Variant Results

or

Results for "Ben-Shalom2017"

Variant Events: 25

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

SCN2A

14280.p1

chr2:
166201311-166201311

C

T

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.C2809T
c.C2809T
c.C2809T

p.R937C
p.R937C
p.R937C

29.0

-

Ben-Shalom2017 T

SCN2A

NDAR_INVTZ957VTW_wes1

chr2:
166201312-166201312

G

A

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.G2810A
c.G2810A
c.G2810A

p.R937H
p.R937H
p.R937H

33.0

-

Ben-Shalom2017 T

SCN2A

11892.p1

chr2:
166201379-166201379

C

A

exonic

De novo

stopgain

NM_001040143
NM_001040142
NM_021007

c.C2877A
c.C2877A
c.C2877A

p.C959X
p.C959X
p.C959X

42.0

-

Ben-Shalom2017 T

SCN2A

11114.p1

chr2:
166210819-166210819

G

T

exonic

De novo

stopgain

NM_001040143
NM_001040142
NM_021007

c.G3037T
c.G3037T
c.G3037T

p.G1013X
p.G1013X
p.G1013X

40.0

-

Ben-Shalom2017 T

SCN2A

D’Gama2015:4849

chr2:
166183366-166183366

C

A

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.C2021A
c.C2021A
c.C2021A

p.T674K
p.T674K
p.T674K

16.28

-

Ben-Shalom2017 T

SCN2A

13544.p1

chr2:
166231378-166231378

T

C

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.T4156C
c.T4156C
c.T4156C

p.C1386R
p.C1386R
p.C1386R

15.44

-

Ben-Shalom2017 T

SCN2A

13642.p1

chr2:
166234111-166234111

C

T

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.C4259T
c.C4259T
c.C4259T

p.T1420M
p.T1420M
p.T1420M

28.0

-

Ben-Shalom2017 T

SCN2A

AN09714

chr2:
166237699-166237699

C

T

exonic

De novo

stopgain

NM_001040143
NM_001040142
NM_021007

c.C4543T
c.C4543T
c.C4543T

p.R1515X
p.R1515X
p.R1515X

43.0

-

Ben-Shalom2017 T

SCN2A

AN08043

chr2:
166237708-166237708

G

C

splicing

De novo

splicing

22.2

-

Ben-Shalom2017 T

SCN2A

DEASD_0262_001

chr2:
166245137-166245137

A

T

splicing

De novo

splicing

12.35

-

Ben-Shalom2017 T

SCN2A

AN04166

chr2:
166245546-166245546

G

A

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.G5230A
c.G5230A
c.G5230A

p.G1744R
p.G1744R
p.G1744R

18.99

-

Ben-Shalom2017 T

SCN2A

2-1291-003

chr2:
166152415-166152415

C

T

exonic

Inherited

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.C82T
c.C82T
c.C82T

p.R28C
p.R28C
p.R28C

23.7

2.0E-4

Ben-Shalom2017 T

SCN2A

2-1337-003

chr2:
166170552-166170583

TGAACAGAAGGAAGCTGAATTTCAGCAGATGC

T

exonic

De novo

frameshift deletion

NM_001040143
NM_001040142
NM_021007

c.1318_1348del
c.1318_1348del
c.1318_1348del

p.E440fs
p.E440fs
p.E440fs

-

Ben-Shalom2017 T

SCN2A

18.s1

chr2:
166231244-166231244

T

G

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.T4022G
c.T4022G
c.T4022G

p.L1341R
p.L1341R
p.L1341R

21.8

-

Ben-Shalom2017 T

SCN2A

ER8490

chr2:
166179824-166179826

TCT

T

exonic

De novo

frameshift deletion

NM_001040143
NM_001040142
NM_021007

c.1831_1832del
c.1831_1832del
c.1831_1832del

p.L611fs
p.L611fs
p.L611fs

-

Ben-Shalom2017 T

SCN2A

ZH60991

chr2:
166201311-166201311

C

T

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.C2809T
c.C2809T
c.C2809T

p.R937C
p.R937C
p.R937C

29.0

-

Ben-Shalom2017 T

SCN2A

OMIM.0008

chr2:
166153563-166153563

C

T

exonic

De novo

stopgain

NM_001040143
NM_001040142
NM_021007

c.C304T
c.C304T
c.C304T

p.R102X
p.R102X
p.R102X

39.0

-

Ben-Shalom2017 T

SCN2A

Ben-Shalom2017:48

chr2:
166234155-166234155

C

T

exonic

De novo

stopgain

NM_001040143
NM_001040142
NM_021007

c.C4303T
c.C4303T
c.C4303T

p.R1435X
p.R1435X
p.R1435X

40.0

-

Ben-Shalom2017 T

SCN2A

14525.p1

chr2:
166152367-166152367

G

A

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.G34A
c.G34A
c.G34A

p.D12N
p.D12N
p.D12N

13.34

-

Ben-Shalom2017 T

SCN2A

ASDFI_732

chr2:
166152578-166152578

A

G

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.A245G
c.A245G
c.A245G

p.D82G
p.D82G
p.D82G

19.73

-

Ben-Shalom2017 T

SCN2A

Codina-Sola2015:ASD_5

chr2:
166179741-166179741

C

T

exonic

De novo

stopgain

NM_001040143
NM_001040142
NM_021007

c.C1747T
c.C1747T
c.C1747T

p.R583X
p.R583X
p.R583X

39.0

-

Ben-Shalom2017 T

SCN2A

AU026A

chr2:
166170231-166170231

G

A

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.G1136A
c.G1136A
c.G1136A

p.R379H
p.R379H
p.R379H

35.0

-

Ben-Shalom2017 T

SCN2A

DEASD_0143_001

chr2:
166170231-166170231

G

A

exonic

De novo

nonsynonymous SNV

NM_001040143
NM_001040142
NM_021007

c.G1136A
c.G1136A
c.G1136A

p.R379H
p.R379H
p.R379H

35.0

-

Ben-Shalom2017 T

SCN2A

220-9736-202

chr2:
166164448-166164448

G

A

splicing

De novo

splicing

25.6

-

Ben-Shalom2017 T

SCN2A

10C109819

chr2:
166183403-166183403

T

TA

exonic

De novo

frameshift insertion

NM_001040143
NM_001040142
NM_021007

c.2058_2059insA
c.2058_2059insA
c.2058_2059insA

p.S686fs
p.S686fs
p.S686fs

-

Ben-Shalom2017 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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