chr19:45412079:C>T Detail (hg19) (APOE)

Information

Genome

Assembly Position
hg19 chr19:45,412,079-45,412,079
hg38 chr19:44,908,822-44,908,822 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000041.3:c.526C>T NP_000032.1:p.Arg176Cys
NM_001302688.1:c.526C>T NP_001289617.1:p.Arg176Cys
NM_001302689.1:c.526C>T NP_001289618.1:p.Arg176Cys
Summary

MGeND

Clinical significance Benign
Variant entry 0
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.053
ToMMo:0.043
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.081

Prediction

ClinVar

Clinical Significance drug response
Review star
Show details
Links
Type Database ID Link
Gene MIM 107741 OMIM
HGNC 613 HGNC
Ensembl ENSG00000130203 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62264686 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2018/05/23 Aged, 100 and over germline MGS000013
(TMGS000027) 		Hiroshi Mori Osaka City University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2005-10-01 no assertion criteria provided Familial type 3 hyperlipoproteinemia germline Detail
Pathogenic 1984-04-01 no assertion criteria provided Hyperlipoproteinemia due to APOE1 germline Detail
Pathogenic 2017-02-21 no assertion criteria provided Familial type 3 hyperlipoproteinemia germline Detail
Pathogenic 1993-05-01 no assertion criteria provided Familial type 3 hyperlipoproteinemia germline Detail
drug response 2021-03-24 reviewed by expert panel germline Detail
Likely benign; other; risk factor 2023-08-01 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
drug response 2010-08-31 no assertion criteria provided unknown Detail
Benign 2019-01-01 criteria provided, single submitter unknown Detail
Benign no assertion criteria provided not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 obesity Prior to multiple testing correction, univariate analysis associated APOE rs4293... BeFree 26043189 Detail
0.008 obesity Prior to multiple testing correction, univariate analysis associated APOE rs4293... BeFree 26043189 Detail
0.196 obesity Prior to multiple testing correction, univariate analysis associated APOE rs4293... BeFree 26043189 Detail
0.391 hyperlipoproteinemia type III NA CLINVAR Detail
0.126 coronary artery disease CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7... BeFree 23050023 Detail
0.125 coronary artery disease CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7... BeFree 23050023 Detail
<0.001 Hyperlipidemia, Familial Combined Variants more frequently identified in isolated hypertriglyceridemias were rs741... BeFree 25176936 Detail
<0.001 Hyperlipidemia, Familial Combined Variants more frequently identified in isolated hypertriglyceridemias were rs741... BeFree 25176936 Detail
0.015 Hyperlipidemia, Familial Combined Variants more frequently identified in isolated hypertriglyceridemias were rs741... BeFree 25176936 Detail
<0.001 Hyperlipidemia, Familial Combined Variants more frequently identified in isolated hypertriglyceridemias were rs741... BeFree 25176936 Detail
0.036 Dyslipidemias After taking into account confounding factors and correcting for multiple compar... BeFree 26043189 Detail
0.019 Alzheimer Disease, Late Onset Two common single-nucleotide polymorphisms (SNPs) in APOE, rs429358 and rs7412, ... BeFree 24448547 Detail
0.202 Hypercholesterolemia [The strong effect of family history suggests a major genetic component for the ... GAD 19494537 Detail
0.009 Complications of Diabetes Mellitus [The strong effect of family history suggests a major genetic component for the ... GAD 19494537 Detail
0.340 myocardial infarction [The strong effect of family history suggests a major genetic component for the ... GAD 19494537 Detail
0.260 Coronary heart disease [Apolipoprotein E, CI and B gene polymorphisms in a sample of patients with coro... GAD 19494537 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) AND Familial type 3 hyperlipoproteinemia ClinVar Detail
NM_000041.3(APOE):c.[434G>A;526C>T] AND Hyperlipoproteinemia due to APOE1 ClinVar Detail
NM_000041.3(APOE):c.[526C>T;725G>A] AND Familial type 3 hyperlipoproteinemia ClinVar Detail
NM_000041.3(APOE):c.[526C>T;761T>A] AND Familial type 3 hyperlipoproteinemia ClinVar Detail
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) AND atorvastatin response - Efficacy ClinVar Detail
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) AND not provided ClinVar Detail
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) AND Warfarin response ClinVar Detail
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) AND Hypercholesterolemia ClinVar Detail
NM_000041.2(APOE):c.526C>T (p.Arg176Cys) AND not specified ClinVar Detail
Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16... DisGeNET Detail
Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16... DisGeNET Detail
Prior to multiple testing correction, univariate analysis associated APOE rs429358, rs7412 and ATG16... DisGeNET Detail
NA DisGeNET Detail
CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7 × 10(-8)), APOA5 rs... DisGeNET Detail
CAD association was replicated and/or verified for 4 loci: SORT1 rs611917 (p=1.7 × 10(-8)), APOA5 rs... DisGeNET Detail
Variants more frequently identified in isolated hypertriglyceridemias were rs7412 in APOE and rs1800... DisGeNET Detail
Variants more frequently identified in isolated hypertriglyceridemias were rs7412 in APOE and rs1800... DisGeNET Detail
Variants more frequently identified in isolated hypertriglyceridemias were rs7412 in APOE and rs1800... DisGeNET Detail
Variants more frequently identified in isolated hypertriglyceridemias were rs7412 in APOE and rs1800... DisGeNET Detail
After taking into account confounding factors and correcting for multiple comparisons only APOE rs42... DisGeNET Detail
Two common single-nucleotide polymorphisms (SNPs) in APOE, rs429358 and rs7412, determine the three ... DisGeNET Detail
[The strong effect of family history suggests a major genetic component for the development of CHD i... DisGeNET Detail
[The strong effect of family history suggests a major genetic component for the development of CHD i... DisGeNET Detail
[The strong effect of family history suggests a major genetic component for the development of CHD i... DisGeNET Detail
[Apolipoprotein E, CI and B gene polymorphisms in a sample of patients with coronary heart disease i... 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
rs7412 dbSNP
Genome
hg19
Position
chr19:45,412,079-45,412,079
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1146
Mean of sample read depth (HGVD)
61.22
Standard deviation of sample read depth (HGVD)
28.00
Number of reference allele (HGVD)
2170
Number of alternative allele (HGVD)
122
Allele Frequency (HGVD)
0.053228621291448515
Gene Symbol (HGVD)
APOE
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))
rs7412
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0435
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
728
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16750
East Asian Chromosome Counts (ExAC)
418
East Asian Allele Counts (ExAC)
34
East Asian Heterozygous Counts (ExAC)
34
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.08133971291866028
Chromosome Counts in All Race (ExAC)
13534
Allele Counts in All Race (ExAC)
972
Heterozygous Counts in All Race (ExAC)
910
Homozygous Counts in All Race (ExAC)
31
Allele Frequency in All Race (ExAC)
0.07181912221072853
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