chr1:43392819:G>T Detail (hg19) (SLC2A1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:43,392,819-43,392,819 |
| hg38 | chr1:42,927,148-42,927,148 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_006516.2:c.1372C>A | NP_006507.2:p.Arg458= |
| Ensemble | ENST00000426263.10:c.1372C>A | ENST00000426263.10:p.Arg458= |
| ENST00000674765.1:c.1030-291C>A |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.043 |
| ToMMo:0.048 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.036 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2016-01-26 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2023-04-11 | criteria provided, multiple submitters, no conflicts | Encephalopathy due to GLUT1 deficiency |
germline
|
Detail |
|
Benign
|
2023-04-11 | criteria provided, multiple submitters, no conflicts | dystonia 9 |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, single submitter | GLUT1 deficiency syndrome 1, autosomal recessive |
germline
|
Detail |
|
Benign
|
2022-06-01 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2016-06-20 | criteria provided, single submitter | Inborn genetic diseases |
germline
|
Detail |
|
Benign
|
2023-04-11 | criteria provided, single submitter | Childhood onset GLUT1 deficiency syndrome 2 |
germline
|
Detail |
|
Benign
|
2023-04-11 | criteria provided, single submitter | Epilepsy, idiopathic generalized, susceptibility to, 12 |
germline
|
Detail |
|
Benign
|
2023-04-11 | criteria provided, single submitter | Hereditary cryohydrocytosis with reduced stomatin |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.240 | Epilepsy, idiopathic generalized, susceptibility to, 12 | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND not specified | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND Encephalopathy due to GLUT1 deficiency | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND Dystonia 9 | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND GLUT1 deficiency syndrome 1, autosomal recessive | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND not provided | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND Inborn genetic diseases | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND Childhood onset GLUT1 deficiency syndrome 2 | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND Epilepsy, idiopathic generalized, susceptibility to, 1... | ClinVar | Detail |
| NM_006516.4(SLC2A1):c.1372C>A (p.Arg458=) AND Hereditary cryohydrocytosis with reduced stomatin | 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
- rs13306758 dbSNP
- Genome
- hg19
- Position
- chr1:43,392,819-43,392,819
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 97.08
- Standard deviation of sample read depth (HGVD)
- 42.12
- Number of reference allele (HGVD)
- 2317
- Number of alternative allele (HGVD)
- 103
- Allele Frequency (HGVD)
- 0.04256198347107438
- Gene Symbol (HGVD)
- SLC2A1
- 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))
- rs13306758
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0478
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 801
- 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)
- 311
- East Asian Heterozygous Counts (ExAC)
- 309
- East Asian Homozygous Counts (ExAC)
- 1
- East Asian Allele Frequency (ExAC)
- 0.035962072155411653
- Chromosome Counts in All Race (ExAC)
- 121344
- Allele Counts in All Race (ExAC)
- 356
- Heterozygous Counts in All Race (ExAC)
- 352
- Homozygous Counts in All Race (ExAC)
- 2
- Allele Frequency in All Race (ExAC)
- 0.0029338080168776373
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