NM_206933.4(USH2A):c.3883C>T (p.Arg1295Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 9, 2024
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:: RCV001047995.15

Allele description [Variation Report for NM_206933.4(USH2A):c.3883C>T (p.Arg1295Ter)]

NM_206933.4(USH2A):c.3883C>T (p.Arg1295Ter)

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.3883C>T (p.Arg1295Ter)

HGVS:

NC_000001.11:g.216198513G>A
NG_009497.2:g.229936C>T
NM_007123.6:c.3883C>T
NM_206933.4:c.3883C>TMANE SELECT
NP_009054.6:p.Arg1295Ter
NP_996816.2:p.Arg1295Ter
NP_996816.3:p.Arg1295Ter
NC_000001.10:g.216371855G>A
NG_009497.1:g.229884C>T
NM_206933.2:c.3883C>T
NM_206933.3:c.3883C>T

Protein change:

R1295*

Links:

dbSNP: rs764797292

NCBI 1000 Genomes Browser:

rs764797292

Molecular consequence:

NM_007123.6:c.3883C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_206933.4:c.3883C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Apodemus agrarius isolate ZY10 D-loop, partial sequence; mitochondrial
Apodemus agrarius isolate ZY10 D-loop, partial sequence; mitochondrial
gi|1756090634|gb|MK329823.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001211984	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 9, 2024)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 10729113, 20507924, 25649381, 10909849, 22004887, 24160897, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001211984

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 9, 2024)

germline

clinical testing

PubMed (7)
[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

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

Novel mutations in the long isoform of the USH2A gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa.

McGee TL, Seyedahmadi BJ, Sweeney MO, Dryja TP, Berson EL.

J Med Genet. 2010 Jul;47(7):499-506. doi: 10.1136/jmg.2009.075143. Epub 2010 May 27.

PubMed [citation]

PMID:: 20507924
PMCID:: PMC3070405

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001211984.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This sequence change creates a premature translational stop signal (p.Arg1295*) 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). This variant is present in population databases (rs764797292, gnomAD 0.002%). This premature translational stop signal has been observed in individuals with Usher syndrome (PMID: 10909849, 22004887, 24160897). ClinVar contains an entry for this variant (Variation ID: 556829). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#	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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