NM_206933.4(USH2A):c.3266del (p.Leu1089fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 20, 2022
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:: RCV002035429.4

Allele description [Variation Report for NM_206933.4(USH2A):c.3266del (p.Leu1089fs)]

NM_206933.4(USH2A):c.3266del (p.Leu1089fs)

Genes:

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

Variant type:

Deletion

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.3266del (p.Leu1089fs)

HGVS:

NC_000001.11:g.216207325del
NG_009497.2:g.221126del
NM_007123.6:c.3266del
NM_206933.4:c.3266delMANE SELECT
NP_009054.6:p.Leu1089fs
NP_996816.3:p.Leu1089fs
NC_000001.10:g.216380665del
NC_000001.10:g.216380667del
NG_009497.1:g.221074del

Protein change:

L1089fs

Links:

dbSNP: rs2102480814

NCBI 1000 Genomes Browser:

rs2102480814

Molecular consequence:

NM_007123.6:c.3266del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_206933.4:c.3266del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus paroxysmal nonkinesiogenic dyskinesia (Pnkd), transcript variant 2,...
Mus musculus paroxysmal nonkinesiogenic dyskinesia (Pnkd), transcript variant 2, mRNA
gi|87239987|ref|NM_025580.2|

Nucleotide
RN7SL806P RNA, 7SL, cytoplasmic 806, pseudogene [Homo sapiens]
RN7SL806P RNA, 7SL, cytoplasmic 806, pseudogene [Homo sapiens]
Gene ID:106479515

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002234510	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 20, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 10729113, 10909849, 20507924, 25649381, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002234510

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 20, 2022)

germline

clinical testing

PubMed (5)
[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

Identification of novel USH2A mutations: implications for the structure of USH2A protein.

Dreyer B, Tranebjaerg L, Rosenberg T, Weston MD, Kimberling WJ, Nilssen O.

Eur J Hum Genet. 2000 Jul;8(7):500-6.

PubMed [citation]

PMID:: 10909849

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002234510.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1451960). This variant has not been reported in the literature in individuals affected with USH2A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu1089Tyrfs*23) 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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