chr13:20189174:G>T Detail (hg38) (GJB2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr13:20,763,313-20,763,313 View the variant detail on this assembly version. |
| hg38 | chr13:20,189,174-20,189,174 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004004.5:c.408C>A | NP_003995.2:p.Tyr136Ter |
| Ensemble | ENST00000382848.5:c.408C>A | ENST00000382848.5:p.Tyr136Ter |
| ENST00000382844.2:c.408C>A | ENST00000382844.2:p.Tyr136Ter |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 6 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.003 |
| ToMMo:0.002 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:[No Data.] |
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
(TMGS000154) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
deafness, autosomal recessive |
germline
|
MGS000001
(TMGS000154) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
deafness, autosomal recessive |
unknown
|
MGS000001
(TMGS000162) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
bilateral sensorineural hearing loss |
unknown
|
MGS000001
(TMGS000162) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Likely pathogenic
|
2014-12-13 | criteria provided, single submitter | Autosomal recessive nonsyndromic hearing loss 1A |
unknown
|
Detail |
|
Pathogenic
|
2017-05-09 | criteria provided, single submitter | Autosomal recessive nonsyndromic hearing loss 1A |
germline
|
Detail |
|
Pathogenic
|
2023-11-28 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.440 | DEAFNESS, AUTOSOMAL RECESSIVE 1A (disorder) | NA | CLINVAR | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_004004.6(GJB2):c.408C>A (p.Tyr136Ter) AND Autosomal recessive nonsyndromic hearing loss 1A | ClinVar | Detail |
| NM_004004.5(GJB2):c.[134G>A;408C>A] AND Autosomal recessive nonsyndromic hearing loss 1A | ClinVar | Detail |
| NM_004004.6(GJB2):c.408C>A (p.Tyr136Ter) 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
- rs786204690 dbSNP
- Genome
- hg38
- Position
- chr13:20,189,174-20,189,174
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- Filtering Status (HGVD)
- LowQual
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 202.40
- Standard deviation of sample read depth (HGVD)
- 90.01
- Number of reference allele (HGVD)
- 2412
- Number of alternative allele (HGVD)
- 8
- Allele Frequency (HGVD)
- 0.003305785123966942
- Gene Symbol (HGVD)
- GJB2
- 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))
- rs786204690
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0018
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 30
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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