A	7: 51,215,879 (GRCm39)		probably null	Het
Apob	G	A	12: 8,051,801 (GRCm39)	G1109D	probably damaging	Het
Arhgef26	A	T	3: 62,288,381 (GRCm39)	N484Y	probably damaging	Het
C6	A	G	15: 4,793,023 (GRCm39)	D376G	probably damaging	Het
Caml	T	C	13: 55,772,986 (GRCm39)		probably null	Het
Capn12	T	C	7: 28,588,077 (GRCm39)	L473S	probably benign	Het
Cdk6	G	A	5: 3,394,553 (GRCm39)		probably null	Het
Cers5	A	T	15: 99,643,805 (GRCm39)	C153S	probably benign	Het
Cfap206	T	C	4: 34,692,530 (GRCm39)	M499V	probably benign	Het
Chd6	A	G	2: 160,791,968 (GRCm39)	M2463T	probably damaging	Het
Chn1	T	C	2: 73,537,350 (GRCm39)	E58G	possibly damaging	Het
Clec4a1	T	C	6: 122,905,001 (GRCm39)	V100A	probably benign	Het
Col7a1	G	C	9: 108,810,130 (GRCm39)		probably benign	Het
Csmd1	A	G	8: 16,246,249 (GRCm39)	V1050A	possibly damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dennd5a	A	T	7: 109,497,889 (GRCm39)	C1044S	probably damaging	Het
Dnah7b	A	G	1: 46,265,048 (GRCm39)	T2181A	probably benign	Het
Dnai1	T	C	4: 41,605,775 (GRCm39)	V255A	probably benign	Het
Dync2h1	A	G	9: 7,135,078 (GRCm39)	C1518R	probably damaging	Het
Dysf	T	C	6: 84,043,981 (GRCm39)	V273A	probably damaging	Het
Eif1	C	T	11: 100,211,223 (GRCm39)		probably benign	Het
Eml3	T	C	19: 8,908,313 (GRCm39)	I58T	probably benign	Het
Fam171b	T	A	2: 83,709,552 (GRCm39)	I408N	probably damaging	Het
Fchsd2	A	G	7: 100,902,747 (GRCm39)	E351G	probably benign	Het
Focad	G	A	4: 88,325,377 (GRCm39)	A81T	possibly damaging	Het
Fpr-rs4	G	A	17: 18,242,748 (GRCm39)	V252I	probably benign	Het
Fryl	A	G	5: 73,222,824 (GRCm39)	L1919P	probably damaging	Het
Gm12185	C	T	11: 48,806,735 (GRCm39)	R152H	probably damaging	Het
Gm14410	C	T	2: 176,885,517 (GRCm39)	G249E	probably damaging	Het
Gm6685	A	T	11: 28,289,706 (GRCm39)	S37T	possibly damaging	Het
Greb1	G	A	12: 16,766,676 (GRCm39)	P374L	probably damaging	Het
Hdac4	A	T	1: 91,940,560 (GRCm39)		probably null	Het
Hecw1	A	T	13: 14,409,010 (GRCm39)	L1099*	probably null	Het
Hivep1	T	C	13: 42,310,966 (GRCm39)	S1069P	probably benign	Het
Itgad	T	C	7: 127,784,959 (GRCm39)	I288T	possibly damaging	Het
Kif9	A	G	9: 110,317,612 (GRCm39)	M96V	possibly damaging	Het
Kncn	T	A	4: 115,741,987 (GRCm39)	V18E	probably damaging	Het
Lrrc74a	G	A	12: 86,805,330 (GRCm39)	G384D	probably damaging	Het
Ltb4r2	T	C	14: 56,000,108 (GRCm39)	V243A	probably damaging	Het
Mtnr1b	T	A	9: 15,774,082 (GRCm39)	I326L	probably benign	Het
Mylip	C	T	13: 45,561,957 (GRCm39)	T253I	probably damaging	Het
Necap1	T	A	6: 122,857,611 (GRCm39)		probably null	Het
Nedd4	C	T	9: 72,633,720 (GRCm39)	P409S	probably damaging	Het
Npat	A	T	9: 53,456,538 (GRCm39)	E36D	probably damaging	Het
Ovch2	C	T	7: 107,384,648 (GRCm39)	V490M	probably damaging	Het
Pax9	T	C	12: 56,756,480 (GRCm39)	S273P	probably benign	Het
Plce1	A	G	19: 38,734,289 (GRCm39)	E1563G	probably damaging	Het
Podxl2	C	A	6: 88,826,299 (GRCm39)	G336*	probably null	Het
Prdm1	A	G	10: 44,322,782 (GRCm39)		probably null	Het
Psme4	T	C	11: 30,803,245 (GRCm39)	I29T	possibly damaging	Het
Ptprd	A	T	4: 75,984,528 (GRCm39)	D780E	probably benign	Het
Retsat	T	C	6: 72,581,918 (GRCm39)	M294T	probably benign	Het
Robo2	A	T	16: 73,764,672 (GRCm39)	V652D	probably damaging	Het
Rptn	C	G	3: 93,305,437 (GRCm39)	H923Q	possibly damaging	Het
Serpinb3d	G	T	1: 107,010,490 (GRCm39)	T66K	probably benign	Het
Setd1b	A	T	5: 123,296,461 (GRCm39)		probably benign	Het
Slc7a10	G	T	7: 34,886,012 (GRCm39)	A36S	possibly damaging	Het
Sstr3	T	A	15: 78,423,788 (GRCm39)	I320F	probably damaging	Het
Syne1	G	T	10: 5,299,071 (GRCm39)	A1005E	probably damaging	Het
Tinagl1	C	T	4: 130,066,725 (GRCm39)	C124Y	probably null	Het
Tm9sf1	C	T	14: 55,873,827 (GRCm39)	R557H	probably damaging	Het
Tmed2	T	A	5: 124,685,055 (GRCm39)	I68K	possibly damaging	Het
Tmem104	A	G	11: 115,134,819 (GRCm39)	T451A	probably benign	Het
Tmem141	T	C	2: 25,511,693 (GRCm39)		probably null	Het
Tmem184a	C	A	5: 139,798,827 (GRCm39)	V41L	probably benign	Het
Tmem39b	C	T	4: 129,580,584 (GRCm39)	V303I	possibly damaging	Het
Tsn	T	C	1: 118,232,939 (GRCm39)	I122V	probably benign	Het
Ttc41	G	T	10: 86,612,527 (GRCm39)	V1267L	probably benign	Het
Uggt1	A	T	1: 36,202,309 (GRCm39)	L1096Q	probably damaging	Het
Usp50	A	T	2: 126,617,713 (GRCm39)	I244N	probably benign	Het
Vil1	A	G	1: 74,471,498 (GRCm39)	S760G	probably benign	Het
Wasf1	T	A	10: 40,813,741 (GRCm39)	V541E	unknown	Het
Zc3h13	G	T	14: 75,581,176 (GRCm39)	S1721I	probably benign	Het
Zfp180	G	T	7: 23,804,530 (GRCm39)	K316N	probably damaging	Het
Zfp582	T	C	7: 6,356,945 (GRCm39)	C253R	probably damaging	Het
Zfp709	TCGACG	TCG	8: 72,644,552 (GRCm39)		probably benign	Het
Zfp759	A	G	13: 67,288,524 (GRCm39)	T692A	probably benign	Het
Zfyve26	A	G	12: 79,329,758 (GRCm39)	V476A	probably benign	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
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'- TAGCACTTCATCCAGGCAGG -3'
(R):5'- TTCCCTTGGAAGCACTGACG -3'

Sequencing Primer
(F):5'- GGCAGCATAACTTCACTAGTTCAG -3'
(R):5'- TCCTCCCCTGGCATGGTAAAG -3'

Posted On

2018-02-28