NM_206933.4(USH2A):c.12394del (p.Leu4132fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 9, 2022
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:: RCV002544691.10

Allele description [Variation Report for NM_206933.4(USH2A):c.12394del (p.Leu4132fs)]

NM_206933.4(USH2A):c.12394del (p.Leu4132fs)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.12394del (p.Leu4132fs)

HGVS:

NC_000001.11:g.215675519del
NG_009497.2:g.752932del
NM_206933.4:c.12394delMANE SELECT
NP_996816.3:p.Leu4132fs
NC_000001.10:g.215848859del
NC_000001.10:g.215848861del
NG_009497.1:g.752880del
NM_206933.2:c.12394del

Protein change:

L4132fs

Links:

dbSNP: rs1558049084

NCBI 1000 Genomes Browser:

rs1558049084

Molecular consequence:

NM_206933.4:c.12394del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens tolloid like 1 (TLL1), transcript variant 1, mRNA
Homo sapiens tolloid like 1 (TLL1), transcript variant 1, mRNA
gi|325652106|ref|NM_012464.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003524072	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 9, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 26445815, 26927203, 10729113, 10909849, 20507924, 25649381, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003524072

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 9, 2022)

germline

clinical testing

PubMed (7)
[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

Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran.

Sloan-Heggen CM, Babanejad M, Beheshtian M, Simpson AC, Booth KT, Ardalani F, Frees KL, Mohseni M, Mozafari R, Mehrjoo Z, Jamali L, Vaziri S, Akhtarkhavari T, Bazazzadegan N, Nikzat N, Arzhangi S, Sabbagh F, Otukesh H, Seifati SM, Khodaei H, Taghdiri M, Meyer NC, et al.

J Med Genet. 2015 Dec;52(12):823-9. doi: 10.1136/jmedgenet-2015-103389. Epub 2015 Oct 7.

PubMed [citation]

PMID:: 26445815
PMCID:: PMC4733363

Visual Prognosis in USH2A-Associated Retinitis Pigmentosa Is Worse for Patients with Usher Syndrome Type IIa Than for Those with Nonsyndromic Retinitis Pigmentosa.

Pierrache LH, Hartel BP, van Wijk E, Meester-Smoor MA, Cremers FP, de Baere E, de Zaeytijd J, van Schooneveld MJ, Cremers CW, Dagnelie G, Hoyng CB, Bergen AA, Leroy BP, Pennings RJ, van den Born LI, Klaver CC.

Ophthalmology. 2016 May;123(5):1151-60. doi: 10.1016/j.ophtha.2016.01.021. Epub 2016 Feb 27.

PubMed [citation]

PMID:: 26927203

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003524072.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with clinical features of USH2A-related conditions (PMID: 26445815, 26927203). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu4132Trpfs*35) 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).

#	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: Nov 3, 2024

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