NM_206933.4(USH2A):c.7168G>T (p.Gly2390Ter) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 18, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001970023.5

Allele description

NM_206933.4(USH2A):c.7168G>T (p.Gly2390Ter)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.7168G>T (p.Gly2390Ter)

HGVS:

NC_000001.11:g.215934748C>A
NG_009497.2:g.493701G>T
NM_206933.4:c.7168G>TMANE SELECT
NP_996816.3:p.Gly2390Ter
NC_000001.10:g.216108090C>A
NG_009497.1:g.493649G>T
NM_206933.2:c.7168G>T
NM_206933.4:c.7168G>T

Protein change:

G2390*

Links:

dbSNP: rs376983577

NCBI 1000 Genomes Browser:

rs376983577

Molecular consequence:

NM_206933.4:c.7168G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002232772	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 3, 2021)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 24944099, 10729113, 10909849, 20507924, 25649381, 28492532
SCV002586942	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 18, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002232772

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 3, 2021)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV002586942

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Apr 18, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Enrichment of LOVD-USHbases with 152 USH2A genotypes defines an extensive mutational spectrum and highlights missense hotspots.

Baux D, Blanchet C, Hamel C, Meunier I, Larrieu L, Faugère V, Vaché C, Castorina P, Puech B, Bonneau D, Malcolm S, Claustres M, Roux AF.

Hum Mutat. 2014 Oct;35(10):1179-86. doi: 10.1002/humu.22608. Epub 2014 Jul 15.

PubMed [citation]

PMID:: 24944099

Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa.

Weston MD, Eudy JD, Fujita S, Yao S, Usami S, Cremers C, Greenberg J, Ramesar R, Martini A, Moller C, Smith RJ, Sumegi J, Kimberling WJ.

Am J Hum Genet. 2000 Apr;66(4):1199-210. Epub 2000 Mar 22. Erratum in: Am J Hum Genet 2000 Jun;66(6):2020. Greenburg J [corrected to Greenberg J].

PubMed [citation]

PMID:: 10729113
PMCID:: PMC1288187

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV002232772.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with Usher syndrome (PMID: 24944099). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly2390*) in the USH2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381).

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

From GeneDx, SCV002586942.2

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 24944099)

#	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		not provided	not provided	not provided	not provided

Last Updated: Feb 14, 2024

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