chr17:12915009:G>A Detail (hg19) (ELAC2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:12,915,009-12,915,009 |
| hg38 | chr17:13,011,692-13,011,692 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_018127.6:c.650C>T | NP_060597.4:p.Ser217Leu |
| NM_173717.1:c.650C>T | NP_776065.1:p.Ser217Leu | |
| NM_001165962.1:c.560-1021C>T |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.032 |
| ToMMo:0.028 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.034 |
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 |
|---|---|---|---|---|---|
Pathogenic
|
2002-01-01 | no assertion criteria provided | Prostate cancer, hereditary, 2 |
germline
|
Detail |
|
Benign
|
2016-01-18 | criteria provided, single submitter | not specified |
germline
|
Detail |
|
Benign
|
2016-02-15 | no assertion criteria provided | not provided |
unknown
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | Combined oxidative phosphorylation defect type 17 |
germline
unknown
|
Detail |
|
Benign
|
2021-09-30 | criteria provided, single submitter | Prostate cancer, hereditary, 2,Combined oxidative phosphorylation defect type 17 |
unknown
|
Detail |
|
Benign
|
2021-09-30 | criteria provided, single submitter | Prostate cancer, hereditary, 2,Combined oxidative phosphorylation defect type 17 |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.240 | Prostate cancer, hereditary, 2 | NA | CLINVAR | Detail | |
| <0.001 | Metastatic Prostate Carcinoma | We examined polymorphisms within ELAC2 (S217L, A541T, E622V), MSR1 (P275A, R293X... | BeFree | 16114055 | Detail |
| <0.001 | Metastatic Prostate Carcinoma | We examined polymorphisms within ELAC2 (S217L, A541T, E622V), MSR1 (P275A, R293X... | BeFree | 16114055 | Detail |
| 0.062 | Malignant neoplasm of prostate | We examined polymorphisms within ELAC2 (S217L, A541T, E622V), MSR1 (P275A, R293X... | BeFree | 16114055 | Detail |
| 0.001 | Hereditary pancreatitis | Furthermore, only the two previously reported missense changes (Ser217Leu and Al... | BeFree | 11254448 | Detail |
| 0.240 | Prostate cancer, hereditary, 2 | Association of HPC2/ELAC2 genotypes and prostate cancer. | UNIPROT | 10986046 | Detail |
| 0.058 | Malignant neoplasm of prostate | Ser217Leu polymorphism of the HPC2/ELAC2 gene associated with prostatic cancer r... | BeFree | 12949798 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_018127.7(ELAC2):c.650C>T (p.Ser217Leu) AND Prostate cancer, hereditary, 2 | ClinVar | Detail |
| NM_018127.7(ELAC2):c.650C>T (p.Ser217Leu) AND not specified | ClinVar | Detail |
| NM_018127.7(ELAC2):c.650C>T (p.Ser217Leu) AND not provided | ClinVar | Detail |
| NM_018127.7(ELAC2):c.650C>T (p.Ser217Leu) AND Combined oxidative phosphorylation defect type 17 | ClinVar | Detail |
| NM_018127.7(ELAC2):c.650C>T (p.Ser217Leu) AND multiple conditions | ClinVar | Detail |
| NM_018127.7(ELAC2):c.650C>T (p.Ser217Leu) AND multiple conditions | ClinVar | Detail |
| NA | DisGeNET | Detail |
| We examined polymorphisms within ELAC2 (S217L, A541T, E622V), MSR1 (P275A, R293X, aIVS5-59c), and RN... | DisGeNET | Detail |
| We examined polymorphisms within ELAC2 (S217L, A541T, E622V), MSR1 (P275A, R293X, aIVS5-59c), and RN... | DisGeNET | Detail |
| We examined polymorphisms within ELAC2 (S217L, A541T, E622V), MSR1 (P275A, R293X, aIVS5-59c), and RN... | DisGeNET | Detail |
| Furthermore, only the two previously reported missense changes (Ser217Leu and Ala541Thr) were identi... | DisGeNET | Detail |
| Association of HPC2/ELAC2 genotypes and prostate cancer. | DisGeNET | Detail |
| Ser217Leu polymorphism of the HPC2/ELAC2 gene associated with prostatic cancer risk in Japanese men. | 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
- rs4792311 dbSNP
- Genome
- hg19
- Position
- chr17:12,915,009-12,915,009
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1205
- Mean of sample read depth (HGVD)
- 56.43
- Standard deviation of sample read depth (HGVD)
- 27.83
- Number of reference allele (HGVD)
- 2333
- Number of alternative allele (HGVD)
- 77
- Allele Frequency (HGVD)
- 0.031950207468879666
- Gene Symbol (HGVD)
- ELAC2
- 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))
- rs4792311
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0279
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 467
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8652
- East Asian Allele Counts (ExAC)
- 292
- East Asian Heterozygous Counts (ExAC)
- 290
- East Asian Homozygous Counts (ExAC)
- 1
- East Asian Allele Frequency (ExAC)
- 0.03374942209893666
- Chromosome Counts in All Race (ExAC)
- 121396
- Allele Counts in All Race (ExAC)
- 32906
- Heterozygous Counts in All Race (ExAC)
- 23100
- Homozygous Counts in All Race (ExAC)
- 4903
- Allele Frequency in All Race (ExAC)
- 0.27106329697848364
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