NM_206933.4(USH2A):c.12497_13811+148del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 1, 2019
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:: RCV001207422.1

Allele description

NM_206933.4(USH2A):c.12497_13811+148del

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.12497_13811+148del

HGVS:

NC_000001.11:g.215673952_215675414del
NC_000001.11:g.215673953_215675415del
NG_009497.1:g.752983_754445del
NG_009497.2:g.753035_754497del
NM_206933.4:c.12497_13811+148delMANE SELECT
NC_000001.10:g.215847295_215848757del
NM_206933.2:c.12497_13811+148del

Molecular consequence:

NM_206933.4:c.12497_13811+148del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001378772	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 1, 2019)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 29588463, 28944237, 17085681, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001378772

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 1, 2019)

germline

clinical testing

PubMed (4)
[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

Combining targeted panel-based resequencing and copy-number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies.

Sanchez-Navarro I, R J da Silva L, Blanco-Kelly F, Zurita O, Sanchez-Bolivar N, Villaverde C, Lopez-Molina MI, Garcia-Sandoval B, Tahsin-Swafiri S, Minguez P, Riveiro-Alvarez R, Lorda I, Sanchez-Alcudia R, Perez-Carro R, Valverde D, Liu Y, Tian L, Hakonarson H, Avila-Fernandez A, Corton M, Ayuso C.

Sci Rep. 2018 Mar 27;8(1):5285. doi: 10.1038/s41598-018-23520-1.

PubMed [citation]

PMID:: 29588463
PMCID:: PMC5869593

Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome.

Neuhaus C, Eisenberger T, Decker C, Nagl S, Blank C, Pfister M, Kennerknecht I, Müller-Hofstede C, Charbel Issa P, Heller R, Beck B, Rüther K, Mitter D, Rohrschneider K, Steinhauer U, Korbmacher HM, Huhle D, Elsayed SM, Taha HM, Baig SM, Stöhr H, Preising M, et al.

Mol Genet Genomic Med. 2017 Sep;5(5):531-552. doi: 10.1002/mgg3.312.

PubMed [citation]

PMID:: 28944237
PMCID:: PMC5606877

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001378772.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant results in the deletion of part of exon 63 (c.12497_13811+148del) of the USH2A gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with USH2A-related conditions. This variant disrupts the p.Thr4337 amino acid residue in USH2A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17085681, 29588463, 28944237, Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). For these reasons, this variant has been classified as 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: Apr 23, 2022

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