NM_206933.4(USH2A):c.10699del (p.Gln3566_Leu3567insTer) AND Usher syndrome type 2A

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Nov 4, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001089579.6

Allele description [Variation Report for NM_206933.4(USH2A):c.10699del (p.Gln3566_Leu3567insTer)]

NM_206933.4(USH2A):c.10699del (p.Gln3566_Leu3567insTer)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.10699del (p.Gln3566_Leu3567insTer)

HGVS:

NC_000001.11:g.215782083del
NG_009497.2:g.646366del
NM_206933.4:c.10699delMANE SELECT
NP_996816.3:p.Gln3566_Leu3567insTer
NC_000001.10:g.215955425del
NG_009497.1:g.646314del
NM_206933.2:c.10699delC
NM_206933.4:c.10699delCMANE SELECT

Links:

dbSNP: rs1661659605

NCBI 1000 Genomes Browser:

rs1661659605

Molecular consequence:

NM_206933.4:c.10699del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Usher syndrome type 2A
Synonyms:: USHER SYNDROME, TYPE IIA; RETINAL DISEASE IN USHER SYNDROME TYPE IIA, MODIFIER OF
Identifiers:: MONDO: MONDO:0010169; MedGen: C1848634; Orphanet: 231178; Orphanet: 886; OMIM: 276901

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001244814	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 29, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002088350	Natera, Inc.	no assertion criteria provided	Pathogenic (Aug 10, 2020)	germline	clinical testing
SCV004101729	DBGen Ocular Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 1, 2020)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004182190	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 4, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001244814.1

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

Description

A heterozygous nonsense variant, NM_206933.2(USH2A):c.10699delC, has been identified in exon 54 of 72 of the USH2A gene. The variant is predicted to result in a premature stop codon at position 3567 of the protein (NP_996816.2(USH2A):p.(Leu3567*)). This variant is predicted to result in loss of protein function either through truncation (including the loss of multiple domains) or nonsense-mediated decay. The variant is absent in population databases (gnomAD). It has not been previously reported in clinical cases however, multiple truncating variants (upstream and downstream) have previously been reported as pathogenic (ClinVar). Based on the information available at the time of curation and in conjunction with the c.2299delG variant, this variant has been classified as PATHOGENIC.NB: This variant has been reclassified as pathogenic due to confirmed compound heterozygous inheritance, consistent with Usher syndrome.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002088350.1

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

#	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

From DBGen Ocular Genomics, SCV004101729.1

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

Description

Class 5 ACMG Guidelines, 2015

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	Blood	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004182190.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

ClinVar

Relating variation to medicine