chr8:142680513:C>T Detail (hg38) (PSCA, JRK)

Information

Genome

Assembly Position
hg19 chr8:143,761,931-143,761,931 View the variant detail on this assembly version.
hg38 chr8:142,680,513-142,680,513

HGVS

Type Transcript Protein
RefSeq NM_005672.4:c.-26C>T
Ensemble ENST00000301258.5:c.-26C>T
ENST00000513264.1:c.-26C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.632
ToMMo:0.641
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.348

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 602470 OMIM
HGNC 9500 HGNC
Ensembl ENSG00000167653 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv35049165 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-07-02 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.010 stomach carcinoma We analyzed 3 SNPs in the PSCA gene (rs2294008, rs9297976 and rs12155758) which ... BeFree 24023815 Detail
0.010 Malignant neoplasm of stomach We analyzed 3 SNPs in the PSCA gene (rs2294008, rs9297976 and rs12155758) which ... BeFree 24023815 Detail
<0.001 gastritis Herein, we aimed to evaluate associations between PSCA (C&gt;T, rs2294008; G&gt;... BeFree 25503145 Detail
0.010 Malignant neoplasm of stomach The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastri... BeFree 25582162 Detail
0.010 Malignant neoplasm of stomach Recently, two genome-wide association studies identified a significant associati... BeFree 20083643 Detail
0.010 Malignant neoplasm of stomach Polymorphisms in prostate stem cell antigen gene rs2294008 increase gastric canc... BeFree 21268123 Detail
<0.001 gastritis Frequency of PSCA rs2294008 C/C genotype in duodenal ulcer was 36.1%, which was ... BeFree 25582162 Detail
0.008 Malignant neoplasm of urinary bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
0.010 stomach carcinoma The C allele of rs2294008 at PSCA was associated with increased risk of duodenal... BeFree 22387998 Detail
0.125 Bladder Neoplasm The present study demonstrates that a genetic variant (rs2294008) discovered by ... BeFree 23266392 Detail
0.243 duodenal ulcer Association of PSCA rs2294008 gene variants with poor prognosis and increased su... BeFree 25721731 Detail
0.010 stomach carcinoma The rs2294008 polymorphism in PSCA increases the risk of noncardia gastric cance... BeFree 21070776 Detail
0.010 stomach carcinoma Association of PSCA rs2294008 gene variants with poor prognosis and increased su... BeFree 25721731 Detail
0.129 Malignant neoplasm of urinary bladder In conclusion, the results suggest that the PSCA rs2294008 (C&gt;T) polymorphism... BeFree 25117309 Detail
0.010 Malignant neoplasm of stomach The variant C allele of the reference SNP rs2294008 in the PSCA gene was associa... BeFree 24962126 Detail
0.003 Gastritis, Atrophic PSCA rs2294008 C&gt;T polymorphism was assessed in H. pylori-positive Japanese p... BeFree 25582162 Detail
0.002 Malignant neoplasm of stomach The results of subgroup analyses (according to histopathology, countries and sou... BeFree 22155405 Detail
0.129 Malignant neoplasm of urinary bladder A multi-stage genome-wide association study of bladder cancer identifies multipl... GWASCAT 20972438 Detail
0.243 duodenal ulcer The C allele of rs2294008 at PSCA was associated with increased risk of duodenal... GWASCAT 22387998 Detail
0.003 Gastritis, Atrophic Carriage of the risk allele (T) of rs2294008 in PSCA was associated with chronic... BeFree 21070776 Detail
0.129 Malignant neoplasm of urinary bladder Three previously established bladder cancer risk-associated SNPs (rs798766 in TA... BeFree 24155119 Detail
0.129 Malignant neoplasm of urinary bladder Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibi... GWASCAT 19648920 Detail
0.004 Carcinoma of bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
0.129 Malignant neoplasm of urinary bladder [Genetic variation in the prostate stem cell antigen gene PSCA confers susceptib... GAD 19648920 Detail
0.010 Malignant neoplasm of stomach Association of the PSCA rs2294008 C&gt;T polymorphism with gastric cancer risk: ... BeFree 22938475 Detail
0.243 duodenal ulcer The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastri... BeFree 25582162 Detail
0.008 gastritis Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are asso... BeFree 25503145 Detail
0.010 stomach carcinoma The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastri... BeFree 25582162 Detail
0.125 Bladder Neoplasm [Genetic variation in the prostate stem cell antigen gene PSCA confers susceptib... GAD 19648920 Detail
0.129 Malignant neoplasm of urinary bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
0.125 Bladder Neoplasm [A multi-stage genome-wide association study of bladder cancer identifies multip... GAD 20972438 Detail
0.007 Carcinoma of bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
<0.001 Carcinoma of bladder Three previously established bladder cancer risk-associated SNPs (rs798766 in TA... BeFree 24155119 Detail
0.010 stomach carcinoma Polymorphisms in prostate stem cell antigen gene rs2294008 increase gastric canc... BeFree 21268123 Detail
0.010 stomach carcinoma Recently, two genome-wide association studies identified a significant associati... BeFree 20083643 Detail
0.012 Malignant neoplasm of urinary bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
0.010 Malignant neoplasm of stomach The rs2294008 polymorphism in PSCA increases the risk of noncardia gastric cance... BeFree 21070776 Detail
0.003 Carcinogenesis Our study showed that rs2294008 in the PSCA gene was associated with increased r... BeFree 21538581 Detail
<0.001 Squamous cell carcinoma of esophagus We found that the T allele of rs2294008, an intronic variant of the PSCA gene at... BeFree 24654646 Detail
0.243 duodenal ulcer [The C allele of rs2294008 at PSCA was associated with increased risk of duodena... GAD 22387998 Detail
0.010 Malignant neoplasm of stomach A genome-wide study performed in a Japanese population identified a strong assoc... BeFree 21681742 Detail
0.010 Malignant neoplasm of stomach We found that the T allele of rs2294008, an intronic variant of the PSCA gene at... BeFree 24654646 Detail
0.010 stomach carcinoma Association of the PSCA rs2294008 C&gt;T polymorphism with gastric cancer risk: ... BeFree 22938475 Detail
0.010 stomach carcinoma We found that the T allele of rs2294008, an intronic variant of the PSCA gene at... BeFree 24654646 Detail
<0.001 Helicobacter pylori infection Two recent genome-wide association studies in Asians have reported the associati... BeFree 25721731 Detail
0.123 Malignant neoplasm of urinary bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
<0.001 gallbladder carcinoma PSCA gene variants (rs2294008 and rs2978974) confer increased susceptibility of ... BeFree 23988503 Detail
0.002 stomach carcinoma The results of subgroup analyses (according to histopathology, countries and sou... BeFree 22155405 Detail
0.004 Carcinoma of bladder Three previously established bladder cancer risk-associated SNPs (rs798766 in TA... BeFree 24155119 Detail
0.004 Carcinoma of bladder In conclusion, the results suggest that the PSCA rs2294008 (C&gt;T) polymorphism... BeFree 25117309 Detail
0.010 Malignant neoplasm of stomach The C allele of rs2294008 at PSCA was associated with increased risk of duodenal... BeFree 22387998 Detail
0.123 Malignant neoplasm of urinary bladder Three previously established bladder cancer risk-associated SNPs (rs798766 in TA... BeFree 24155119 Detail
0.003 Carcinogenesis Our study showed that the rs2294008 polymorphism in the PSCA gene is associated ... BeFree 25374226 Detail
<0.001 gastritis Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are asso... BeFree 25503145 Detail
<0.001 gastric ulcer The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastri... BeFree 25582162 Detail
<0.001 Carcinoma of bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
0.010 stomach carcinoma A genome-wide study performed in a Japanese population identified a strong assoc... BeFree 21681742 Detail
0.003 Carcinoma of bladder In the meta-analysis, the reported risk allele for four SNPs were significantly ... BeFree 22711262 Detail
0.010 stomach carcinoma The variant C allele of the reference SNP rs2294008 in the PSCA gene was associa... BeFree 24962126 Detail
0.010 Malignant neoplasm of stomach Association of PSCA rs2294008 gene variants with poor prognosis and increased su... BeFree 25721731 Detail
0.017 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.015 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.010 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.124 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
<0.001 Malignant neoplasm of stomach Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.010 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
<0.001 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.004 stomach carcinoma Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (r... BeFree 26554163 Detail
0.027 Carcinoma of bladder These findings suggest that seven bladder cancer risk-associated variants (rs964... BeFree 24740636 Detail
0.107 Malignant neoplasm of urinary bladder These findings suggest that seven bladder cancer risk-associated variants (rs964... BeFree 24740636 Detail
<0.001 gastric adenocarcinoma Two SNPs of rs2294008 (C&gt;T) and rs2976392 (G&gt;A) were identified to be asso... BeFree 26006239 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005672.5(PSCA):c.-26C>T AND not provided ClinVar Detail
We analyzed 3 SNPs in the PSCA gene (rs2294008, rs9297976 and rs12155758) which were previously foun... DisGeNET Detail
We analyzed 3 SNPs in the PSCA gene (rs2294008, rs9297976 and rs12155758) which were previously foun... DisGeNET Detail
Herein, we aimed to evaluate associations between PSCA (C&gt;T, rs2294008; G&gt;A, rs2976392), MUC1 ... DisGeNET Detail
The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastric mucosal atrophy, f... DisGeNET Detail
Recently, two genome-wide association studies identified a significant association between the prost... DisGeNET Detail
Polymorphisms in prostate stem cell antigen gene rs2294008 increase gastric cancer risk in Chinese. DisGeNET Detail
Frequency of PSCA rs2294008 C/C genotype in duodenal ulcer was 36.1%, which was significantly higher... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
The C allele of rs2294008 at PSCA was associated with increased risk of duodenal ulcer (odds ratio (... DisGeNET Detail
The present study demonstrates that a genetic variant (rs2294008) discovered by bladder cancer genom... DisGeNET Detail
Association of PSCA rs2294008 gene variants with poor prognosis and increased susceptibility to gast... DisGeNET Detail
The rs2294008 polymorphism in PSCA increases the risk of noncardia gastric cancer and its precursors... DisGeNET Detail
Association of PSCA rs2294008 gene variants with poor prognosis and increased susceptibility to gast... DisGeNET Detail
In conclusion, the results suggest that the PSCA rs2294008 (C&gt;T) polymorphism is a risk factor fo... DisGeNET Detail
The variant C allele of the reference SNP rs2294008 in the PSCA gene was associated with a significa... DisGeNET Detail
PSCA rs2294008 C&gt;T polymorphism was assessed in H. pylori-positive Japanese patients (n = 488) wi... DisGeNET Detail
The results of subgroup analyses (according to histopathology, countries and sources of controls) in... DisGeNET Detail
A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loc... DisGeNET Detail
The C allele of rs2294008 at PSCA was associated with increased risk of duodenal ulcer (odds ratio (... DisGeNET Detail
Carriage of the risk allele (T) of rs2294008 in PSCA was associated with chronic atrophic gastritis ... DisGeNET Detail
Three previously established bladder cancer risk-associated SNPs (rs798766 in TACC3, rs9642880 in MY... DisGeNET Detail
Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary blad... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
[Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bla... DisGeNET Detail
Association of the PSCA rs2294008 C&gt;T polymorphism with gastric cancer risk: evidence from a meta... DisGeNET Detail
The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastric mucosal atrophy, f... DisGeNET Detail
Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are associated with GC and H... DisGeNET Detail
The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastric mucosal atrophy, f... DisGeNET Detail
[Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bla... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
[A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility lo... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
Three previously established bladder cancer risk-associated SNPs (rs798766 in TACC3, rs9642880 in MY... DisGeNET Detail
Polymorphisms in prostate stem cell antigen gene rs2294008 increase gastric cancer risk in Chinese. DisGeNET Detail
Recently, two genome-wide association studies identified a significant association between the prost... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
The rs2294008 polymorphism in PSCA increases the risk of noncardia gastric cancer and its precursors... DisGeNET Detail
Our study showed that rs2294008 in the PSCA gene was associated with increased risks of gastric canc... DisGeNET Detail
We found that the T allele of rs2294008, an intronic variant of the PSCA gene at 8q24 that was previ... DisGeNET Detail
[The C allele of rs2294008 at PSCA was associated with increased risk of duodenal ulcer (odds ratio ... DisGeNET Detail
A genome-wide study performed in a Japanese population identified a strong association between SNP r... DisGeNET Detail
We found that the T allele of rs2294008, an intronic variant of the PSCA gene at 8q24 that was previ... DisGeNET Detail
Association of the PSCA rs2294008 C&gt;T polymorphism with gastric cancer risk: evidence from a meta... DisGeNET Detail
We found that the T allele of rs2294008, an intronic variant of the PSCA gene at 8q24 that was previ... DisGeNET Detail
Two recent genome-wide association studies in Asians have reported the association between the PSCA ... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
PSCA gene variants (rs2294008 and rs2978974) confer increased susceptibility of gallbladder carcinom... DisGeNET Detail
The results of subgroup analyses (according to histopathology, countries and sources of controls) in... DisGeNET Detail
Three previously established bladder cancer risk-associated SNPs (rs798766 in TACC3, rs9642880 in MY... DisGeNET Detail
In conclusion, the results suggest that the PSCA rs2294008 (C&gt;T) polymorphism is a risk factor fo... DisGeNET Detail
The C allele of rs2294008 at PSCA was associated with increased risk of duodenal ulcer (odds ratio (... DisGeNET Detail
Three previously established bladder cancer risk-associated SNPs (rs798766 in TACC3, rs9642880 in MY... DisGeNET Detail
Our study showed that the rs2294008 polymorphism in the PSCA gene is associated with the risk of bla... DisGeNET Detail
Polymorphisms of PSCA (rs2976392, rs2294008) and MUC1 (rs4072037) genes are associated with GC and H... DisGeNET Detail
The PSCA rs2294008 C&gt;T polymorphism may be acting through induction of gastric mucosal atrophy, f... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
A genome-wide study performed in a Japanese population identified a strong association between SNP r... DisGeNET Detail
In the meta-analysis, the reported risk allele for four SNPs were significantly associated with incr... DisGeNET Detail
The variant C allele of the reference SNP rs2294008 in the PSCA gene was associated with a significa... DisGeNET Detail
Association of PSCA rs2294008 gene variants with poor prognosis and increased susceptibility to gast... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
Genetic Variation of BCL2 (rs2279115), NEIL2 (rs804270), LTA (rs909253), PSCA (rs2294008) and PLCE1 ... DisGeNET Detail
These findings suggest that seven bladder cancer risk-associated variants (rs9642880, rs2294008, rs7... DisGeNET Detail
These findings suggest that seven bladder cancer risk-associated variants (rs9642880, rs2294008, rs7... DisGeNET Detail
Two SNPs of rs2294008 (C&gt;T) and rs2976392 (G&gt;A) were identified to be associated with GAC risk... 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
rs2294008 dbSNP
Genome
hg38
Position
chr8:142,680,513-142,680,513
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
537
Mean of sample read depth (HGVD)
100.69
Standard deviation of sample read depth (HGVD)
33.00
Number of reference allele (HGVD)
395
Number of alternative allele (HGVD)
679
Allele Frequency (HGVD)
0.6322160148975792
Gene Symbol (HGVD)
PSCA
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))
rs2294008
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6412
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10746
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
790
East Asian Allele Counts (ExAC)
275
East Asian Heterozygous Counts (ExAC)
189
East Asian Homozygous Counts (ExAC)
43
East Asian Allele Frequency (ExAC)
0.34810126582278483
Chromosome Counts in All Race (ExAC)
22222
Allele Counts in All Race (ExAC)
10281
Heterozygous Counts in All Race (ExAC)
5683
Homozygous Counts in All Race (ExAC)
2299
Allele Frequency in All Race (ExAC)
0.46264962649626495
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