NM_206933.4(USH2A):c.3788G>A (p.Trp1263Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 14, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000793284.6

Allele description [Variation Report for NM_206933.4(USH2A):c.3788G>A (p.Trp1263Ter)]

NM_206933.4(USH2A):c.3788G>A (p.Trp1263Ter)

Genes:

USH2A-AS1:USH2A antisense RNA 1 [Gene - HGNC]
USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.3788G>A (p.Trp1263Ter)

HGVS:

NC_000001.11:g.216199650C>T
NG_009497.2:g.228799G>A
NM_007123.6:c.3788G>A
NM_206933.4:c.3788G>AMANE SELECT
NP_009054.6:p.Trp1263Ter
NP_996816.3:p.Trp1263Ter
NC_000001.10:g.216372992C>T
NG_009497.1:g.228747G>A
NM_206933.2:c.3788G>A

Protein change:

W1263*

Links:

dbSNP: rs1572042090

NCBI 1000 Genomes Browser:

rs1572042090

Molecular consequence:

NM_007123.6:c.3788G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_206933.4:c.3788G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus synaptotagmin-like 5 (Sytl5), transcript variant 2, mRNA
Mus musculus synaptotagmin-like 5 (Sytl5), transcript variant 2, mRNA
gi|595582194|ref|NM_001290728.1|

Nucleotide
Homo sapiens V-set and transmembrane domain containing 4 (VSTM4), transcript var...
Homo sapiens V-set and transmembrane domain containing 4 (VSTM4), transcript variant 2, mRNA
gi|190341100|ref|NM_144984.2|

Nucleotide
Eleocharis quinqueflora (1)
Taxonomy

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000932632	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 14, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 21686329, 10729113, 10909849, 20507924, 25649381, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000932632

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 14, 2023)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Seven novel mutations in the long isoform of the USH2A gene in Chinese families with nonsyndromic retinitis pigmentosa and Usher syndrome Type II.

Xu W, Dai H, Lu T, Zhang X, Dong B, Li Y.

Mol Vis. 2011;17:1537-52. Epub 2011 Jun 9.

PubMed [citation]

PMID:: 21686329
PMCID:: PMC3115748

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000932632.3

#	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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 640289). This premature translational stop signal has been observed in individual(s) with Usher syndrome type IIA (PMID: 21686329). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp1263*) 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

Last Updated: Sep 29, 2024

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