chr6:31778272:G>A Detail (hg19) (HSPA1L)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:31,778,272-31,778,272 |
| hg38 | chr6:31,810,495-31,810,495 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_005527.3:c.1478C>T | NP_005518.3:p.Thr493Met |
| Ensemble | ENST00000375654.5:c.1478C>T | ENST00000375654.5:p.Thr493Met |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | |
| GWAS entry | 1 |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.922 |
| ToMMo:0.916 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.825 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
biliary cirrhosis, primary |
not provided
|
MGS000089
(TMGS000168) |
Minoru Nakamura Minoru Nakamura |
National Hospital Organization Nagasaki Medical Center National Hospital Organization Nagasaki Medical Center |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2019-10-21 | criteria provided, single submitter | HSPA1L-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Leukemia, Lymphocytic, Acute, L1 | To systematically evaluate their associations with childhood acute lymphoblastic... | BeFree | 20012387 | Detail |
| <0.001 | Leukemia, Lymphocytic, Acute, L1 | To systematically evaluate their associations with childhood acute lymphoblastic... | BeFree | 20012387 | Detail |
| <0.001 | Organ dysfunction syndrome | We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... | BeFree | 24383711 | Detail |
| <0.001 | Organ dysfunction syndrome | We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... | BeFree | 24383711 | Detail |
| <0.001 | Organ dysfunction syndrome | We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... | BeFree | 24383711 | Detail |
| <0.001 | Organ dysfunction syndrome | We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... | BeFree | 24383711 | Detail |
| <0.001 | Organ dysfunction syndrome | We evaluated the role of single nucleotide polymorphisms for five genes: bacteri... | BeFree | 24383711 | Detail |
| 0.007 | Diabetes Mellitus, Insulin-Dependent | NA | GAD | Detail | |
| <0.001 | High altitude pulmonary edema | We focused on 5 common polymorphisms within HSPA1A (rs1043618 and rs1008438), HS... | BeFree | 19351530 | Detail |
| 0.006 | bipolar disorder | We have further studied a previously investigated sample of 187 major depressive... | BeFree | 19582769 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_005527.4(HSPA1L):c.1478C>T (p.Thr493Met) AND HSPA1L-related disorder | ClinVar | Detail |
| To systematically evaluate their associations with childhood acute lymphoblastic leukemia (ALL), we ... | DisGeNET | Detail |
| To systematically evaluate their associations with childhood acute lymphoblastic leukemia (ALL), we ... | DisGeNET | Detail |
| We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... | DisGeNET | Detail |
| We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... | DisGeNET | Detail |
| We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... | DisGeNET | Detail |
| We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... | DisGeNET | Detail |
| We evaluated the role of single nucleotide polymorphisms for five genes: bactericidal permeability i... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| We focused on 5 common polymorphisms within HSPA1A (rs1043618 and rs1008438), HSPA1B (rs1061581 and ... | DisGeNET | Detail |
| We have further studied a previously investigated sample of 187 major depressive disorder (MDD) pati... | 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
- -
- Genome
- hg19
- Position
- chr6:31,778,272-31,778,272
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1172
- Mean of sample read depth (HGVD)
- 205.47
- Standard deviation of sample read depth (HGVD)
- 80.56
- Number of reference allele (HGVD)
- 182
- Number of alternative allele (HGVD)
- 2162
- Allele Frequency (HGVD)
- 0.9223549488054608
- Gene Symbol (HGVD)
- HSPA1L
- 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))
- rs2227956
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.9165
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 15361
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8642
- East Asian Allele Counts (ExAC)
- 7130
- East Asian Heterozygous Counts (ExAC)
- 1208
- East Asian Homozygous Counts (ExAC)
- 2961
- East Asian Allele Frequency (ExAC)
- 0.8250404998842861
- Chromosome Counts in All Race (ExAC)
- 121270
- Allele Counts in All Race (ExAC)
- 104924
- Heterozygous Counts in All Race (ExAC)
- 13614
- Homozygous Counts in All Race (ExAC)
- 45655
- Allele Frequency in All Race (ExAC)
- 0.8652098622907561
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