Mutagenetix > Incidental Mutation

Incidental Mutation 'R5580:Syngap1'

438442

Institutional Source

Beutler Lab

Gene Symbol

Syngap1

Ensembl Gene

ENSMUSG00000067629

Gene Name

synaptic Ras GTPase activating protein 1 homolog (rat)

Synonyms

Syngap

MMRRC Submission

043134-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5580 (G1)

Quality Score

213

Status

Not validated

Chromosome

Chromosomal Location

27160227-27191408 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 27181305 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 9 (A9T)

Gene Model

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

AlphaFold

F6SEU4

Predicted Effect

possibly damaging
Transcript: ENSMUST00000081285
AA Change: A1019T

PolyPhen 2 Score 0.666 (Sensitivity: 0.86; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000080038
Gene: ENSMUSG00000067629
AA Change: A1019T

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

possibly damaging
Transcript: ENSMUST00000177932
AA Change: A1078T

PolyPhen 2 Score 0.483 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000137587
Gene: ENSMUSG00000067629
AA Change: A1078T

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
AA Change: A1062T

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000141245
Gene: ENSMUSG00000067629
AA Change: A1062T

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: A1078T

PolyPhen 2 Score 0.884 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000141686
Gene: ENSMUSG00000067629
AA Change: A1078T

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 damaging
Transcript: ENSMUST00000201186
AA Change: A9T

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)

Predicted Effect

unknown
Transcript: ENSMUST00000201349
AA Change: A1077T

SMART Domains

Protein: ENSMUSP00000144666
Gene: ENSMUSG00000067629
AA Change: A1077T

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: A1064T

SMART Domains

Protein: ENSMUSP00000144248
Gene: ENSMUSG00000067629
AA Change: A1064T

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: A1019T

PolyPhen 2 Score 0.859 (Sensitivity: 0.83; Specificity: 0.93)

Predicted Effect

probably benign
Transcript: ENSMUST00000229490
AA Change: A1078T

PolyPhen 2 Score 0.216 (Sensitivity: 0.91; Specificity: 0.88)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000231853
AA Change: A905T

PolyPhen 2 Score 0.884 (Sensitivity: 0.82; Specificity: 0.94)

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 benign
Transcript: ENSMUST00000202049

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.2%

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: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410002F23Rik	A	G	7: 43,900,664 (GRCm39)	T73A	possibly damaging	Het
A1bg	A	T	15: 60,790,881 (GRCm39)	V365E	probably benign	Het
Abcg5	A	C	17: 84,967,582 (GRCm39)	V406G	probably damaging	Het
Adamts12	A	G	15: 11,152,086 (GRCm39)	Y192C	probably benign	Het
Add3	C	T	19: 53,233,642 (GRCm39)	S649L	probably damaging	Het
Adgrg6	A	T	10: 14,286,228 (GRCm39)	C1129*	probably null	Het
Arsb	T	A	13: 93,944,053 (GRCm39)	V248D	probably damaging	Het
AW554918	A	T	18: 25,472,922 (GRCm39)	N39I	probably damaging	Het
Cacna1b	A	T	2: 24,540,566 (GRCm39)	I1383N	probably damaging	Het
Caprin2	A	T	6: 148,760,232 (GRCm39)	V625D	possibly damaging	Het
Cd9	A	G	6: 125,441,420 (GRCm39)	L67P	probably damaging	Het
Cdh5	T	A	8: 104,852,126 (GRCm39)	Y80*	probably null	Het
Csf2ra	A	G	19: 61,214,655 (GRCm39)	L223P	probably damaging	Het
Cyp2c67	T	C	19: 39,604,094 (GRCm39)	K421E	probably damaging	Het
Dzank1	T	C	2: 144,348,098 (GRCm39)	R223G	probably damaging	Het
Emilin2	A	G	17: 71,582,225 (GRCm39)	V167A	probably benign	Het
Eps8l3	A	G	3: 107,788,919 (GRCm39)	T81A	probably damaging	Het
Esrra	T	C	19: 6,897,755 (GRCm39)	M1V	probably null	Het
Evpl	C	A	11: 116,125,058 (GRCm39)	A135S	probably benign	Het
Fam193a	A	G	5: 34,578,132 (GRCm39)	I209V	probably benign	Het
Fbxl19	C	A	7: 127,350,168 (GRCm39)	C253*	probably null	Het
Fer1l5	T	A	1: 36,424,539 (GRCm39)	Y305*	probably null	Het
Fzd2	A	C	11: 102,496,665 (GRCm39)	I370L	probably damaging	Het
Gnl3	T	C	14: 30,737,242 (GRCm39)	K212R	probably benign	Het
Golm1	A	G	13: 59,790,179 (GRCm39)	L207P	probably benign	Het
Gphn	T	A	12: 78,538,818 (GRCm39)	F155I	probably damaging	Het
Grhl1	G	A	12: 24,659,739 (GRCm39)	G500S	probably benign	Het
Gucd1	C	A	10: 75,346,968 (GRCm39)	G55V	possibly damaging	Het
Haus6	A	T	4: 86,517,503 (GRCm39)	I287K	possibly damaging	Het
Hmcn1	G	A	1: 150,453,290 (GRCm39)	P5342S	probably benign	Het
Hspa12a	A	G	19: 58,788,092 (GRCm39)	S577P	probably benign	Het
Ido2	T	A	8: 25,040,882 (GRCm39)	I113F	possibly damaging	Het
Ifrd2	C	T	9: 107,469,511 (GRCm39)	P396S	probably damaging	Het
Igkv4-86	T	A	6: 68,887,990 (GRCm39)		probably benign	Het
Ipo11	A	G	13: 107,037,255 (GRCm39)	V196A	probably benign	Het
Itih2	T	C	2: 10,128,287 (GRCm39)	E138G	probably damaging	Het
Kidins220	T	G	12: 25,097,896 (GRCm39)	C1179G	probably benign	Het
Kif20b	T	A	19: 34,927,128 (GRCm39)		probably null	Het
Klk1	T	A	7: 43,878,238 (GRCm39)	Y63N	probably benign	Het
L3mbtl3	T	G	10: 26,179,604 (GRCm39)	D517A	unknown	Het
Lars1	G	T	18: 42,347,916 (GRCm39)	P969H	probably damaging	Het
Lrp1	C	T	10: 127,424,389 (GRCm39)	V766I	probably benign	Het
Lrrc8c	A	G	5: 105,755,553 (GRCm39)	I443V	probably benign	Het
Lsg1	T	C	16: 30,387,985 (GRCm39)	M439V	probably null	Het
Magi2	T	A	5: 20,420,422 (GRCm39)	M286K	probably benign	Het
Med11	T	C	11: 70,342,891 (GRCm39)		probably null	Het
Med13l	A	G	5: 118,889,695 (GRCm39)	K1819E	possibly damaging	Het
Ms4a14	T	A	19: 11,280,590 (GRCm39)	Q656L	probably benign	Het
Muc5b	A	G	7: 141,415,084 (GRCm39)	T2677A	possibly damaging	Het
Myo7a	A	T	7: 97,722,367 (GRCm39)	L1186H	probably damaging	Het
Naca	C	A	10: 127,876,462 (GRCm39)		probably benign	Het
Nbeal1	T	C	1: 60,281,761 (GRCm39)	I828T	probably benign	Het
Ncor1	A	T	11: 62,280,604 (GRCm39)	C75*	probably null	Het
Nepn	A	C	10: 52,280,398 (GRCm39)	S497R	probably damaging	Het
Nf2	A	G	11: 4,753,689 (GRCm39)	F222L	probably damaging	Het
Nlrp9b	A	C	7: 19,757,089 (GRCm39)	T109P	probably damaging	Het
Nr1h4	A	T	10: 89,352,302 (GRCm39)	F22I	probably benign	Het
Ogg1	A	G	6: 113,306,337 (GRCm39)	Y178C	probably damaging	Het
Or1e22	G	T	11: 73,377,036 (GRCm39)	P205T	probably benign	Het
Or4b12	C	A	2: 90,096,694 (GRCm39)	V27L	probably benign	Het
Or5b119	T	A	19: 13,456,791 (GRCm39)	Y257F	probably damaging	Het
Or5b21	G	A	19: 12,839,168 (GRCm39)	V10M	possibly damaging	Het
Or5d14	A	T	2: 87,880,668 (GRCm39)	M100K	possibly damaging	Het
Osr1	G	A	12: 9,629,325 (GRCm39)	R66Q	probably damaging	Het
Pi4ka	A	G	16: 17,098,951 (GRCm39)	S1978P	probably damaging	Het
Pik3c2g	A	T	6: 139,603,531 (GRCm39)	Q239L	probably damaging	Het
Pin1rt1	A	G	2: 104,544,670 (GRCm39)	I154T	probably damaging	Het
Pkdcc	A	G	17: 83,527,511 (GRCm39)	T230A	probably damaging	Het
Por	A	T	5: 135,762,675 (GRCm39)	I430F	probably damaging	Het
Prb1c	T	C	6: 132,338,432 (GRCm39)	N262S	unknown	Het
Prkcsh	T	A	9: 21,922,551 (GRCm39)		probably null	Het
Pros1	A	G	16: 62,746,689 (GRCm39)		probably null	Het
Pus10	T	A	11: 23,622,556 (GRCm39)	L59I	probably benign	Het
Pxmp2	A	G	5: 110,431,542 (GRCm39)	V67A	possibly damaging	Het
Rab3gap1	C	A	1: 127,858,727 (GRCm39)	A612E	probably benign	Het
Rpap2	A	G	5: 107,768,011 (GRCm39)	E206G	probably benign	Het
Rpl31	C	T	1: 39,409,108 (GRCm39)	R41C	probably benign	Het
Ryr3	C	T	2: 112,672,293 (GRCm39)	G1393R	probably damaging	Het
Scara5	T	C	14: 65,968,528 (GRCm39)	M267T	probably benign	Het
Sema5a	A	T	15: 32,575,031 (GRCm39)	I380F	probably benign	Het
Slc36a3	A	G	11: 55,026,279 (GRCm39)	S180P	probably benign	Het
Slc44a5	A	G	3: 153,966,922 (GRCm39)	K536R	probably benign	Het
Smg1	T	C	7: 117,748,125 (GRCm39)		probably benign	Het
Spata31d1e	A	T	13: 59,890,070 (GRCm39)	D583E	probably benign	Het
Strc	T	C	2: 121,205,493 (GRCm39)	K879R	probably damaging	Het
Swt1	T	C	1: 151,260,206 (GRCm39)	E731G	probably benign	Het
Tex15	C	T	8: 34,062,457 (GRCm39)	T903I	probably damaging	Het
Tg	A	G	15: 66,557,149 (GRCm39)	I937V	possibly damaging	Het
Tm9sf4	T	C	2: 153,024,350 (GRCm39)	Y58H	probably damaging	Het
Tsen2	A	T	6: 115,554,941 (GRCm39)	D458V	probably damaging	Het
Ttn	T	A	2: 76,748,146 (GRCm39)	D4301V	probably benign	Het
Txk	C	A	5: 72,864,932 (GRCm39)	L314F	probably damaging	Het
Ube3b	A	G	5: 114,553,384 (GRCm39)	T919A	probably benign	Het
Ubn2	A	G	6: 38,460,187 (GRCm39)	M641V	probably damaging	Het
Usp4	C	T	9: 108,243,058 (GRCm39)	T242I	probably benign	Het
Usp53	A	G	3: 122,727,883 (GRCm39)	S900P	probably benign	Het
Vmn1r225	T	C	17: 20,723,101 (GRCm39)	Y181H	probably damaging	Het
Vmn1r83	T	A	7: 12,055,800 (GRCm39)	I86L	probably benign	Het
Vmn2r65	T	C	7: 84,596,802 (GRCm39)	I84M	probably damaging	Het
Vstm2b	A	G	7: 40,552,050 (GRCm39)	H126R	probably damaging	Het
Zfp524	A	T	7: 5,021,416 (GRCm39)	I315F	probably benign	Het
Zfp975	A	T	7: 42,314,513 (GRCm39)	L20*	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
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'- CTCTCGCTTCAGGACAGTCTAC -3'
(R):5'- ACCAGACTACACTGTTGCTTCC -3'

Sequencing Primer
(F):5'- TTCAGGACAGTCTACAGCACATG -3'
(R):5'- GACTACACTGTTGCTTCCCTCCC -3'

Posted On

2016-10-26