ClinVar Genomic variation as it relates to human health
NM_004004.6(GJB2):c.249C>G (p.Phe83Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_004004.6(GJB2):c.249C>G (p.Phe83Leu)
Variation ID: 44732 Accession: VCV000044732.41
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 13q12.11 13: 20189333 (GRCh38) [ NCBI UCSC ] 13: 20763472 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jan 31, 2015 Oct 8, 2024 Jan 31, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_004004.6:c.249C>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_003995.2:p.Phe83Leu missense NC_000013.11:g.20189333G>C NC_000013.10:g.20763472G>C NG_008358.1:g.8643C>G LRG_1350:g.8643C>G LRG_1350t1:c.249C>G LRG_1350p1:p.Phe83Leu P29033:p.Phe83Leu - Protein change
- F83L
- Other names
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- Canonical SPDI
- NC_000013.11:20189332:G:C
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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functionally_normal; Sequence Ontology [ SO:0002219]
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00040 (C)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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1000 Genomes Project 0.00040
1000 Genomes Project 30x 0.00047
Trans-Omics for Precision Medicine (TOPMed) 0.00147
The Genome Aggregation Database (gnomAD) 0.00150
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00238
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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GJB2 | Dosage sensitivity unlikely | No evidence available |
GRCh38 GRCh37 |
570 | 637 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Benign (2) |
criteria provided, multiple submitters, no conflicts
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Feb 11, 2015 | RCV000037828.18 | |
Likely benign (3) |
criteria provided, multiple submitters, no conflicts
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May 9, 2017 | RCV000175768.9 | |
Likely benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV000274859.5 | |
Likely benign (1) |
criteria provided, single submitter
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Apr 27, 2017 | RCV000374467.5 | |
Benign/Likely benign (7) |
criteria provided, multiple submitters, no conflicts
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Jan 31, 2024 | RCV000757329.21 | |
Likely benign (1) |
criteria provided, single submitter
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Aug 31, 2020 | RCV001257146.1 | |
Likely benign (1) |
criteria provided, single submitter
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Nov 1, 2021 | RCV002504896.1 | |
GJB2-related disorder
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Likely benign (1) |
no assertion criteria provided
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Feb 28, 2020 | RCV004534805.2 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Benign
(Jun 26, 2012)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000061490.5
First in ClinVar: May 03, 2013 Last updated: Jan 31, 2015 |
Comment:
Phe83Leu in exon 2 of GJB2: This variant is not expected to have clinical signif icance because it has been identified in 0.3% (28/8572) of … (more)
Phe83Leu in exon 2 of GJB2: This variant is not expected to have clinical signif icance because it has been identified in 0.3% (28/8572) of European American chr omosomes and 0.07% (3/4403) of African American chromosomes from a broad populat ion by the NHLBI Exome sequencing project (http://evs.gs.washington.edu/EVS/; db SNP rs111033218). In addition, this has been observed at equal frequencies in af fected individuals and controls (Scott 1998, Heathcote 2000, Prasad 2000, Rabion et 2000, Pandya 2003, Bruzzone 2003, Frei 2004, Roux 2004, Sinnathuray 2004, Che ng 2005, Santos 2005, Frei 2006, Tang 2006, Ramsebner 2007, Ross 2007, Picotti 2 009, Lee 2009, Kimani 2010). Furthermore, functional studies revealed that the v ariant protein behaves similar to that of the wild type protein (Bruzzone 2003). (less)
Number of individuals with the variant: 16
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Likely benign
(Feb 18, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Athena Diagnostics
Accession: SCV001143663.1
First in ClinVar: Jan 18, 2020 Last updated: Jan 18, 2020 |
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Likely benign
(Nov 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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Mutilating keratoderma
Autosomal dominant keratitis-ichthyosis-hearing loss syndrome Palmoplantar keratoderma-deafness syndrome Knuckle pads, deafness AND leukonychia syndrome Autosomal recessive nonsyndromic hearing loss 1A X-linked mixed hearing loss with perilymphatic gusher Autosomal dominant nonsyndromic hearing loss 3A Ichthyosis, hystrix-like, with hearing loss
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002808036.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Likely benign
(Jul 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000977443.3
First in ClinVar: Aug 26, 2019 Last updated: Mar 04, 2023 |
Comment:
This variant is associated with the following publications: (PMID: 22995991, 9600457, 26778469, 30828346, 25262649, 20956747, 15070423, 12505163, 24158611, 20981092, 12325027, 25388846, 30245029, 33096615)
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Likely benign
(May 09, 2017)
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criteria provided, single submitter
Method: clinical testing
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Deafness, autosomal recessive 1A
Affected status: yes, no
Allele origin:
germline
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Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia
Accession: SCV000599739.1
First in ClinVar: Sep 19, 2017 Last updated: Sep 19, 2017 |
Observation 1:
Number of individuals with the variant: 2
Observation 2:
Number of individuals with the variant: 1
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Benign
(Feb 11, 2015)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000227323.5
First in ClinVar: Jun 28, 2015 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 2
Sex: mixed
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Likely benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Autosomal dominant nonsyndromic hearing loss 3A
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000383024.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
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Likely benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Ichthyosis, hystrix-like, with hearing loss
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000383022.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
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Likely benign
(Apr 27, 2017)
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criteria provided, single submitter
Method: clinical testing
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Autosomal recessive nonsyndromic hearing loss 1A
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000383021.3
First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. (less)
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Likely benign
(Aug 31, 2020)
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criteria provided, single submitter
Method: clinical testing
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Nonsyndromic hearing loss and deafness
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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INGEBI, INGEBI / CONICET
Accession: SCV001433662.1
First in ClinVar: Sep 27, 2020 Last updated: Sep 27, 2020 |
Comment:
Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of c.249C>G variant (p.Phe83Leu) in GJB2 gene is 0,28% (404/ … (more)
Based on ACMG/AMP guidelines and Hearing Loss Expert Panel specific criteria: the filtering allele frequency of c.249C>G variant (p.Phe83Leu) in GJB2 gene is 0,28% (404/ 29116 European non-Finnish chromosomes with 95% CI) from Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which meets the allele frequency threshold defined by the ClinGen Hearing Loss Expert Panel for considering supporting evidence against pathogenicity for autosomal recessive hearing loss variants (BS1_Supporting). The p.Phe83Leu change has been identified in trans with a pathogenic dominant variant in a family case with KID syndrome applying to BP2 rule (PMID: 10633135). Functional studies demonstrated that p.Phe83Leu mutant generated electrical conductance like the wild type in Xenopus laevis oocytes. Besides, 100% of dye transfer was detected in HeLa cells expressing p.Phe83Leu mutant (PMID:12505163). Hence, this evidence meets BS3_Sup standard. Therefore, this variant meets criteria to be classified as likely benign for autosomal recessive non-syndromic hearing loss: (BS1_Supporting, BP2 and BS3_Supporting). (less)
Number of individuals with the variant: 2
Clinical Features:
Prelingual profound hearing loss (present)
Sex: mixed
Ethnicity/Population group: Caucasian
Geographic origin: Argentina
Tissue: blood
Secondary finding: no
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Benign
(Sep 13, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885512.4
First in ClinVar: Feb 18, 2019 Last updated: Mar 04, 2023 |
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Likely benign
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001032575.6
First in ClinVar: Dec 17, 2019 Last updated: Feb 14, 2024 |
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Likely benign
(-)
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criteria provided, single submitter
Method: not provided
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005219303.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
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Likely benign
(Feb 28, 2020)
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no assertion criteria provided
Method: clinical testing
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GJB2-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004748349.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
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Benign
(Apr 19, 2020)
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no assertion criteria provided
Method: clinical testing
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Autosomal recessive deafness type 1A
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV001453870.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001957893.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Likely benign
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001965984.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021 |
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
Help
A brief description of the result of this method for this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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functionally_normal
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INGEBI, INGEBI / CONICET
Accession: SCV001433662.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Sensorineural hearing loss in a pediatric population: association of congenital cytomegalovirus infection with intracranial abnormalities. | Kimani JW | Archives of otolaryngology--head & neck surgery | 2010 | PMID: 20956747 |
Audiologic and temporal bone imaging findings in patients with sensorineural hearing loss and GJB2 mutations. | Lee KH | The Laryngoscope | 2009 | PMID: 19235794 |
Correlation between GJB2 mutations and audiological deficits: personal experience. | Picciotti PM | European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery | 2009 | PMID: 18668259 |
High incidence of GJB2 mutations during screening of newborns for hearing loss in Austria. | Ramsebner R | Ear and hearing | 2007 | PMID: 17485979 |
GJB2 and GJB6 mutations in children with congenital cytomegalovirus infection. | Ross SA | Pediatric research | 2007 | PMID: 17426645 |
DNA sequence analysis of GJB2, encoding connexin 26: observations from a population of hearing impaired cases and variable carrier rates, complex genotypes, and ethnic stratification of alleles among controls. | Tang HY | American journal of medical genetics. Part A | 2006 | PMID: 17041943 |
Connexin 26 variants and auditory neuropathy/dys-synchrony among children in schools for the deaf. | Cheng X | American journal of medical genetics. Part A | 2005 | PMID: 16222667 |
GJB2 mutations in hearing impairment: identification of a broad clinical spectrum for improved genetic counseling. | Frei K | The Laryngoscope | 2005 | PMID: 15744158 |
Hearing impairment in Dutch patients with connexin 26 (GJB2) and connexin 30 (GJB6) mutations. | Santos RL | International journal of pediatric otorhinolaryngology | 2005 | PMID: 15656949 |
Auditory perception and speech discrimination after cochlear implantation in patients with connexin 26 (GJB2) gene-related deafness. | Sinnathuray AR | Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology | 2004 | PMID: 15547422 |
Screening for monogenetic del(GJB6-D13S1830) and digenic del(GJB6-D13S1830)/GJB2 patterns of inheritance in deaf individuals from Eastern Austria. | Frei K | Hearing research | 2004 | PMID: 15464308 |
Molecular epidemiology of DFNB1 deafness in France. | Roux AF | BMC medical genetics | 2004 | PMID: 15070423 |
Frequency and distribution of GJB2 (connexin 26) and GJB6 (connexin 30) mutations in a large North American repository of deaf probands. | Pandya A | Genetics in medicine : official journal of the American College of Medical Genetics | 2003 | PMID: 12865758 |
Loss-of-function and residual channel activity of connexin26 mutations associated with non-syndromic deafness. | Bruzzone R | FEBS letters | 2003 | PMID: 12505163 |
Genetic testing for hereditary hearing loss: connexin 26 (GJB2) allele variants and two novel deafness-causing mutations (R32C and 645-648delTAGA). | Prasad S | Human mutation | 2000 | PMID: 11102979 |
Molecular basis of childhood deafness resulting from mutations in the GJB2 (connexin 26) gene. | Rabionet R | Human genetics | 2000 | PMID: 10982180 |
A connexin 26 mutation causes a syndrome of sensorineural hearing loss and palmoplantar hyperkeratosis (MIM 148350). | Heathcote K | Journal of medical genetics | 2000 | PMID: 10633135 |
Identification of mutations in the connexin 26 gene that cause autosomal recessive nonsyndromic hearing loss. | Scott DA | Human mutation | 1998 | PMID: 9600457 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GJB2 | - | - | - | - |
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Text-mined citations for rs111033218 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.