chr1:66102257:G>A Detail (hg19) (LEPR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:66,102,257-66,102,257 |
| hg38 | chr1:65,636,574-65,636,574 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_002303.5:c.3057G>A | NP_002294.2:p.Pro1019= |
| Ensemble | ENST00000349533.11:c.3057G>A | ENST00000349533.11:p.Pro1019= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.854 |
| ToMMo:0.859 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.871 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2018-01-13 | criteria provided, multiple submitters, no conflicts | Obesity due to leptin receptor gene deficiency |
germline
|
Detail |
|
Benign
|
2016-06-14 | criteria provided, single submitter | Monogenic Non-Syndromic Obesity |
germline
|
Detail |
|
Benign
|
2017-07-26 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.440 | obesity | The aim of this study was to evaluate the effect of the G3057A (rs62589000) LEPR... | BeFree | 20304616 | Detail |
| 0.239 | Diabetes Mellitus, Non-Insulin-Dependent | To investigate the relationship between human leptin receptor (LEPR) gene G3057A... | BeFree | 18713300 | Detail |
| 0.641 | obesity | The G3057A LEPR polymorphism is associated with obesity in Tunisian women. | BeFree | 20304616 | Detail |
| 0.008 | obesity | The aim of this study was to evaluate the effect of the G3057A (rs62589000) LEPR... | BeFree | 20304616 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002303.6(LEPR):c.3057G>A (p.Pro1019=) AND Obesity due to leptin receptor gene deficiency | ClinVar | Detail |
| NM_002303.6(LEPR):c.3057G>A (p.Pro1019=) AND Monogenic Non-Syndromic Obesity | ClinVar | Detail |
| NM_002303.6(LEPR):c.3057G>A (p.Pro1019=) AND not specified | ClinVar | Detail |
| NM_002303.6(LEPR):c.3057G>A (p.Pro1019=) AND not provided | ClinVar | Detail |
| The aim of this study was to evaluate the effect of the G3057A (rs62589000) LEPR polymorphism on obe... | DisGeNET | Detail |
| To investigate the relationship between human leptin receptor (LEPR) gene G3057A polymorphism and ty... | DisGeNET | Detail |
| The G3057A LEPR polymorphism is associated with obesity in Tunisian women. | DisGeNET | Detail |
| The aim of this study was to evaluate the effect of the G3057A (rs62589000) LEPR polymorphism on obe... | 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
- rs1805096 dbSNP
- Genome
- hg19
- Position
- chr1:66,102,257-66,102,257
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 89.45
- Standard deviation of sample read depth (HGVD)
- 45.07
- Number of reference allele (HGVD)
- 353
- Number of alternative allele (HGVD)
- 2067
- Allele Frequency (HGVD)
- 0.8541322314049586
- Gene Symbol (HGVD)
- LEPR
- 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))
- rs1805096
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.8595
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 14406
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8634
- East Asian Allele Counts (ExAC)
- 7517
- East Asian Heterozygous Counts (ExAC)
- 979
- East Asian Homozygous Counts (ExAC)
- 3269
- East Asian Allele Frequency (ExAC)
- 0.8706277507528376
- Chromosome Counts in All Race (ExAC)
- 120424
- Allele Counts in All Race (ExAC)
- 54506
- Heterozygous Counts in All Race (ExAC)
- 27778
- Homozygous Counts in All Race (ExAC)
- 13364
- Allele Frequency in All Race (ExAC)
- 0.4526174184547931
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