chr13:20763421:AT> Detail (hg19) (GJB2)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr13:20,763,421-20,763,422 |
| hg38 | chr13:20,189,282-20,189,283 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_004004.5:c.299_300delAT | NP_003995.2:p.His100ArgfsTer14 |
| Ensemble | ENST00000382844.2:c.299_300delAT | ENST00000382844.2:p.His100ArgfsTer14 |
| ENST00000382848.5:c.299_300delAT | ENST00000382848.5:p.His100ArgfsTer14 |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 2 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:<0.001 |
| ToMMo:<0.001 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:<0.001 |
Prediction
ClinVar
| Clinical Significance |
Pathogenic
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
deafness, autosomal recessive |
germline
|
MGS000001
(TMGS000137) |
Kenjiro Kosaki | Keio University | ||||
|
Pathogenic
|
other |
germline
|
MGS000001
(TMGS000154) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Pathogenic
|
2023-06-02 | criteria provided, multiple submitters, no conflicts | Autosomal recessive nonsyndromic hearing loss 1A |
germline
inherited
unknown
|
Detail |
|
Pathogenic
|
2019-08-12 | criteria provided, single submitter | Rare genetic deafness |
germline
|
Detail |
|
Pathogenic
|
2024-01-16 | criteria provided, multiple submitters, no conflicts | not provided |
germline
unknown
|
Detail |
|
Pathogenic
|
criteria provided, single submitter | Autosomal recessive nonsyndromic hearing loss 1A,Autosomal recessive nonsyndromic hearing loss 1B |
germline
|
Detail | |
|
Pathogenic
|
criteria provided, single submitter | Autosomal recessive nonsyndromic hearing loss 1A,Autosomal recessive nonsyndromic hearing loss 1B |
germline
|
Detail | |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2021-08-19 | criteria provided, single submitter | Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A,Ichthyosis, hystrix-like, with hearing loss,X-linked mixed hearing loss with perilymphatic gusher,palmoplantar keratoderma-deafness syndrome,Knuckle pads, deafness AND leukonychia syndrome,Mutilating keratoderma |
unknown
|
Detail |
|
Pathogenic
|
2023-07-28 | no assertion criteria provided | autism spectrum disorder |
unknown
|
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.299_300del (p.His100fs) AND Autosomal recessive nonsyndromic hearing loss 1A | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND Rare genetic deafness | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND not provided | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND multiple conditions | ClinVar | Detail |
| NM_004004.6(GJB2):c.299_300del (p.His100fs) AND Autism spectrum disorder | 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
- rs111033204 dbSNP
- Genome
- hg19
- Position
- chr13:20,763,421-20,763,422
- Variant Type
- snv
- Reference Allele
- AT
- Alternative Allele
- -
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 194.47
- Standard deviation of sample read depth (HGVD)
- 87.36
- Number of reference allele (HGVD)
- 2418
- Number of alternative allele (HGVD)
- 2
- Allele Frequency (HGVD)
- 8.264462809917355E-4
- 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))
- rs111033204
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0005
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8646
- East Asian Allele Counts (ExAC)
- 5
- East Asian Heterozygous Counts (ExAC)
- 5
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 5.783021050196623E-4
- Chromosome Counts in All Race (ExAC)
- 121252
- Allele Counts in All Race (ExAC)
- 5
- Heterozygous Counts in All Race (ExAC)
- 5
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 4.123643321347277E-5
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