chr11:116662407:G>C Detail (hg19) (APOA5, LOC108491825)

Information

Genome

Assembly Position
hg19 chr11:116,662,407-116,662,407
hg38 chr11:116,791,691-116,791,691 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001166598.1:c.56C>G NP_001160070.1:p.Ser19Trp
NM_052968.4:c.56C>G NP_443200.2:p.Ser19Trp
Ensemble ENST00000542499.5:c.56C>G ENST00000542499.5:p.Ser19Trp
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606368 OMIM
HGNC 17288 HGNC
Ensembl ENSG00000110243 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv44157307 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2002-11-15 no assertion criteria provided Hypertriglyceridemia 1 germline Detail
Benign 2024-01-31 criteria provided, single submitter not provided germline Detail
Benign 2019-02-11 criteria provided, single submitter germline Detail
Benign 2022-04-07 criteria provided, single submitter Hypertriglyceridemia 1,Familial type 5 hyperlipoproteinemia unknown Detail
Benign 2022-04-07 criteria provided, single submitter Hypertriglyceridemia 1,Familial type 5 hyperlipoproteinemia unknown Detail
Likely benign 2023-07-18 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.004 obesity We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C... BeFree 18596051 Detail
0.002 Ischemic Cerebrovascular Accident Apolipoprotein A5 gene C56G variant confers risk for the development of large-ve... BeFree 18274806 Detail
0.012 atherosclerosis We examined the relationship of APOA5 -1131T&gt;C and S19W with lipid subfractio... BeFree 14729863 Detail
0.019 obesity In current study two SNPs rs662799 risk allele G (P = 0.03) and rs3135506 risk a... BeFree 24402875 Detail
0.019 obesity We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C... BeFree 18596051 Detail
0.144 Metabolic syndrome X The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (A... BeFree 21749608 Detail
0.250 obesity In summary, we identified significant interactions for APOA5 S19W and LPL m107 f... BeFree 19629056 Detail
0.004 Ischemic stroke Apolipoprotein A5 gene C56G variant confers risk for the development of large-ve... BeFree 18274806 Detail
0.004 Hyperlipoproteinemia Type I Association of APOA5 -1131T&gt;C and S19W gene polymorphisms with both mild hype... BeFree 18468520 Detail
<0.001 Diabetes We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C... BeFree 18596051 Detail
0.150 coronary artery disease The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high leve... BeFree 16682041 Detail
0.002 Diabetes We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C... BeFree 18596051 Detail
0.101 Metabolic syndrome X The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (A... BeFree 21749608 Detail
0.031 Coronary heart disease However, there is no evidence that APOA5 S19W, -12,238T &gt; C, APOA4 T347S and ... BeFree 16321685 Detail
0.144 Coronary heart disease The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high leve... BeFree 16682041 Detail
0.002 arteriosclerosis We examined the relationship of APOA5 -1131T&gt;C and S19W with lipid subfractio... BeFree 14729863 Detail
0.139 coronary artery disease The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high leve... BeFree 16682041 Detail
<0.001 diabetes mellitus We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C... BeFree 18596051 Detail
0.005 HIV Infections In conclusion, polymorphisms in genes associated to the development of atherogen... BeFree 25500319 Detail
0.003 Hypertensive disease Association of APOA5 rs662799 and rs3135506 polymorphisms with arterial hyperten... BeFree 24684850 Detail
0.129 Metabolic syndrome X The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (A... BeFree 21749608 Detail
0.031 Coronary heart disease The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high leve... BeFree 16682041 Detail
0.009 Cerebrovascular accident This pool of samples was previously investigated for haplotype tagging minor all... BeFree 20158509 Detail
0.019 obesity In summary, we identified significant interactions for APOA5 S19W and LPL m107 f... BeFree 19629056 Detail
0.033 Coronary Arteriosclerosis The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high leve... BeFree 16682041 Detail
0.021 Coronary heart disease However, there is no evidence that APOA5 S19W, -12,238T &gt; C, APOA4 T347S and ... BeFree 16321685 Detail
0.139 coronary artery disease Therefore, the present study aimed to elucidate the relationship of four single ... BeFree 18801202 Detail
0.034 Coronary Arteriosclerosis The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high leve... BeFree 16682041 Detail
0.034 Coronary Arteriosclerosis The APOA5 variant S19W was also associated with minimal lumen diameter (MLD) of ... BeFree 19878569 Detail
0.007 diabetes mellitus We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C... BeFree 18596051 Detail
0.171 Metabolic syndrome X The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (A... BeFree 21749608 Detail
<0.001 Hashimoto Disease We analyzed the associations of seven polymorphisms of genes involved in lipid m... BeFree 25587205 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001371904.1(APOA5):c.56C>G (p.Ser19Trp) AND Hypertriglyceridemia 1 ClinVar Detail
NM_001371904.1(APOA5):c.56C>G (p.Ser19Trp) AND not provided ClinVar Detail
NM_001371904.1(APOA5):c.56C>G (p.Ser19Trp) AND Cardiovascular phenotype ClinVar Detail
NM_001371904.1(APOA5):c.56C>G (p.Ser19Trp) AND multiple conditions ClinVar Detail
NM_001371904.1(APOA5):c.56C>G (p.Ser19Trp) AND multiple conditions ClinVar Detail
NM_001371904.1(APOA5):c.56C>G (p.Ser19Trp) AND not specified ClinVar Detail
We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C, APOE, GCKR, TRIB1 ... DisGeNET Detail
Apolipoprotein A5 gene C56G variant confers risk for the development of large-vessel associated isch... DisGeNET Detail
We examined the relationship of APOA5 -1131T&gt;C and S19W with lipid subfractions and progression o... DisGeNET Detail
In current study two SNPs rs662799 risk allele G (P = 0.03) and rs3135506 risk allele C (P = 0.05) o... DisGeNET Detail
We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C, APOE, GCKR, TRIB1 ... DisGeNET Detail
The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (APOA5), C482T (APOC3)... DisGeNET Detail
In summary, we identified significant interactions for APOA5 S19W and LPL m107 for obesity in Caribb... DisGeNET Detail
Apolipoprotein A5 gene C56G variant confers risk for the development of large-vessel associated isch... DisGeNET Detail
Association of APOA5 -1131T&gt;C and S19W gene polymorphisms with both mild hypertriglyceridemia and... DisGeNET Detail
We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C, APOE, GCKR, TRIB1 ... DisGeNET Detail
The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high levels of triglycerides ... DisGeNET Detail
We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C, APOE, GCKR, TRIB1 ... DisGeNET Detail
The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (APOA5), C482T (APOC3)... DisGeNET Detail
However, there is no evidence that APOA5 S19W, -12,238T &gt; C, APOA4 T347S and APCC3 -482C &gt; T S... DisGeNET Detail
The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high levels of triglycerides ... DisGeNET Detail
We examined the relationship of APOA5 -1131T&gt;C and S19W with lipid subfractions and progression o... DisGeNET Detail
The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high levels of triglycerides ... DisGeNET Detail
We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C, APOE, GCKR, TRIB1 ... DisGeNET Detail
In conclusion, polymorphisms in genes associated to the development of atherogenic dyslipidemia, esp... DisGeNET Detail
Association of APOA5 rs662799 and rs3135506 polymorphisms with arterial hypertension in Moroccan pat... DisGeNET Detail
The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (APOA5), C482T (APOC3)... DisGeNET Detail
The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high levels of triglycerides ... DisGeNET Detail
This pool of samples was previously investigated for haplotype tagging minor alleles of apolipoprote... DisGeNET Detail
In summary, we identified significant interactions for APOA5 S19W and LPL m107 for obesity in Caribb... DisGeNET Detail
The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high levels of triglycerides ... DisGeNET Detail
However, there is no evidence that APOA5 S19W, -12,238T &gt; C, APOA4 T347S and APCC3 -482C &gt; T S... DisGeNET Detail
Therefore, the present study aimed to elucidate the relationship of four single nucleotide polymorph... DisGeNET Detail
The -1131 T&gt;C and S19W APOA5 gene polymorphisms are associated with high levels of triglycerides ... DisGeNET Detail
The APOA5 variant S19W was also associated with minimal lumen diameter (MLD) of coronary atheroscler... DisGeNET Detail
We found that: (i) genotypes, including those of APOA5 S19W, APOA5 -1131T &gt; C, APOE, GCKR, TRIB1 ... DisGeNET Detail
The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (APOA5), C482T (APOC3)... DisGeNET Detail
We analyzed the associations of seven polymorphisms of genes involved in lipid metabolism (APOA5 rs3... 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
rs3135506 dbSNP
Genome
hg19
Position
chr11:116,662,407-116,662,407
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1201
Mean of sample read depth (HGVD)
47.01
Standard deviation of sample read depth (HGVD)
21.21
Number of reference allele (HGVD)
2397
Number of alternative allele (HGVD)
5
Allele Frequency (HGVD)
0.0020815986677768525
Gene Symbol (HGVD)
APOA5
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))
rs3135506
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0008
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
14
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
5780
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4602076124567473E-4
Chromosome Counts in All Race (ExAC)
87240
Allele Counts in All Race (ExAC)
6894
Heterozygous Counts in All Race (ExAC)
6368
Homozygous Counts in All Race (ExAC)
263
Allele Frequency in All Race (ExAC)
0.07902338376891334
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