NM_206933.4(USH2A):c.7075_7076del (p.Leu2359fs) AND Usher syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 31, 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:: RCV003226420.1

Allele description [Variation Report for NM_206933.4(USH2A):c.7075_7076del (p.Leu2359fs)]

NM_206933.4(USH2A):c.7075_7076del (p.Leu2359fs)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.7075_7076del (p.Leu2359fs)

HGVS:

NC_000001.11:g.215965361_215965362del
NG_009497.2:g.463087_463088del
NM_206933.4:c.7075_7076delMANE SELECT
NP_996816.3:p.Leu2359fs
NC_000001.10:g.216138703_216138704del
NG_009497.1:g.463035_463036del
NM_206933.2:c.7075_7076del
NM_206933.2:c.7075_7076delTT

Protein change:

L2359fs

Links:

dbSNP: rs1667314337

NCBI 1000 Genomes Browser:

rs1667314337

Molecular consequence:

NM_206933.4:c.7075_7076del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Usher syndrome
Synonyms:: Usher Syndromes; Usher's syndrome
Identifiers:: MONDO: MONDO:0019501; MeSH: D052245; MedGen: C0271097; Orphanet: 886; OMIM: PS276900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003922465	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Mar 31, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003922465

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Mar 31, 2023)

germline

clinical testing

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

Citation Link

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

Genetic and clinical findings of panel-based targeted exome sequencing in a northeast Chinese cohort with retinitis pigmentosa.

Sun Y, Li W, Li JK, Wang ZS, Bai JY, Xu L, Xing B, Yang W, Wang ZW, Wang LS, He W, Chen F.

Mol Genet Genomic Med. 2020 Apr;8(4):e1184. doi: 10.1002/mgg3.1184. Epub 2020 Feb 26.

PubMed [citation]

PMID:: 32100970
PMCID:: PMC7196472

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003922465.1

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

Description

Variant summary: USH2A c.7075_7076delTT (p.Leu2359AsnfsX17) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 251282 control chromosomes (gnomAD). c.7075_7076delTT has been reported in the literature in at least one individual affected with retinitis pigmentosa which belongs to the Usher syndrome phenotype spectrum (Sun_2020). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely 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: Feb 20, 2024

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