chr17:42911000:G>T Detail (hg38) (G6PC1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:41,063,017-41,063,017 View the variant detail on this assembly version. |
| hg38 | chr17:42,911,000-42,911,000 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000151.3:c.648G>T | NP_000142.2:p.Leu216= |
| NM_001270397.1:c.*40G>T | ||
| Ensemble | ENST00000253801.7:c.648G>T | ENST00000253801.7:p.Leu216= |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 5 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.002 |
| ToMMo:0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.001 |
Prediction
ClinVar
| Clinical Significance |
Pathogenic
Likely pathogenic
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000174) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000179) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
Likely pathogenic
|
2024-01-28 | criteria provided, multiple submitters, no conflicts | Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
germline
unknown
|
Detail |
|
Pathogenic
|
2022-04-11 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.123 | Glucose-6-phosphate transport defect | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000151.4(G6PC1):c.648G>T (p.Leu216=) AND Glycogen storage disease due to glucose-6-phosphatase de... | ClinVar | Detail |
| NM_000151.4(G6PC1):c.648G>T (p.Leu216=) AND not provided | ClinVar | Detail |
| NA | 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
- rs80356484 dbSNP
- Genome
- hg38
- Position
- chr17:42,911,000-42,911,000
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 175.06
- Standard deviation of sample read depth (HGVD)
- 73.85
- Number of reference allele (HGVD)
- 2414
- Number of alternative allele (HGVD)
- 6
- Allele Frequency (HGVD)
- 0.0024793388429752068
- Gene Symbol (HGVD)
- G6PC
- 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))
- rs80356484
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0013
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 21
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 11
- East Asian Heterozygous Counts (ExAC)
- 11
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.0012710885139819736
- Chromosome Counts in All Race (ExAC)
- 121406
- Allele Counts in All Race (ExAC)
- 11
- Heterozygous Counts in All Race (ExAC)
- 11
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 9.060507717905211E-5
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