chr13:20763294:G>A Detail (hg19) (GJB2)

Information

Genome

Assembly Position
hg19 chr13:20,763,294-20,763,294
hg38 chr13:20,189,155-20,189,155 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004004.5:c.427C>T NP_003995.2:p.Arg143Trp
Ensemble ENST00000382844.2:c.427C>T ENST00000382844.2:p.Arg143Trp
ENST00000382848.5:c.427C>T ENST00000382848.5:p.Arg143Trp
Summary

MGeND

Clinical significance Pathogenic
Variant entry 8
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 tgv47910839 TogoVar
COSMIC
MONDO
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 deafness, autosomal recessive 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
Pathogenic 2019-12-24 criteria provided, multiple submitters, no conflicts Autosomal recessive nonsyndromic hearing loss 1A germline inherited unknown Detail
Pathogenic 2013-02-08 criteria provided, single submitter germline Detail
Pathogenic 2019-05-14 criteria provided, single submitter Rare genetic deafness germline Detail
Pathogenic 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2021-08-03 criteria provided, single submitter Knuckle pads, deafness AND leukonychia syndrome,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,X-linked mixed hearing loss with perilymphatic gusher,Mutilating keratoderma,palmoplantar keratoderma-deafness syndrome,Ichthyosis, hystrix-like, with hearing loss,Autosomal recessive nonsyndromic hearing loss 1A,Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2014-10-02 no assertion criteria provided germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2021-12-10 criteria provided, single submitter Autosomal recessive nonsyndromic hearing loss 1A,Ichthyosis, hystrix-like, with hearing loss,Autosomal dominant nonsyndromic hearing loss 3A,Mutilating keratoderma,Autosomal dominant keratitis-ichthyosis-hearing loss syndrome,Knuckle pads, deafness AND leukonychia syndrome,palmoplantar keratoderma-deafness syndrome germline Detail
Pathogenic 2016-01-01 criteria provided, single submitter Autosomal dominant nonsyndromic hearing loss 3A unknown Detail
Pathogenic 2020-08-21 criteria provided, single submitter Nonsyndromic genetic hearing loss germline Detail
not provided no assertion provided Autosomal recessive nonsyndromic hearing loss 1A unknown Detail
Pathogenic 2024-02-03 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
0.345 Sensorineural Hearing Loss (disorder) Further studies are required to determine the exact mechanism by which mutant (V... BeFree 12562518 Detail
0.065 Hearing Loss, Mixed Conductive-Sensorineural It was confirmed that GJB2 mutations are an important cause of hearing loss in t... BeFree 10633133 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Autosomal recessive nonsyndromic hearing loss 1A ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Hearing impairment ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Rare genetic deafness ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND not provided ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Hearing loss ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND multiple conditions ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Autosomal dominant nonsyndromic hearing loss 3A ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Nonsyndromic genetic hearing loss ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND Autosomal recessive nonsyndromic hearing loss 1A ClinVar Detail
NM_004004.6(GJB2):c.427C>T (p.Arg143Trp) AND GJB2-related disorder ClinVar Detail
NA DisGeNET Detail
Further studies are required to determine the exact mechanism by which mutant (V84L), (V95M), and (R... DisGeNET Detail
It was confirmed that GJB2 mutations are an important cause of hearing loss in this population, with... 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
rs80338948 dbSNP
Genome
hg19
Position
chr13:20,763,294-20,763,294
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
192.11
Standard deviation of sample read depth (HGVD)
85.71
Number of reference allele (HGVD)
2416
Number of alternative allele (HGVD)
2
Allele Frequency (HGVD)
8.271298593879239E-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))
rs80338948
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0007
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.317497103128621E-4
Chromosome Counts in All Race (ExAC)
121050
Allele Counts in All Race (ExAC)
20
Heterozygous Counts in All Race (ExAC)
20
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.6522098306484924E-4
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