chr19:44908684:T>C Detail (hg38) (APOE)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr19:45,411,941-45,411,941 View the variant detail on this assembly version.
hg38	chr19:44,908,684-44,908,684

HGVS

APOE

Type	Transcript	Protein
RefSeq	NM_000041.3:c.388T>C	NP_000032.1:p.Cys130Arg
	NM_001302688.1:c.388T>C	NP_001289617.1:p.Cys130Arg
	NM_001302689.1:c.388T>C	NP_001289618.1:p.Cys130Arg
	NM_001302690.1:c.388T>C	NP_001289619.1:p.Cys130Arg
	NM_001302691.1:c.388T>C	NP_001289620.1:p.Cys130Arg
Ensemble	ENST00000252486.9:c.388T>C	ENST00000252486.9:p.Cys130Arg

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.119
	ToMMo:0.100
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.150

Prediction

ClinVar

Clinical Significance	Conflicting classifications of pathogenicity; other; risk factor
Review star
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Links

APOE

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	tgv62264649	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
not provided	2023-06-08	no assertion provided	Familial type 3 hyperlipoproteinemia	germline	Detail
Pathogenic Established risk allele	2022-06-27	no assertion criteria provided	Alzheimer disease 2	germline unknown	Detail
Pathogenic	1993-05-01	no assertion criteria provided	Familial type 3 hyperlipoproteinemia	germline	Detail
Pathogenic	2017-02-15	no assertion criteria provided	APOE4(-)-FREIBURG	germline	Detail
association	2019-11-22	no assertion criteria provided		germline	Detail
Conflicting interpretations of pathogenicity; other; risk factor	2022-10-01	criteria provided, conflicting interpretations	not provided	germline	Detail
risk factor	2019-01-16	criteria provided, single submitter	Primary degenerative dementia of the Alzheimer type, presenile onset	germline	Detail
drug response	2010-08-31	no assertion criteria provided		unknown	Detail
Likely pathogenic	2019-06-27	criteria provided, single submitter	Alzheimer disease	germline unknown	Detail
Likely pathogenic	2020-05-27	no assertion criteria provided	familial hypercholesterolemia	germline	Detail
Pathogenic	2020-03-24	criteria provided, single submitter	Alzheimer disease 4	unknown	Detail
Uncertain significance	2019-01-01	criteria provided, single submitter	Lipoprotein glomerulopathy	unknown	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
0.009	Primary Progressive Aphasia (disorder)	Inside this region of 16.3 kb, LD (r2 = 0.14) between TOMM40 (rs157590) and APOE...	BeFree	22710912	Detail
<0.001	Primary Progressive Aphasia (disorder)	Inside this region of 16.3 kb, LD (r2 = 0.14) between TOMM40 (rs157590) and APOE...	BeFree	22710912	Detail
0.006	Cognitive changes	Patients were also genotyped for three polymorphisms associated with cognitive c...	BeFree	25080285	Detail
0.007	dementia	When adjusted for CSF Aß42, the association of rs429358 with dementia is greatly...	BeFree	20847432	Detail
0.036	Dyslipidemias	After taking into account confounding factors and correcting for multiple compar...	BeFree	26043189	Detail
0.005	Presenile dementia	When adjusted for CSF Aß42, the association of rs429358 with dementia is greatly...	BeFree	20847432	Detail
0.019	Alzheimer Disease, Late Onset	Two common single-nucleotide polymorphisms (SNPs) in APOE, rs429358 and rs7412, ...	BeFree	24448547	Detail
<0.001	Down syndrome	As expected, the most strongly associated SNP was the APOE ɛ4 rs429358 variant (...	BeFree	20946940	Detail
0.440	Alzheimer's disease	[In addition to known candidate genes, APOE, TOMM40, and one hypothetical gene L...	GAD	21123754	Detail
0.030	Down syndrome	As expected, the most strongly associated SNP was the APOE ɛ4 rs429358 variant (...	BeFree	20946940	Detail
0.133	Down syndrome	As expected, the most strongly associated SNP was the APOE ɛ4 rs429358 variant (...	BeFree	20946940	Detail
<0.001	Cognitive changes	Patients were also genotyped for three polymorphisms associated with cognitive c...	BeFree	25080285	Detail
0.142	Lewy Body Disease	Genome-wide significance was observed for clinico-pathologic AD dementia, NPs, N...	GWASCAT	25188341	Detail
<0.001	Cognitive changes	Patients were also genotyped for three polymorphisms associated with cognitive c...	BeFree	25080285	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000041.3(APOE):c.[388T>C;478C>T] AND Familial type 3 hyperlipoproteinemia	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND Alzheimer disease 2	ClinVar	Detail
NM_000041.3(APOE):c.[388T>C;805C>G] AND Familial type 3 hyperlipoproteinemia	ClinVar	Detail
NM_000041.3(APOE):c.[137T>C;388T>C] AND APOE4(-)-FREIBURG	ClinVar	Detail
NM_000041.3(APOE):c.[305C>G;388T>C] AND APOE5 VARIANT	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND not provided	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND Primary degenerative dementia of the Alzheimer type, pr...	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND Warfarin response	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND Alzheimer disease	ClinVar	Detail
NM_000041.3(APOE):c.[137T>C;388T>C] AND Familial hypercholesterolemia	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND Alzheimer disease 4	ClinVar	Detail
NM_000041.4(APOE):c.388T>C (p.Cys130Arg) AND Lipoprotein glomerulopathy	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
Inside this region of 16.3 kb, LD (r2 = 0.14) between TOMM40 (rs157590) and APOE (rs429358) was obse...	DisGeNET	Detail
Inside this region of 16.3 kb, LD (r2 = 0.14) between TOMM40 (rs157590) and APOE (rs429358) was obse...	DisGeNET	Detail
Patients were also genotyped for three polymorphisms associated with cognitive change in Parkinson's...	DisGeNET	Detail
When adjusted for CSF Aß42, the association of rs429358 with dementia is greatly reduced but remains...	DisGeNET	Detail
After taking into account confounding factors and correcting for multiple comparisons only APOE rs42...	DisGeNET	Detail
When adjusted for CSF Aß42, the association of rs429358 with dementia is greatly reduced but remains...	DisGeNET	Detail
Two common single-nucleotide polymorphisms (SNPs) in APOE, rs429358 and rs7412, determine the three ...	DisGeNET	Detail
As expected, the most strongly associated SNP was the APOE ɛ4 rs429358 variant (HR=2.47 [1.58, 3.87]...	DisGeNET	Detail
[In addition to known candidate genes, APOE, TOMM40, and one hypothetical gene LOC100129500 partiall...	DisGeNET	Detail
As expected, the most strongly associated SNP was the APOE ɛ4 rs429358 variant (HR=2.47 [1.58, 3.87]...	DisGeNET	Detail
As expected, the most strongly associated SNP was the APOE ɛ4 rs429358 variant (HR=2.47 [1.58, 3.87]...	DisGeNET	Detail
Patients were also genotyped for three polymorphisms associated with cognitive change in Parkinson's...	DisGeNET	Detail
Genome-wide significance was observed for clinico-pathologic AD dementia, NPs, NFTs, CAA, and LBD wi...	DisGeNET	Detail
Patients were also genotyped for three polymorphisms associated with cognitive change in Parkinson's...	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: rs387906567 dbSNP
Genome: hg38
Position: chr19:44,908,684-44,908,684
Variant Type: snv
Reference Allele: T
Alternative Allele: C
Filtering Status (HGVD): PASS
# of samples (HGVD): 914
Mean of sample read depth (HGVD): 16.54
Standard deviation of sample read depth (HGVD): 7.03
Number of reference allele (HGVD): 1610
Number of alternative allele (HGVD): 218
Allele Frequency (HGVD): 0.11925601750547046
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)): rs429358
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.1002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 1679
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16756
East Asian Chromosome Counts (ExAC): 1044
East Asian Allele Counts (ExAC): 157
East Asian Heterozygous Counts (ExAC): 145
East Asian Homozygous Counts (ExAC): 6
East Asian Allele Frequency (ExAC): 0.1503831417624521
Chromosome Counts in All Race (ExAC): 28926
Allele Counts in All Race (ExAC): 5332
Heterozygous Counts in All Race (ExAC): 4692
Homozygous Counts in All Race (ExAC): 320
Allele Frequency in All Race (ExAC): 0.18433243448800388

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