chr5:96393270:G>C Detail (hg38) (CAST, PCSK1, LOC101929710)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr5:95,728,974-95,728,974 View the variant detail on this assembly version. |
| hg38 | chr5:96,393,270-96,393,270 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000439.4:c.1993C>G | NP_000430.3:p.Gln665Glu |
| NM_001177875.1:c.1852C>G | NP_001171346.1:p.Gln618Glu | |
| Ensemble | ENST00000311106.8:c.1993C>G | ENST00000311106.8:p.Gln665Glu |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.213 |
| ToMMo:0.210 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.308 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Likely benign
|
2016-06-14 | criteria provided, single submitter | Obesity due to prohormone convertase I deficiency |
germline
|
Detail |
|
Likely benign
|
2016-06-14 | criteria provided, single submitter | Monogenic Non-Syndromic Obesity |
germline
|
Detail |
|
Benign
|
2017-12-19 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.097 | Diabetes Mellitus, Non-Insulin-Dependent | Single nucleotide polymorphisms (SNPs) in PCSK1, namely, rs6234, rs6235, and rs2... | BeFree | 24964673 | Detail |
| <0.001 | Overweight | In this study, we found modest evidence for association of the PCSK1 rs6234 with... | BeFree | 20498726 | Detail |
| 0.230 | obesity | Association of PCSK1 rs6234 with obesity and related traits in a Chinese Han pop... | BeFree | 20498726 | Detail |
| 0.230 | obesity | [Association of PCSK1 rs6234 with obesity and related traits in a Chinese Han po... | GAD | 20498726 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000439.5(PCSK1):c.1993C>G (p.Gln665Glu) AND Obesity due to prohormone convertase I deficiency | ClinVar | Detail |
| NM_000439.5(PCSK1):c.1993C>G (p.Gln665Glu) AND Monogenic Non-Syndromic Obesity | ClinVar | Detail |
| NM_000439.5(PCSK1):c.1993C>G (p.Gln665Glu) AND not specified | ClinVar | Detail |
| NM_000439.5(PCSK1):c.1993C>G (p.Gln665Glu) AND not provided | ClinVar | Detail |
| Single nucleotide polymorphisms (SNPs) in PCSK1, namely, rs6234, rs6235, and rs271939 have been link... | DisGeNET | Detail |
| In this study, we found modest evidence for association of the PCSK1 rs6234 with BMI and overweight ... | DisGeNET | Detail |
| Association of PCSK1 rs6234 with obesity and related traits in a Chinese Han population. | DisGeNET | Detail |
| [Association of PCSK1 rs6234 with obesity and related traits in a Chinese Han population.] | 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
- rs6234 dbSNP
- Genome
- hg38
- Position
- chr5:96,393,270-96,393,270
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1197
- Mean of sample read depth (HGVD)
- 88.76
- Standard deviation of sample read depth (HGVD)
- 38.00
- Number of reference allele (HGVD)
- 1885
- Number of alternative allele (HGVD)
- 509
- Allele Frequency (HGVD)
- 0.21261487050960734
- Gene Symbol (HGVD)
- PCSK1
- Homozygous Counts in All Race (ExAC)
- 4507
- 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))
- rs6234
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.2098
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3517
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8630
- East Asian Allele Counts (ExAC)
- 2662
- East Asian Heterozygous Counts (ExAC)
- 1896
- East Asian Homozygous Counts (ExAC)
- 383
- East Asian Allele Frequency (ExAC)
- 0.30845886442641945
- Chromosome Counts in All Race (ExAC)
- 121318
- Allele Counts in All Race (ExAC)
- 32607
- Heterozygous Counts in All Race (ExAC)
- 23593
- Allele Frequency in All Race (ExAC)
- 0.26877297680476103
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