chr16:55697923:G>A Detail (hg38) (SLC6A2)

Information

Genome

Assembly Position
hg19 chr16:55,731,835-55,731,835 View the variant detail on this assembly version.
hg38 chr16:55,697,923-55,697,923

HGVS

Type Transcript Protein
RefSeq NM_001172504.1:c.1287G>A NP_001165975.1:p.Thr429=
NM_001043.3:c.1287G>A NP_001034.1:p.Thr429=
NM_001172502.1:c.972G>A NP_001165973.1:p.Thr324=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.251
ToMMo:0.255
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.304

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 163970 OMIM
HGNC 11048 HGNC
Ensembl ENSG00000103546 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55587064 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2020-09-28 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.011 Unipolar Depression In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.040 major depressive disorder In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.038 Mental Depression In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.009 depressive disorder In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.016 major depressive disorder In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.008 Unipolar Depression In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.005 Unipolar Depression In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.014 major depressive disorder In self-identified white patients with major depressive disorder (N=126) treated... BeFree 22727709 Detail
0.005 Unipolar Depression Different combinations of T-182C and the G1287A polymorphisms of NET gene might ... BeFree 26061302 Detail
0.014 major depressive disorder Different combinations of T-182C and the G1287A polymorphisms of NET gene might ... BeFree 26061302 Detail
0.005 Unipolar Depression Association between major depressive disorder and the norepinephrine transporter... BeFree 23648227 Detail
0.014 major depressive disorder Association between major depressive disorder and the norepinephrine transporter... BeFree 23648227 Detail
0.043 attention deficit hyperactivity disorder The 1287 G/A polymorphism of the norepinephrine transporter gene (NET) is involv... BeFree 21569456 Detail
0.128 Hypertensive disease A silent G1287A nucleotide substitution in exon 9 of the NET gene was studied in... BeFree 17124432 Detail
0.043 attention deficit hyperactivity disorder Regional brain perfusion before and after treatment with methylphenidate may be ... BeFree 22405810 Detail
0.005 Unipolar Depression No association of the G1287A polymorphism in the norepinephrine transporter gene... BeFree 17917281 Detail
0.043 attention deficit hyperactivity disorder Additive regression analyses controlling for ADHD symptom severity, age, sex, IQ... BeFree 23609393 Detail
0.014 major depressive disorder No association of the G1287A polymorphism in the norepinephrine transporter gene... BeFree 17917281 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001172501.3(SLC6A2):c.1287G>A (p.Thr429=) AND not provided ClinVar Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
In self-identified white patients with major depressive disorder (N=126) treated with open-label dul... DisGeNET Detail
Different combinations of T-182C and the G1287A polymorphisms of NET gene might increase morbidity r... DisGeNET Detail
Different combinations of T-182C and the G1287A polymorphisms of NET gene might increase morbidity r... DisGeNET Detail
Association between major depressive disorder and the norepinephrine transporter polymorphisms T-182... DisGeNET Detail
Association between major depressive disorder and the norepinephrine transporter polymorphisms T-182... DisGeNET Detail
The 1287 G/A polymorphism of the norepinephrine transporter gene (NET) is involved in commission err... DisGeNET Detail
A silent G1287A nucleotide substitution in exon 9 of the NET gene was studied in human conditions in... DisGeNET Detail
Regional brain perfusion before and after treatment with methylphenidate may be associated with the ... DisGeNET Detail
No association of the G1287A polymorphism in the norepinephrine transporter gene and susceptibility ... DisGeNET Detail
Additive regression analyses controlling for ADHD symptom severity, age, sex, IQ, and final dose of ... DisGeNET Detail
No association of the G1287A polymorphism in the norepinephrine transporter gene and susceptibility ... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5569 dbSNP
Genome
hg38
Position
chr16:55,697,923-55,697,923
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
107.47
Standard deviation of sample read depth (HGVD)
53.61
Number of reference allele (HGVD)
1802
Number of alternative allele (HGVD)
605
Allele Frequency (HGVD)
0.2513502285002077
Gene Symbol (HGVD)
SLC6A2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs5569
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2554
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4281
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
2624
East Asian Heterozygous Counts (ExAC)
1820
East Asian Homozygous Counts (ExAC)
402
East Asian Allele Frequency (ExAC)
0.3040556199304751
Chromosome Counts in All Race (ExAC)
121276
Allele Counts in All Race (ExAC)
36929
Heterozygous Counts in All Race (ExAC)
24723
Homozygous Counts in All Race (ExAC)
6103
Allele Frequency in All Race (ExAC)
0.30450377650977933
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