chr1:53716416:G>A Detail (hg19) (LRP8)

Information

Genome

Assembly Position
hg19 chr1:53,716,416-53,716,416
hg38 chr1:53,250,744-53,250,744 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_017522.4:c.2010C>T NP_059992.3:p.Asp670=
NM_004631.4:c.2622C>T NP_004622.2:p.Asp874=
NM_033300.3:c.2112C>T NP_150643.2:p.Asp704=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.715
ToMMo:0.706
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.726

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 602600 OMIM
HGNC 6700 HGNC
Ensembl ENSG00000157193 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1539178 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 schizophrenia HIMS replication analysis supported rs439401 (APOE regulatory region), and rs229... BeFree 22419519 Detail
Annotation

Annotations

DescrptionSourceLinks
HIMS replication analysis supported rs439401 (APOE regulatory region), and rs2297660 and rs3737983 (... 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
-
Genome
hg19
Position
chr1:53,716,416-53,716,416
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
83.33
Standard deviation of sample read depth (HGVD)
35.10
Number of reference allele (HGVD)
688
Number of alternative allele (HGVD)
1730
Allele Frequency (HGVD)
0.7154673283705542
Gene Symbol (HGVD)
LRP8
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))
rs3737983
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7057
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11828
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8646
East Asian Allele Counts (ExAC)
6280
East Asian Heterozygous Counts (ExAC)
1752
East Asian Homozygous Counts (ExAC)
2264
East Asian Allele Frequency (ExAC)
0.7263474439046959
Chromosome Counts in All Race (ExAC)
121364
Allele Counts in All Race (ExAC)
48730
Heterozygous Counts in All Race (ExAC)
27252
Homozygous Counts in All Race (ExAC)
10738
Allele Frequency in All Race (ExAC)
0.4015193961965657
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