NC_000001.10:g.(?_216011333)_(216040512_?)del AND Usher syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 19, 2020
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:: RCV001449694.4

Allele description [Variation Report for NC_000001.10:g.(?_216011333)_(216040512_?)del]

NC_000001.10:g.(?_216011333)_(216040512_?)del

Gene:: USH2A:usherin [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 1q41
Genomic location:: Chr1: 216011333 - 216040512 (on Assembly GRCh37)
Preferred name:: NC_000001.10:g.(?_216011333)_(216040512_?)del
HGVS:: NC_000001.10:g.(?_216011333)_(216040512_?)del
This HGVS expression did not pass validation
Observations:: 1

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
SCV001652946	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely pathogenic (Jun 19, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001652946

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely pathogenic
(Jun 19, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV001652946.1

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

Description

The deletion of exons 43-47 in USH2A has not been previously reported in individuals with Usher syndrome and has not been observed in population studies such as the Database of Genomic Variants or ExAC. Please note that exact breakpoints could not be determined due to limitations of the testing methodology. This deletion is in-frame and removes 4% (689 of 15609 nucleotides) of the coding sequence. Several smaller deletions impacting exons encompassed by this deletion have been reported in individuals with Usher syndrome and/or hearing loss. In summary, while additional evidence is needed to confirm its impact, the variant is likely pathogenic. ACMG/AMP criteria applied: PVS1_Strong, PM2.

#	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		1	not provided	1	not provided

Last Updated: Dec 24, 2022

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