chr13:20189282:AT> Detail (hg38) (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 1
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
Links
Type Database ID Link
Gene MIM 121011 OMIM
HGNC 4284 HGNC
Ensembl ENSG00000165474 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv47910879 TogoVar
COSMIC
MONDO
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
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

DescrptionSourceLinks
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
hg38
Position
chr13:20,189,282-20,189,283
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
Genome browser