chr19:11227602:C>T Detail (hg19) (LDLR)

Information

Genome

Assembly Position
hg19 chr19:11,227,602-11,227,602
hg38 chr19:11,116,926-11,116,926 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001195800.1:c.1269C>T NP_001182729.1:p.Asn423=
NM_001195799.1:c.1650C>T NP_001182728.1:p.Asn550=
NM_001195803.1:c.1392C>T NP_001182732.1:p.Asn464=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.129
ToMMo:0.123
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.176

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606945 OMIM
HGNC 6547 HGNC
Ensembl ENSG00000130164 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61199987 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-12-31 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign Likely benign 2023-03-30 criteria provided, multiple submitters, no conflicts Hypercholesterolemia, familial, 1 germline unknown Detail
Benign 2024-02-01 criteria provided, single submitter familial hypercholesterolemia germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
Benign 2015-12-08 criteria provided, single submitter germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 cerebral infarction The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Ta... BeFree 22621231 Detail
0.018 Cerebrovascular accident The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Ta... BeFree 22621231 Detail
0.291 Hypertensive disease Our results not only demonstrated potential interactions of APOE epsilon2/epsilo... BeFree 18851860 Detail
0.152 Cardiovascular Diseases In a previous study, analysis of the genetic LDLR variant rs688 provided evidenc... BeFree 24295502 Detail
0.035 Alzheimer's disease We previously identified a single nucleotide polymorphism (SNP), rs688:C>T, t... BeFree 20232416 Detail
0.123 Coronary heart disease The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARC... BeFree 20810930 Detail
<0.001 Coronary Arteriosclerosis The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARC... BeFree 20810930 Detail
0.126 coronary artery disease The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARC... BeFree 20810930 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND not specified ClinVar Detail
NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND Hypercholesterolemia, familial, 1 ClinVar Detail
NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND Familial hypercholesterolemia ClinVar Detail
NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND not provided ClinVar Detail
NM_000527.5(LDLR):c.1773C>T (p.Asn591=) AND Cardiovascular phenotype ClinVar Detail
The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Taiwanese population a... DisGeNET Detail
The LDLR analysis based on the haplotypes rs688 and rs5925 was conducted in a Taiwanese population a... DisGeNET Detail
Our results not only demonstrated potential interactions of APOE epsilon2/epsilon3/epsilon4 and LDLR... DisGeNET Detail
In a previous study, analysis of the genetic LDLR variant rs688 provided evidence suggesting that ge... DisGeNET Detail
We previously identified a single nucleotide polymorphism (SNP), rs688:C&gt;T, that modulates LDLR e... DisGeNET Detail
The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (... DisGeNET Detail
The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (... DisGeNET Detail
The aim of this study was to evaluate 3 single nucleotide polymorphisms in SMARCA4-LDLR gene locus (... 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
rs688 dbSNP
Genome
hg19
Position
chr19:11,227,602-11,227,602
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
109.90
Standard deviation of sample read depth (HGVD)
53.94
Number of reference allele (HGVD)
2107
Number of alternative allele (HGVD)
313
Allele Frequency (HGVD)
0.12933884297520662
Gene Symbol (HGVD)
LDLR
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))
rs688
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1233
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2066
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
1525
East Asian Heterozygous Counts (ExAC)
1267
East Asian Homozygous Counts (ExAC)
129
East Asian Allele Frequency (ExAC)
0.1763413506012951
Chromosome Counts in All Race (ExAC)
121396
Allele Counts in All Race (ExAC)
45902
Heterozygous Counts in All Race (ExAC)
26978
Homozygous Counts in All Race (ExAC)
9462
Allele Frequency in All Race (ExAC)
0.37811789515305283
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