Variant Results

or

Results for "SYNGAP1"

Variant Events: 88

Gene Gene symbol on which the variant is located	ID Subject Identifier from the original study	Location Genomic location of the reference allele	REF Reference allele	ALT Alternate allele	Context Variant functional categories	Variant validation performed by an orthogonal method and reported	Inheritance Reported inheritance status	Effects Variant effect on transcript per Annovar	Transcript Transcript used for the cDNA/Protein mutation	cDNA cDNA variant notation	Protein Protein variant notation	CADD-Phred v1.0 CADD phred-like score. This is phred-like rank score based on whole genome CADD raw scores	ExAC v0.3 ExAC population frequency (version 0.3)	Sources Source(s) where variants from this event are reported

SYNGAP1

08C77304

chr6:
33411384-33411384

C

T

exonic

Unknown

nonsynonymous SNV

NM_006772

c.C3055T

p.R1019C

16.89

3.303E-5

Stessman2017 T

SYNGAP1

PN400508

chr6:
33419613-33419615

CAG

C

exonic

Unknown

frameshift deletion

NM_006772

c.3963_3964del

p.P1321fs

-

0.0037

Leblond2019 E

SYNGAP1

M02073

chr6:
33405522-33405522

C

G

exonic

De novo

stopgain

NM_006772

c.C840G

p.Y280X

34.0

-

Guo2018 T
Li2017 T
Stessman2017 T
Wang2016 T

SYNGAP1

217-14271-3940

chr6:
33399974-33399975

CA

C

exonic

De novo

frameshift deletion

NM_006772

c.333delA

p.P111fs

-

O’Roak2014 T

SYNGAP1

212-21043-1

chr6:
33408610-33408611

TC

T

exonic

De novo

frameshift deletion

NM_006772

c.1782delC

p.F594fs

-

O’Roak2014 T

SYNGAP1

16

chr6:
33402928-33402928

G

A

splicing

De novo

splicing

16.05

-

O’Roak2014 T

SYNGAP1

G01-GEA-137-HI

chr6:
33409384-33409384

G

GCC

exonic

De novo

frameshift insertion

NM_006772

c.2142_2143insCC

p.L714fs

-

Fu2022 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

BO14/09

chr6:
33410958-33410958

C

CT

exonic

De novo

frameshift insertion

NM_006772

c.2630dupT

p.L877fs

-

O’Roak2014 T

SYNGAP1

ER53899

chr6:
33405933-33405935

TAA

T

exonic

De novo

frameshift deletion

NM_006772

c.1252_1253del

p.K418fs

-

O’Roak2014 T

SYNGAP1

13073.p1

chr6:
33408650-33408652

CTT

C

exonic

De novo

frameshift deletion

NM_006772

c.1822_1823del

p.F608fs

-

Dong2014 E
Iossifov2014 E
Ji2016 E
Kosmicki2017 E
O’Roak2014 T
Satterstrom2020 E
Wilfert2021 G
Willsey2013 E
Zhou2022 GE

SYNGAP1

Mahjani2021:37

chr6:
33411123-33411123

T

C

exonic

nonsynonymous SNV

NM_006772

c.T2794C

p.F932L

21.4

-

Mahjani2021 E

SYNGAP1

14277.p1

chr6:
33410913-33410913

A

AACCTGGTTAGTGTGTTGGTTAGTAGGCCTAGTATGAGGAGCGTTATGGAGTGGAAGTGAAATCACATGGCT

exonic

De novo

stopgain

NM_006772

c.2584_2585insACCTGGTTAGTGTGTTGGTTAGTAGGCCTAGTATGAGGAGCGTTATGGAGTGGAAGTGAAATCACATGGCT

p.N862_L863delinsNLVSVLVSRPSMRSVMEWKX

-

Satterstrom2020 E

SYNGAP1

08C74220

chr6:
33399974-33399975

CA

C

exonic

De novo

frameshift deletion

NM_006772

c.333delA

p.P111fs

-

Fu2022 E

SYNGAP1

SSC06095

chr6:
33403326-33403326

G

A

exonic

nonsynonymous SNV

NM_006772

c.G698A

p.C233Y

23.4

-

Antaki2022 GE

SYNGAP1

12804_p1

chr6:
33403326-33403326

G

A

exonic

De novo

nonsynonymous SNV

NM_006772

c.G698A

p.C233Y

23.4

-

Fu2022 E

SYNGAP1

SP0084433

chr6:
33403302-33403302

C

G

exonic

De novo

stopgain

NM_006772

c.C674G

p.S225X

37.0

-

Antaki2022 GE
Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

F10841-1

chr6:
33408690-33408690

C

T

exonic

De novo

stopgain

NM_006772

c.C1861T

p.R621X

39.0

-

Fu2022 E

SYNGAP1

Ishay2021:33

chr6:
33408600-33408600

G

A

exonic

Inherited

nonsynonymous SNV

NM_006772

c.G1771A

p.A591T

22.6

-

Ishay2021 E

SYNGAP1

Ishay2021:35

chr6:
33408600-33408600

G

A

exonic

Inherited

nonsynonymous SNV

NM_006772

c.G1771A

p.A591T

22.6

-

Ishay2021 E

SYNGAP1

Ishay2021:34

chr6:
33408600-33408600

G

A

exonic

Inherited

nonsynonymous SNV

NM_006772

c.G1771A

p.A591T

22.6

-

Ishay2021 E

SYNGAP1

SP0005275

chr6:
33412306-33412306

C

T

exonic

De novo

nonsynonymous SNV

NM_006772

c.C3494T

p.S1165L

21.6

-

Antaki2022 GE
Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SSC04046

chr6:
33411699-33411699

G

T

exonic

stopgain

NM_006772

c.G3370T

p.G1124X

41.0

-

Antaki2022 GE

SYNGAP1

SP0038495

chr6:
33419606-33419606

G

GCCCCCCCCCCCCCCCCCCCCCCCCC

exonic

De novo

frameshift insertion

NM_006772

c.3955_3956insCCCCCCCCCCCCCCCCCCCCCCCCC

p.A1319fs

-

Fu2022 E

SYNGAP1

SP0005693

chr6:
33419606-33419606

G

GCCCCCCCCCCCCCCCCCCCCCC

exonic

De novo

frameshift insertion

NM_006772

c.3955_3956insCCCCCCCCCCCCCCCCCCCCCC

p.A1319fs

-

Fu2022 E

SYNGAP1

SP0080242

chr6:
33408546-33408546

C

T

exonic

De novo

nonsynonymous SNV

NM_006772

c.C1717T

p.R573W

17.32

-

Antaki2022 GE
Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SP0025466

chr6:
33405712-33405712

G

A

exonic

De novo

nonsynonymous SNV

NM_006772

c.G1030A

p.G344S

22.1

-

Antaki2022 GE
Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

11254_p1

chr6:
33400029-33400029

G

A

exonic

De novo

synonymous SNV

NM_006772

c.G387A

p.S129S

-

Fu2022 E

SYNGAP1

MAC1188

chr6:
33411093-33411093

C

T

exonic

De novo

stopgain

NM_006772

c.C2764T

p.R922X

39.0

-

Fu2022 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SP0037844

chr6:
33410949-33410949

C

T

exonic

De novo

stopgain

NM_006772

c.C2620T

p.Q874X

40.0

-

Antaki2022 GE
Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SSC06347

chr6:
33408650-33408652

CTT

C

exonic

De novo

frameshift deletion

NM_006772

c.1822_1823del

p.F608fs

-

Antaki2022 GE
Fu2022 E
Trost2022 G

SYNGAP1

Codina-Sola2015:ASD_3

chr6:
33391308-33391308

G

A

exonic

Maternal

nonsynonymous SNV

NM_006772

c.G122A

p.R41H

16.77

8.236E-6

Codina-Sola2015 E

SYNGAP1

SP0050807

chr6:
33414343-33414343

G

A

intronic

De novo

-

Fu2022 E
Trost2022 G

SYNGAP1

GX0516.p1

chr6:
33410757-33410757

C

T

exonic

Paternal

nonsynonymous SNV

NM_006772

c.C2428T

p.R810C

20.5

-

Guo2018 T

SYNGAP1

SP0015357

chr6:
33393573-33393573

A

G

splicing

De novo

splicing

15.68

-

Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SP0036848

chr6:
33419606-33419606

G

GGCCCCCCC

exonic

De novo

frameshift insertion

NM_006772

c.3955_3956insGCCCCCCC

p.A1319fs

-

Fu2022 E

SYNGAP1

SP0052624

chr6:
33408577-33408580

ACAT

A

exonic

De novo

nonframeshift deletion

NM_006772

c.1749_1751del

p.583_584del

-

Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SP0144158

chr6:
33419657-33419657

G

A

exonic

De novo

nonsynonymous SNV

NM_006772

c.G4006A

p.E1336K

15.0

-

Fu2022 E
Zhou2022 GE

SYNGAP1

M19759

Complex Event; expand row to view variants

Unknown

frameshift deletion, frameshift substitution

NM_006772
NM_006772

c.3545delA
c.3544_3545T

p.E1182fs
N/A

-

Guo2018 T
Wang2016 T

SYNGAP1

M16067

chr6:
33411159-33411159

G

A

exonic

Paternal

nonsynonymous SNV

NM_006772

c.G2830A

p.G944S

12.14

8.293E-6

Guo2018 T
Wang2016 T

SYNGAP1

118_15mr

chr6:
33410665-33410665

G

A

splicing

De novo

splicing

17.02

-

Fu2022 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

Chen2021:71

chr6:
33400564-33400564

C

T

exonic

De novo

stopgain

NM_006772

c.C490T

p.R164X

34.0

-

Chen2021 GET

SYNGAP1

EGAN00001101065

chr6:
33400493-33400493

C

T

exonic

De novo

nonsynonymous SNV

NM_006772

c.C419T

p.S140F

20.9

-

Fu2022 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

Chen2021:70

chr6:
33405509-33405510

CC

C

exonic

De novo

frameshift deletion

NM_006772

c.828delC

p.P276fs

-

Chen2021 GET

SYNGAP1

Wang2023:466

chr6:
33411228-33411228

C

T

exonic

De novo

stopgain

NM_006772

c.C2899T

p.R967X

40.0

-

Wang2023 E

SYNGAP1

SP0006795

chr6:
33408918-33408918

A

G

intronic

De novo

-

7.0E-4

Trost2022 G

SYNGAP1

Miyake2023:7544

chr6:
33409439-33409439

C

T

exonic

De novo

stopgain

NM_006772

c.C2197T

p.Q733X

40.0

-

Miyake2023 E

SYNGAP1

NDAR_INVRT684RNC_wes1

chr6:
33410717-33410717

A

C

exonic

De novo

synonymous SNV

NM_006772

c.A2388C

p.P796P

-

2.503E-5

Lim2017 E

SYNGAP1

AU138A

chr6:
33391326-33391326

G

A

exonic

De novo

nonsynonymous SNV

NM_006772

c.G140A

p.R47Q

15.24

-

DeRubeis2014 E
Fu2022 E
Kosmicki2017 E
Lim2017 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

NDAR_INVDU502HMU_wes1

chr6:
33405763-33405763

C

T

exonic

De novo

stopgain

NM_006772

c.C1081T

p.Q361X

37.0

-

DeRubeis2014 E
Fu2022 E
Kosmicki2017 E
Lim2017 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

JASD_Fam0063

chr6:
33409439-33409439

C

T

exonic

De novo

stopgain

NM_006772

c.C2197T

p.Q733X

40.0

-

Takata2018 E

SYNGAP1

09C80386

chr6:
33408610-33408611

TC

T

exonic

De novo

frameshift deletion

NM_006772

c.1782delC

p.F594fs

-

DeRubeis2014 E
Fu2022 E
Kosmicki2017 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

AU087A

chr6:
33411228-33411228

C

T

exonic

De novo

stopgain

NM_006772

c.C2899T

p.R967X

40.0

-

DeRubeis2014 E
Fu2022 E
Kosmicki2017 E
Lim2017 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

NDAR_INVZX362NCN_wes1

chr6:
33414451-33414455

GAACA

G

exonic

De novo

frameshift deletion

NM_006772

c.3683_3686del

p.E1228fs

-

DeRubeis2014 E
Fu2022 E
Kosmicki2017 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

11254.p1

chr6:
33400029-33400029

G

A

exonic

De novo

synonymous SNV

NM_006772

c.G387A

p.S129S

-

Krumm2015 E
Satterstrom2020 E
Trost2022 G

SYNGAP1

SSC11011

chr6:
33410913-33410913

A

AACCTGGTTAGTGTGTTGGTTAGTAGGCCTAGTATGAGGAGCGTTATGGAGTGGAAGTGAAATCACATGGCT

exonic

De novo

stopgain

NM_006772

c.2584_2585insACCTGGTTAGTGTGTTGGTTAGTAGGCCTAGTATGAGGAGCGTTATGGAGTGGAAGTGAAATCACATGGCT

p.N862_L863delinsNLVSVLVSRPSMRSVMEWKX

-

Trost2022 G

SYNGAP1

3-0438-000

chr6:
33406693-33406698

ACTGGT

A

exonic

De novo

nonframeshift deletion

NM_006772

c.1674_1676del

p.558_559del

-

Yuen2016 G

SYNGAP1

3-0438-000

chr6:
33406690-33406690

C

CA

exonic

De novo

frameshift insertion

NM_006772

c.1670_1671insA

p.S557fs

-

Trost2022 G
Yuen2016 G
Zhou2022 GE

SYNGAP1

SP0234769

chr6:
33403340-33403340

G

T

exonic

stopgain

NM_006772

c.G712T

p.E238X

38.0

-

Zhou2022 GE

SYNGAP1

SMHC01629s000

chr6:
33399974-33399975

CA

C

exonic

De novo

frameshift deletion

NM_006772

c.333delA

p.P111fs

-

Yuan2023 E

SYNGAP1

SP0248679

chr6:
33400532-33400532

C

A

exonic

nonsynonymous SNV

NM_006772

c.C458A

p.T153N

9.279

-

Zhou2022 GE

SYNGAP1

11504.p1

chr6:
33400029-33400029

G

A

exonic

De novo

synonymous SNV

NM_006772

c.G387A

p.S129S

-

Iossifov2014 E
Kosmicki2017 E

SYNGAP1

SP0184840

chr6:
33405559-33405560

CG

C

exonic

De novo

frameshift deletion

NM_006772

c.878delG

p.R293fs

-

Trost2022 G
Zhou2022 GE

SYNGAP1

12804.p1

chr6:
33403326-33403326

G

A

exonic

De novo

nonsynonymous SNV

NM_006772

c.G698A

p.C233Y

23.4

-

Iossifov2014 E
Ji2016 E
Kosmicki2017 E
Krupp2017 E
Lim2017 E
O’Roak2014 T
Satterstrom2020 E
Trost2022 G
Wilfert2021 G
Zhou2022 GE

SYNGAP1

12237.p1

chr6:
33411673-33411673

T

TTGGGGGCAG

exonic

De novo

nonframeshift insertion

NM_006772

c.3344_3345insTGGGGGCAG

p.I1115delinsIGGS

-

Wilfert2021 G
Zhou2022 GE

SYNGAP1

14001.p1

chr6:
33411384-33411384

C

T

exonic

De novo

nonsynonymous SNV

NM_006772

c.C3055T

p.R1019C

16.89

3.303E-5

Iossifov2014 E
Ji2016 E
Kosmicki2017 E
Lim2017 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

Valentino2021:36

chr6:
33410665-33410665

G

A

splicing

De novo

splicing

17.02

-

Valentino2021 E

SYNGAP1

M20609

chr6:
33411159-33411159

G

A

exonic

Maternal

nonsynonymous SNV

NM_006772

c.G2830A

p.G944S

12.14

8.293E-6

Guo2018 T
Wang2016 T

SYNGAP1

12237.p1

chr6:
33411699-33411699

G

T

exonic

De novo

stopgain

NM_006772

c.G3370T

p.G1124X

41.0

-

Wilfert2021 G
Zhou2022 GE

SYNGAP1

PN400330

chr6:
33419613-33419615

CAG

C

exonic

Unknown

frameshift deletion

NM_006772

c.3963_3964del

p.P1321fs

-

0.0037

Leblond2019 E

SYNGAP1

GX0132.p1

chr6:
33405577-33405577

C

T

exonic

Maternal

nonsynonymous SNV

NM_006772

c.C895T

p.R299C

20.3

-

Guo2018 T

SYNGAP1

13804.p1

chr6:
33388092-33388092

C

T

exonic

synonymous SNV

NM_006772

c.C51T

p.S17S

-

Zhou2022 GE

SYNGAP1

80001103406

chr6:
33414425-33414427

ATG

A

exonic

De novo

frameshift deletion

NM_006772

c.3657_3658del

p.Y1219fs

-

Fu2022 E
Satterstrom2020 E
Trost2022 G
Zhou2022 GE

SYNGAP1

05C51696

chr6:
33412317-33412317

G

A

exonic

Unknown

nonsynonymous SNV

NM_006772

c.G3505A

p.E1169K

35.0

-

Stessman2017 T

SYNGAP1

GX0345.p1

chr6:
33411594-33411594

G

C

exonic

Maternal

nonsynonymous SNV

NM_006772

c.G3265C

p.G1089R

13.57

-

Guo2018 T

SYNGAP1

SP0093825

chr6:
33408737-33408737

T

C

exonic

synonymous SNV

NM_006772

c.T1908C

p.F636F

-

Zhou2022 GE

SYNGAP1

GX0313.p1

chr6:
33411159-33411159

G

A

exonic

Maternal

nonsynonymous SNV

NM_006772

c.G2830A

p.G944S

12.14

8.293E-6

Guo2018 T

SYNGAP1

JS0008.p1

chr6:
33412222-33412222

A

A/C

exonic

Paternal

-

Guo2018 T

SYNGAP1

11054.p1

chr6:
33400029-33400029

G

A

exonic

synonymous SNV

NM_006772

c.G387A

p.S129S

-

Zhou2022 GE

SYNGAP1

Mahjani2021:129

chr6:
33414425-33414427

ATG

A

exonic

frameshift deletion

NM_006772

c.3657_3658del

p.Y1219fs

-

Mahjani2021 E

SYNGAP1

SP0006454

chr6:
33403084-33403084

T

C

splicing

De novo

splicing

18.83

-

Feliciano2019 E
Fu2022 E
Trost2022 G
Zhou2022 GE

SYNGAP1

SP0124549

chr6:
33414351-33414351

G

A

splicing

22.1

-

Zhou2022 GE

SYNGAP1

Lee2020:142

chr6:
33405662-33405662

T

C

exonic

nonsynonymous SNV

NM_006772

c.T980C

p.L327P

20.4

-

Lee2020 T

SYNGAP1

A0238

chr6:
33400564-33400564

C

T

exonic

De novo

stopgain

NM_006772

c.C490T

p.R164X

34.0

-

Xiong2019 ET

SYNGAP1

5-0005-003

chr6:
33411051-33411051

C

T

exonic

De novo

stopgain

NM_006772

c.C2722T

p.Q908X

40.0

-

Trost2022 G
Zhou2022 GE

SYNGAP1

1-0552-003

chr6:
33397577-33397590

CTGTGTGTGTGTGT

CTGTGTGTGTGT

intronic

De novo

-

Yuen2017 G

SYNGAP1

3-0661-000

chr6:
33417987-33417987

C

T

intronic

De novo

-

Trost2022 G
Yuen2017 G

SYNGAP1

1-0408-003

chr6:
33408465-33408465

T

TTC

intronic

De novo

-

2.0E-4

Yuen2016 G

SYNGAP1

Stessman2017:ASD_1073-1

chr6:
33408690-33408690

C

T

exonic

Inherited

stopgain

NM_006772

c.C1861T

p.R621X

39.0

-

Stessman2017 T

Source Variant Information

, -

Source:

Paper alias:

No records found.

Paper Information

Title
Authors
Technology
Variant source
Cohorts
Design
URL
Pubmed
Subject count	The number of subjects for this study could not be determined directly from the variant data; the value given is that reported by the authors in the publication.
Variant event count
Curation notes	View
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