chr19:11230881:T>C Detail (hg19) (LDLR)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr19:11,230,881-11,230,881 |
hg38 | chr19:11,120,205-11,120,205 View the variant detail on this assembly version. |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_001195800.1:c.1455T>C | NP_001182729.1:p.Val485= |
NM_001195799.1:c.1836T>C | NP_001182728.1:p.Val612= | |
NM_001195803.1:c.1578T>C | NP_001182732.1:p.Val526= |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.177 |
ToMMo:0.175 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.220 |
Prediction
ClinVar
Clinical Significance |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
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2021-06-10 | criteria provided, multiple submitters, no conflicts | Hypercholesterolemia, familial, 1 |
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Detail |
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2018-02-07 | criteria provided, multiple submitters, no conflicts | not specified |
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Detail |
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2024-02-01 | criteria provided, single submitter | familial hypercholesterolemia |
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Detail |
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2023-11-29 | criteria provided, single submitter | not provided |
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Detail |
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2015-12-08 | criteria provided, single submitter |
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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 |
<0.001 | Hashimoto Disease | We analyzed the associations of seven polymorphisms of genes involved in lipid m... | BeFree | 25587205 | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND Hypercholesterolemia, familial, 1 | ClinVar | Detail |
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND not specified | ClinVar | Detail |
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND Familial hypercholesterolemia | ClinVar | Detail |
NM_000527.5(LDLR):c.1959T>C (p.Val653=) AND not provided | ClinVar | Detail |
NM_000527.5(LDLR):c.1959T>C (p.Val653=) 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 |
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
- rs5925 dbSNP
- Genome
- hg19
- Position
- chr19:11,230,881-11,230,881
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 194.75
- Standard deviation of sample read depth (HGVD)
- 87.01
- Number of reference allele (HGVD)
- 1992
- Number of alternative allele (HGVD)
- 428
- Allele Frequency (HGVD)
- 0.1768595041322314
- 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))
- rs5925
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1752
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2936
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8626
- East Asian Allele Counts (ExAC)
- 1902
- East Asian Heterozygous Counts (ExAC)
- 1494
- East Asian Homozygous Counts (ExAC)
- 204
- East Asian Allele Frequency (ExAC)
- 0.22049617435659633
- Chromosome Counts in All Race (ExAC)
- 121264
- Allele Counts in All Race (ExAC)
- 49618
- Heterozygous Counts in All Race (ExAC)
- 28210
- Homozygous Counts in All Race (ExAC)
- 10704
- Allele Frequency in All Race (ExAC)
- 0.4091733737960153
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