chr13:20189349:G> Detail (hg38) (GJB2)

Information

Genome

Assembly Position
hg19 chr13:20,763,488-20,763,488 
hg38 chr13:20,189,349-20,189,349

HGVS

Type Transcript Protein
RefSeq NM_004004.5:c.233delC NP_003995.2:p.Leu79CysfsTer3
Ensemble ENST00000382844.2:c.233delC ENST00000382844.2:p.Leu79CysfsTer3
ENST00000382848.5:c.233delC ENST00000382848.5:p.Leu79CysfsTer3
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.010
ToMMo:0.006
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.005

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 tgv47910914 TogoVar
COSMIC COSM2265391 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 unknown germline inherited maternal Detail
Pathogenic 2009-02-01 no assertion criteria provided Deafness, digenic, GJB2/GJB3 germline Detail
Pathogenic 2013-02-08 criteria provided, single submitter germline Detail
Pathogenic 2018-09-14 reviewed by expert panel Nonsyndromic genetic hearing loss germline Detail
Pathogenic 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Pathogenic 2016-03-08 criteria provided, single submitter Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2016-03-18 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A germline Detail
Pathogenic 2016-03-18 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A germline Detail
Pathogenic 2015-03-20 no assertion criteria provided germline Detail
Pathogenic 2012-02-10 criteria provided, single submitter Rare genetic deafness germline 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
not provided no assertion provided Autosomal recessive nonsyndromic hearing loss 1A unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2022-04-11 criteria provided, single submitter Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Mutilating keratoderma,Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant nonsyndromic hearing loss 3A,Autosomal recessive nonsyndromic hearing loss 1A,palmoplantar keratoderma-deafness syndrome,X-linked mixed hearing loss with perilymphatic gusher unknown Detail
Pathogenic 2023-07-28 no assertion criteria provided autism spectrum disorder unknown Detail
Pathogenic 2023-07-27 criteria provided, single submitter GJB2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.440 DEAFNESS, AUTOSOMAL RECESSIVE 1A (disorder) NA CLINVAR Detail
0.065 Hearing Loss, Mixed Conductive-Sensorineural A total of 199 (19.6%) babies were found to have at least 1 mutated allele on th... BeFree 21811586 Detail
0.065 Hearing Loss, Mixed Conductive-Sensorineural Accordingly, we developed a method for the simultaneous detection of seven mutat... BeFree 23469187 Detail
0.120 DEAFNESS, DIGENIC, GJB2/GJB3 (disorder) NA CLINVAR Detail
0.016 Hearing Loss, Mixed Conductive-Sensorineural Accordingly, we developed a method for the simultaneous detection of seven mutat... BeFree 23469187 Detail
0.065 Hearing Loss, Mixed Conductive-Sensorineural The c.235delC of GJB2 gene is the hotspot mutation of the hearing loss populatio... BeFree 24256046 Detail
0.002 Hearing Loss, Mixed Conductive-Sensorineural Accordingly, we developed a method for the simultaneous detection of seven mutat... BeFree 23469187 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Autosomal recessive nonsyndromic hearing loss 1A ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Deafness, digenic, GJB2/GJB3 ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Hearing impairment ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Nonsyndromic genetic hearing loss ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND not provided ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Autosomal dominant nonsyndromic hearing loss 3A ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Hearing loss ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Rare genetic deafness ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Autosomal recessive nonsyndromic hearing loss 1A ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND Autism spectrum disorder ClinVar Detail
NM_004004.6(GJB2):c.235del (p.Leu79fs) AND GJB2-related disorder ClinVar Detail
NA DisGeNET Detail
A total of 199 (19.6%) babies were found to have at least 1 mutated allele on the NGS for deafness, ... DisGeNET Detail
Accordingly, we developed a method for the simultaneous detection of seven mutations (c.235delC of G... DisGeNET Detail
NA DisGeNET Detail
Accordingly, we developed a method for the simultaneous detection of seven mutations (c.235delC of G... DisGeNET Detail
The c.235delC of GJB2 gene is the hotspot mutation of the hearing loss population in the Silk Road r... DisGeNET Detail
Accordingly, we developed a method for the simultaneous detection of seven mutations (c.235delC of G... 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
rs80338943 dbSNP
Genome
hg38
Position
chr13:20,189,349-20,189,349
Variant Type
snv
Reference Allele
G
Alternative Allele
-
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
150.82
Standard deviation of sample read depth (HGVD)
71.38
Number of reference allele (HGVD)
2396
Number of alternative allele (HGVD)
24
Allele Frequency (HGVD)
0.009917355371900827
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))
rs80338943
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0059
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
99
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8648
East Asian Allele Counts (ExAC)
43
East Asian Heterozygous Counts (ExAC)
43
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0049722479185938945
Chromosome Counts in All Race (ExAC)
121376
Allele Counts in All Race (ExAC)
44
Heterozygous Counts in All Race (ExAC)
44
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.625098866332718E-4
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