chr10:96058298:C>T Detail (hg19) (PLCE1)

Information

Genome

Assembly Position
hg19 chr10:96,058,298-96,058,298
hg38 chr10:94,298,541-94,298,541 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001288989.1:c.5330C>T NP_001275918.1:p.Thr1777Ile
NM_016341.3:c.5330C>T NP_057425.3:p.Thr1777Ile
NM_001165979.2:c.4304C>T NP_001159451.1:p.Thr1435Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.257
ToMMo:0.250
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.234

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 608414 OMIM
HGNC 17175 HGNC
Ensembl ENSG00000138193 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv40247046 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2021-10-25 criteria provided, multiple submitters, no conflicts Nephrotic syndrome, type 3 germline Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2022-09-27 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.010 Esophageal Neoplasms Phospholipase C epsilon 1 (PLCE1 rs2274223A>G, rs3765524C>T and rs7922612C... BeFree 24935391 Detail
0.128 Malignant neoplasm of esophagus Phospholipase C epsilon 1 (PLCE1 rs2274223A>G, rs3765524C>T and rs7922612C... BeFree 24935391 Detail
0.124 Malignant neoplasm of stomach A notable signal was rs2274223, a nonsynonymous SNP located in PLCE1, for gastri... BeFree 20729852 Detail
0.003 esophageal carcinoma Phospholipase C epsilon 1 (PLCE1 rs2274223A>G, rs3765524C>T and rs7922612C... BeFree 24935391 Detail
0.122 Stomach Neoplasms [A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and ... GAD 20729852 Detail
0.121 dengue shock syndrome Genome-wide association study identifies susceptibility loci for dengue shock sy... GWASCAT 22001756 Detail
0.123 Severe Dengue [Genome-wide association study identifies susceptibility loci for dengue shock s... GAD 22001756 Detail
0.128 Malignant neoplasm of esophagus A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and e... GWASCAT 20729852 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
Annotation

Annotations

DescrptionSourceLinks
NM_016341.4(PLCE1):c.5330C>T (p.Thr1777Ile) AND not specified ClinVar Detail
NM_016341.4(PLCE1):c.5330C>T (p.Thr1777Ile) AND Nephrotic syndrome, type 3 ClinVar Detail
NM_016341.4(PLCE1):c.5330C>T (p.Thr1777Ile) AND not provided ClinVar Detail
NM_016341.4(PLCE1):c.5330C>T (p.Thr1777Ile) AND Focal segmental glomerulosclerosis ClinVar Detail
Phospholipase C epsilon 1 (PLCE1 rs2274223A&gt;G, rs3765524C&gt;T and rs7922612C&gt;T) polymorphisms... DisGeNET Detail
Phospholipase C epsilon 1 (PLCE1 rs2274223A&gt;G, rs3765524C&gt;T and rs7922612C&gt;T) polymorphisms... DisGeNET Detail
A notable signal was rs2274223, a nonsynonymous SNP located in PLCE1, for gastric cancer (P = 8.40 x... DisGeNET Detail
Phospholipase C epsilon 1 (PLCE1 rs2274223A&gt;G, rs3765524C&gt;T and rs7922612C&gt;T) polymorphisms... DisGeNET Detail
[A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous ... DisGeNET Detail
Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and P... DisGeNET Detail
[Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and ... DisGeNET Detail
A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous c... 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

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
rs3765524 dbSNP
Genome
hg19
Position
chr10:96,058,298-96,058,298
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
88.69
Standard deviation of sample read depth (HGVD)
41.30
Number of reference allele (HGVD)
1794
Number of alternative allele (HGVD)
620
Allele Frequency (HGVD)
0.25683512841756423
Gene Symbol (HGVD)
PLCE1
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))
rs3765524
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2495
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4182
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8578
East Asian Allele Counts (ExAC)
2006
East Asian Heterozygous Counts (ExAC)
1558
East Asian Homozygous Counts (ExAC)
224
East Asian Allele Frequency (ExAC)
0.2338540452319888
Chromosome Counts in All Race (ExAC)
120696
Allele Counts in All Race (ExAC)
32726
Heterozygous Counts in All Race (ExAC)
22904
Homozygous Counts in All Race (ExAC)
4911
Allele Frequency in All Race (ExAC)
0.2711440312852124
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