chr19:50858501:T>C Detail (hg38) (KLK3)

Information

Genome

Assembly Position
hg19 chr19:51,361,757-51,361,757 View the variant detail on this assembly version.
hg38 chr19:50,858,501-50,858,501

HGVS

Type Transcript Protein
RefSeq NM_001030048.1:c.536T>C NP_001025219.1:p.Ile179Thr
NM_001648.2:c.536T>C NP_001639.1:p.Ile179Thr
NM_001030047.1:c.536T>C NP_001025218.1:p.Ile179Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:[No Data.]
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 176820 OMIM
HGNC 6364 HGNC
Ensembl ENSG00000142515 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62517395 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
0.262 Malignant neoplasm of prostate Genome-wide association scan for variants associated with early-onset prostate c... GWASCAT 24740154 Detail
<0.001 Neoplasm Metastasis Patients with CYP3A5*3/*3 and KLK3 I179T CC/TC genotypes had increased OR 2.30, ... BeFree 18306354 Detail
0.262 Malignant neoplasm of prostate Genetic variation in prostate-specific antigen-detected prostate cancer and the ... GWASCAT 24753544 Detail
0.021 Neoplasm Metastasis Patients with CYP3A5*3/*3 and KLK3 I179T CC/TC genotypes had increased OR 2.30, ... BeFree 18306354 Detail
0.262 Malignant neoplasm of prostate The genotypes of 4 single nucleotide polymorphisms previously associated with se... BeFree 23246478 Detail
0.080 prostate carcinoma The genotypes of 4 single nucleotide polymorphisms previously associated with se... BeFree 23246478 Detail
Annotation

Annotations

DescrptionSourceLinks
Genome-wide association scan for variants associated with early-onset prostate cancer. DisGeNET Detail
Patients with CYP3A5*3/*3 and KLK3 I179T CC/TC genotypes had increased OR 2.30, 95% CI 1.16-4.58 for... DisGeNET Detail
Genetic variation in prostate-specific antigen-detected prostate cancer and the effect of control se... DisGeNET Detail
Patients with CYP3A5*3/*3 and KLK3 I179T CC/TC genotypes had increased OR 2.30, 95% CI 1.16-4.58 for... DisGeNET Detail
The genotypes of 4 single nucleotide polymorphisms previously associated with serum prostate specifi... DisGeNET Detail
The genotypes of 4 single nucleotide polymorphisms previously associated with serum prostate specifi... 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
chr19:50,858,501-50,858,501
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
91.63
Standard deviation of sample read depth (HGVD)
43.44
Number of reference allele (HGVD)
2417
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1356492969396195E-4
Gene Symbol (HGVD)
KLK3
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.469010175763182E-4
Chromosome Counts in All Race (ExAC)
121290
Allele Counts in All Race (ExAC)
6701
Heterozygous Counts in All Race (ExAC)
6245
Homozygous Counts in All Race (ExAC)
228
Allele Frequency in All Race (ExAC)
0.05524775331849287
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