chr1:55524237:G>A Detail (hg19) (PCSK9)

Information

Genome

Assembly Position
hg19 chr1:55,524,237-55,524,237
hg38 chr1:55,058,564-55,058,564 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_174936.3:c.1420G>A NP_777596.2:p.Val474Ile
Ensemble ENST00000713786.1:c.1543G>A ENST00000713786.1:p.Val515Ile
ENST00000673903.1:c.1045G>A ENST00000673903.1:p.Val349Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.965
ToMMo:0.969
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.991

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607786 OMIM
HGNC 20001 HGNC
Ensembl ENSG00000169174 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv1591739 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 2017-06-22 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline Detail
Likely benign 2017-04-27 criteria provided, single submitter hypobetalipoproteinemia germline Detail
Benign Likely benign 2024-02-05 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, autosomal dominant, 3 germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
Benign 2015-12-08 criteria provided, single submitter germline Detail
Benign 2023-02-09 no assertion criteria provided familial hypercholesterolemia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.025 Coronary heart disease In the present study, we have determined the relative frequency of the R46L, I47... BeFree 17550346 Detail
0.162 Hypercholesterolemia No association tests were performed for R46L variant because of its very low fre... BeFree 24793346 Detail
0.163 Hypercholesterolemia, Familial In the present study, we have determined the relative frequency of the R46L, I47... BeFree 17550346 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND not specified ClinVar Detail
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND Hypobetalipoproteinemia ClinVar Detail
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND Hypercholesterolemia, autosomal dominant, 3 ClinVar Detail
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND not provided ClinVar Detail
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND Cardiovascular phenotype ClinVar Detail
NM_174936.4(PCSK9):c.1420G>A (p.Val474Ile) AND Familial hypercholesterolemia ClinVar Detail
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variant... DisGeNET Detail
No association tests were performed for R46L variant because of its very low frequency, whereas the ... DisGeNET Detail
In the present study, we have determined the relative frequency of the R46L, I474V and E670G variant... 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
chr1:55,524,237-55,524,237
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
59.97
Standard deviation of sample read depth (HGVD)
27.61
Number of reference allele (HGVD)
85
Number of alternative allele (HGVD)
2327
Allele Frequency (HGVD)
0.964759535655058
Gene Symbol (HGVD)
PCSK9
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))
rs562556
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9687
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16235
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)
8572
East Asian Heterozygous Counts (ExAC)
74
East Asian Homozygous Counts (ExAC)
4249
East Asian Allele Frequency (ExAC)
0.991441128845709
Chromosome Counts in All Race (ExAC)
121300
Allele Counts in All Race (ExAC)
103643
Heterozygous Counts in All Race (ExAC)
14741
Homozygous Counts in All Race (ExAC)
44451
Allele Frequency in All Race (ExAC)
0.8544352844187963
Genome browser