NM_206933.4(USH2A):c.12299ACA[1] (p.Asn4101del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 7, 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:: RCV002557893.3

Allele description [Variation Report for NM_206933.4(USH2A):c.12299ACA[1] (p.Asn4101del)]

NM_206933.4(USH2A):c.12299ACA[1] (p.Asn4101del)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.12299ACA[1] (p.Asn4101del)

HGVS:

NC_000001.11:g.215675607TGT[1]
NC_000001.11:g.215675607_215675609TGT[1]
NG_009497.2:g.752837ACA[1]
NM_206933.4:c.12299ACA[1]MANE SELECT
NP_996816.3:p.Asn4101del
NC_000001.10:g.215848949TGT[1]
NC_000001.10:g.215848949_215848951del
NG_009497.1:g.752785ACA[1]
NM_206933.2:c.12302_12304del

Protein change:

N4101del

Links:

dbSNP: rs1657997491

NCBI 1000 Genomes Browser:

rs1657997491

Molecular consequence:

NM_206933.4:c.12299ACA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens homeobox B1 (HOXB1), mRNA
Homo sapiens homeobox B1 (HOXB1), mRNA
gi|1519245153|ref|NM_002144.4|

Nucleotide
Leiocottus hirundo NADH dehydrogenase subunit 1 gene, partial cds; mitochondrial
Leiocottus hirundo NADH dehydrogenase subunit 1 gene, partial cds; mitochondrial
gi|155543544|gb|EF521357.1|

Nucleotide
Oligocottus rimensis NADH dehydrogenase subunit 1 gene, partial cds; mitochondri...
Oligocottus rimensis NADH dehydrogenase subunit 1 gene, partial cds; mitochondrial
gi|155543540|gb|EF521355.1|

Nucleotide
Aizoaceae phosphoenolpyruvate carboxylase isoform 1E2 gene, exon 8 and partial c...
Aizoaceae phosphoenolpyruvate carboxylase isoform 1E2 gene, exon 8 and partial cds.
PopSet: 2033629136

PopSet
Homo sapiens chromosome 19 clone CTD-2659N19, complete sequence
Homo sapiens chromosome 19 clone CTD-2659N19, complete sequence
gi|15799583|gnl|lanlchgs|2659N19|gb 8761.6|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003524048	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 7, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27460420, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003524048

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 7, 2022)

germline

clinical testing

PubMed (2)
[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

An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients.

Bonnet C, Riahi Z, Chantot-Bastaraud S, Smagghe L, Letexier M, Marcaillou C, Lefèvre GM, Hardelin JP, El-Amraoui A, Singh-Estivalet A, Mohand-Saïd S, Kohl S, Kurtenbach A, Sliesoraityte I, Zobor D, Gherbi S, Testa F, Simonelli F, Banfi S, Fakin A, Glavač D, Jarc-Vidmar M, et al.

Eur J Hum Genet. 2016 Dec;24(12):1730-1738. doi: 10.1038/ejhg.2016.99. Epub 2016 Jul 27.

PubMed [citation]

PMID:: 27460420
PMCID:: PMC5117943

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003524048.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant, c.12302_12304del, results in the deletion of 1 amino acid(s) of the USH2A protein (p.Asn4101del), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 865868). This variant has been observed in individual(s) with USH2A-related conditions (PMID: 27460420). This variant is not present in population databases (gnomAD no frequency).

#	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: Sep 29, 2024

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