chr3:119431989:C>T Detail (hg38) (TMEM39A)

Information

Genome

Assembly Position
hg19 chr3:119,150,836-119,150,836 View the variant detail on this assembly version.
hg38 chr3:119,431,989-119,431,989

HGVS

Type Transcript Protein
RefSeq NM_018266.2:c.1459G>A NP_060736.1:p.Ala487Thr
Ensemble ENST00000319172.10:c.1459G>A ENST00000319172.10:p.Ala487Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.089
ToMMo:0.098
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.079

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM
HGNC 25600 HGNC
Ensembl ENSG00000176142 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv13923975 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Autoimmune Diseases Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
0.010 multiple sclerosis Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
<0.001 multiple sclerosis Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
0.001 multiple sclerosis Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
<0.001 multiple sclerosis Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
0.002 Autoimmune Diseases Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
<0.001 multiple sclerosis Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
<0.001 multiple sclerosis Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
<0.001 Autoimmune Diseases Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7... BeFree 22194214 Detail
Annotation

Annotations

DescrptionSourceLinks
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... DisGeNET Detail
Replication extended to the following polymorphisms: PKN2 (rs305217), GTF2B (rs7538427), EPHA4 (rs15... 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
-
Genome
hg38
Position
chr3:119,431,989-119,431,989
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
40.79
Standard deviation of sample read depth (HGVD)
17.08
Number of reference allele (HGVD)
2194
Number of alternative allele (HGVD)
214
Allele Frequency (HGVD)
0.0888704318936877
Gene Symbol (HGVD)
TMEM39A
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))
rs1132200
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0983
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1647
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8520
East Asian Allele Counts (ExAC)
675
East Asian Heterozygous Counts (ExAC)
623
East Asian Homozygous Counts (ExAC)
26
East Asian Allele Frequency (ExAC)
0.07922535211267606
Chromosome Counts in All Race (ExAC)
119352
Allele Counts in All Race (ExAC)
14650
Heterozygous Counts in All Race (ExAC)
12520
Homozygous Counts in All Race (ExAC)
1065
Allele Frequency in All Race (ExAC)
0.12274616261143509
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