NM_004004.6(GJB2):c.487A>G (p.Met163Val) AND Autosomal dominant nonsyndromic hearing loss 3A

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 8, 2024
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001787816.4

Allele description [Variation Report for NM_004004.6(GJB2):c.487A>G (p.Met163Val)]

NM_004004.6(GJB2):c.487A>G (p.Met163Val)

Gene:

GJB2:gap junction protein beta 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q12.11

Genomic location:

Preferred name:

NM_004004.6(GJB2):c.487A>G (p.Met163Val)

HGVS:

NC_000013.11:g.20189095T>C
NG_008358.1:g.8881A>G
NM_004004.6:c.487A>GMANE SELECT
NP_003995.2:p.Met163Val
LRG_1350t1:c.487A>G
LRG_1350:g.8881A>G
LRG_1350p1:p.Met163Val
NC_000013.10:g.20763234T>C
NM_004004.5:c.487A>G
c.487A>G

Protein change:

M163V

Links:

dbSNP: rs80338949

NCBI 1000 Genomes Browser:

rs80338949

Molecular consequence:

NM_004004.6:c.487A>G - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

loss_of_function_variant [Sequence Ontology: SO:0002054]

Condition(s)

Name:: Autosomal dominant nonsyndromic hearing loss 3A
Synonyms:: Deafness, autosomal dominant 3a
Identifiers:: MONDO: MONDO:0011103; MedGen: C2675750; Orphanet: 90635; OMIM: 601544

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ARL6IP4 ARF like GTPase 6 interacting protein 4 [Homo sapiens]
ARL6IP4 ARF like GTPase 6 interacting protein 4 [Homo sapiens]
Gene ID:51329

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002029256	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005073752	Laboratory of Prof. Karen Avraham, Tel Aviv University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 8, 2024)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002029256

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 5, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005073752

Laboratory of Prof. Karen Avraham, Tel Aviv University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 8, 2024)

germline

research

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
Jewish	germline	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genome-Nilou Lab, SCV002029256.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Prof. Karen Avraham, Tel Aviv University, SCV005073752.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Jewish	1	not provided	not provided	research	PubMed (1)

Description

Pathogenic by Deafness Variation Database and autosomal dominant according to PMID: 37892203

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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