Variant Results

or

Results for "VPS39"

Variant Events: 22

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

VPS39

10C114376

chr15:
42470650-42470650

T

C

exonic

De novo

synonymous SNV

NM_015289
NM_001301138

c.A837G
c.A870G

p.G279G
p.G290G

-

Lim2017 E

VPS39

Lim2017:5321

chr15:
42461938-42461938

A

G

exonic

De novo

nonsynonymous SNV

NM_015289
NM_001301138

c.T1217C
c.T1250C

p.I406T
p.I417T

16.53

-

Lim2017 E

VPS39

1-0571-003

chr15:
42467940-42467940

T

C

intronic

De novo

-

Yuen2017 G

VPS39

PN400369

chr15:
42457972-42457972

C

A

exonic

Unknown

nonsynonymous SNV

NM_015289
NM_001301138

c.G1723T
c.G1756T

p.D575Y
p.D586Y

15.53

0.0034

Leblond2019 E

VPS39

iHART2298

chr15:
42454229-42454229

C

T

splicing

Maternal

splicing

19.63

-

Ruzzo2019 G

VPS39

11957.p1

chr15:
42454487-42454487

C

T

intronic

De novo

-

Satterstrom2020 E

VPS39

MT_17.3

chr15:
42455876-42455876

G

A

exonic

De novo

stopgain

NM_015289
NM_001301138

c.C2077T
c.C2110T

p.Q693X
p.Q704X

37.0

-

Trost2022 G
Zhou2022 GE

VPS39

1-0630-003

chr15:
42483181-42483181

T

C

intronic

De novo

-

Trost2022 G

VPS39

PN400350

chr15:
42457972-42457972

C

A

exonic

Unknown

nonsynonymous SNV

NM_015289
NM_001301138

c.G1723T
c.G1756T

p.D575Y
p.D586Y

15.53

0.0034

Leblond2019 E

VPS39

5321

chr15:
42461938-42461938

A

G

exonic

De novo

nonsynonymous SNV

NM_015289
NM_001301138

c.T1217C
c.T1250C

p.I406T
p.I417T

16.53

-

Fu2022 E
Trost2022 G

VPS39

MSSNG00131-003

chr15:
42464768-42464768

C

T

intronic

De novo

-

Trost2022 G

VPS39

1-0552-003

Complex Event; expand row to view variants

De novo

-

Trost2022 G
Yuen2017 G

VPS39

1-1122-003

chr15:
42480254-42480254

G

A

intronic

De novo

-

Trost2022 G

VPS39

mAGRE2298

chr15:
42454229-42454229

C

T

splicing

Maternal

splicing

19.63

-

Cirnigliaro2023 G

VPS39

SSC04242

chr15:
42454487-42454487

C

T

intronic

De novo

-

Trost2022 G

VPS39

PN400383

chr15:
42457972-42457972

C

A

exonic

Unknown

nonsynonymous SNV

NM_015289
NM_001301138

c.G1723T
c.G1756T

p.D575Y
p.D586Y

15.53

0.0034

Leblond2019 E

VPS39

PN400264

chr15:
42457972-42457972

C

A

exonic

Unknown

nonsynonymous SNV

NM_015289
NM_001301138

c.G1723T
c.G1756T

p.D575Y
p.D586Y

15.53

0.0034

Leblond2019 E

VPS39

11056.p1

chr15:
42461938-42461938

A

G

exonic

De novo

nonsynonymous SNV

NM_015289
NM_001301138

c.T1217C
c.T1250C

p.I406T
p.I417T

16.53

-

Iossifov2014 E
Ji2016 E
Kosmicki2017 E
Krupp2017 E
O’Roak2012b E
Satterstrom2020 E
Wilfert2021 G
Zhou2022 GE

VPS39

2-1188-003

chr15:
42481142-42481142

C

T

intronic

De novo

-

Yuen2017 G

VPS39

PN400491

chr15:
42457972-42457972

C

A

exonic

Unknown

nonsynonymous SNV

NM_015289
NM_001301138

c.G1723T
c.G1756T

p.D575Y
p.D586Y

15.53

0.0034

Leblond2019 E

VPS39

SP0091972

chr15:
42466028-42466028

C

T

exonic

De novo

nonsynonymous SNV

NM_015289
NM_001301138

c.G983A
c.G1016A

p.S328N
p.S339N

11.16

-

Fu2022 E
Trost2022 G
Zhou2022 GE

VPS39

PN400253

chr15:
42457972-42457972

C

A

exonic

Unknown

nonsynonymous SNV

NM_015289
NM_001301138

c.G1723T
c.G1756T

p.D575Y
p.D586Y

15.53

0.0034

Leblond2019 E

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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