VCV001723233.2 - ClinVar

NM_206933.4(USH2A):c.3837del (p.Leu1278_Tyr1279insTer)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_206933.4(USH2A):c.3837del (p.Leu1278_Tyr1279insTer)

Variation ID: 1723233 Accession: VCV001723233.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 1q41 1: 216198559 (GRCh38) [ NCBI UCSC ] 1: 216371901 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 19, 2022	Feb 14, 2024	Jul 25, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_206933.4:c.3837del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_996816.3:p.Leu1278_Tyr1279insTer	nonsense
NM_007123.6:c.3837del	NP_009054.6:p.Leu1278_Tyr1279insTer	nonsense
NC_000001.11:g.216198559del
NC_000001.10:g.216371901del
NG_009497.2:g.229890del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000001.11:216198558:G:

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
USH2A		-	-	GRCh38 GRCh37	7071	8566
USH2A-AS1	-	-	-	GRCh38	-	730

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Usher syndrome type 2A	Pathogenic (1)	criteria provided, single submitter	Oct 19, 2022	RCV002308509.1
not provided	Pathogenic (1)	criteria provided, single submitter	Jul 25, 2023	RCV003565515.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Oct 19, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Usher syndrome type 2A (Autosomal recessive inheritance) Affected status: yes Allele origin: unknown	Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen Accession: SCV002585005.1 First in ClinVar: Nov 19, 2022 Last updated: Nov 19, 2022	Comment: The variant results in a reading frame shift leading to a premature stop codon and thus with high probability to loss of function of the … (more) The variant results in a reading frame shift leading to a premature stop codon and thus with high probability to loss of function of the corresponding protein. The variant is not listed in control collectives (gnomAD) and has not yet been described in the ClinVar database or in the literature. In case of stop or nonsense variants in a gene that matches the phenotype, in which "loss of function" changes represent a known pathomechanism, there is a high probability of pathogenetic relevance. The variant was observed in trans with a known pathogenic variant. The variant is currently to be regarded as a "likely pathogenic variant" (ACMG criteria). (less) Age: 20-29 years Sex: male
Pathogenic (Jul 25, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004308852.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Publications: PubMed (4) PubMed: 10729113‚ 10909849‚ 20507924‚ 25649381 Comment: This sequence change creates a premature translational stop signal (p.Tyr1279) in the USH2A gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Tyr1279) 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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with USH2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1723233). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

The variant results in a reading frame shift leading to a premature stop codon and thus with high probability to loss of function of the corresponding protein. The variant is not listed in control collectives (gnomAD) and has not yet been described in the ClinVar database or in the literature. In case of stop or nonsense variants in a gene that matches the phenotype, in which "loss of function" changes represent a known pathomechanism, there is a high probability of pathogenetic relevance. The variant was observed in trans with a known pathogenic variant. The variant is currently to be regarded as a "likely pathogenic variant" (ACMG criteria).

Comment:

This sequence change creates a premature translational stop signal (p.Tyr1279*) 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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with USH2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1723233). For these reasons, this variant has been classified as Pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants.	Lenassi E	European journal of human genetics : EJHG	2015	PMID: 25649381
Novel mutations in the long isoform of the USH2A gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa.	McGee TL	Journal of medical genetics	2010	PMID: 20507924
Identification of novel USH2A mutations: implications for the structure of USH2A protein.	Dreyer B	European journal of human genetics : EJHG	2000	PMID: 10909849
Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa.	Weston MD	American journal of human genetics	2000	PMID: 10729113

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_206933.4(USH2A):c.3837del (p.Leu1278_Tyr1279insTer)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...