NM_206933.4(USH2A):c.3176C>T (p.Pro1059Leu) AND Usher syndrome type 2A

Germline classification:: Uncertain significance (3 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:: RCV001100918.7

Allele description [Variation Report for NM_206933.4(USH2A):c.3176C>T (p.Pro1059Leu)]

NM_206933.4(USH2A):c.3176C>T (p.Pro1059Leu)

Genes:

USH2A-AS1:USH2A antisense RNA 1 [Gene - HGNC]
USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.3176C>T (p.Pro1059Leu)

HGVS:

NC_000001.11:g.216207413G>A
NG_009497.2:g.221036C>T
NM_007123.6:c.3176C>T
NM_206933.4:c.3176C>TMANE SELECT
NP_009054.5:p.Pro1059Leu
NP_009054.6:p.Pro1059Leu
NP_996816.3:p.Pro1059Leu
NC_000001.10:g.216380755G>A
NG_009497.1:g.220984C>T
NM_007123.5:c.3176C>T
NM_206933.2:c.3176C>T

Protein change:

P1059L

Links:

dbSNP: rs547581739

NCBI 1000 Genomes Browser:

rs547581739

Molecular consequence:

NM_007123.6:c.3176C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_206933.4:c.3176C>T - missense variant - [Sequence Ontology: SO:0001583]

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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PREDICTED: Rattus norvegicus NLR family, CARD domain containing 4 (Nlrc4), trans...
PREDICTED: Rattus norvegicus NLR family, CARD domain containing 4 (Nlrc4), transcript variant X4, mRNA
gi|2678950427|ref|XM_063261612.1|

Nucleotide
PREDICTED: Rattus norvegicus NLR family, CARD domain containing 4 (Nlrc4), trans...
PREDICTED: Rattus norvegicus NLR family, CARD domain containing 4 (Nlrc4), transcript variant X5, misc_RNA
gi|2678950429|ref|XR_010052054.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001257464	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 28, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22952768, 15325563, 20507924 Citation Link,
SCV002093938	Natera, Inc.	no assertion criteria provided	Uncertain significance (Jan 20, 2020)	germline	clinical testing
SCV004182368	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 4, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001257464

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 28, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV002093938

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Jan 20, 2020)

germline

clinical testing

SCV004182368

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 4, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.

Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M, D'Amico F, Ziviello C, Simonelli F, Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V.

PLoS One. 2012;7(8):e43799. doi: 10.1371/journal.pone.0043799. Epub 2012 Aug 29.

PubMed [citation]

PMID:: 22952768
PMCID:: PMC3430670

Comprehensive screening of the USH2A gene in Usher syndrome type II and non-syndromic recessive retinitis pigmentosa.

Seyedahmadi BJ, Rivolta C, Keene JA, Berson EL, Dryja TP.

Exp Eye Res. 2004 Aug;79(2):167-73.

PubMed [citation]

PMID:: 15325563

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001257464.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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 Natera, Inc., SCV002093938.1

#	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 Genome-Nilou Lab, SCV004182368.1

#	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: Nov 10, 2024

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