NM_206933.4(USH2A):c.3945T>C (p.Asn1315=) AND Usher syndrome type 2A

Germline classification:: Benign (3 submissions)
Last evaluated:: Jul 1, 2021
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:: RCV001100534.15

Allele description [Variation Report for NM_206933.4(USH2A):c.3945T>C (p.Asn1315=)]

NM_206933.4(USH2A):c.3945T>C (p.Asn1315=)

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.3945T>C (p.Asn1315=)

Other names:

p.N1315N:AAT>AAC

HGVS:

NC_000001.11:g.216198451A>G
NG_009497.2:g.229998T>C
NM_007123.6:c.3945T>C
NM_206933.4:c.3945T>CMANE SELECT
NP_009054.6:p.Asn1315=
NP_996816.3:p.Asn1315=
NC_000001.10:g.216371793A>G
NG_009497.1:g.229946T>C
NM_007123.5:c.3945T>C
NM_206933.2:c.3945T>C
NM_206933.3:c.3945T>C
c.3945T>C
p.Asn1315Asn

Links:

dbSNP: rs41303257

NCBI 1000 Genomes Browser:

rs41303257

Molecular consequence:

NM_007123.6:c.3945T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_206933.4:c.3945T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001257059	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 22004887, 11311042, 15241801 Citation Link,
SCV001462272	Natera, Inc.	no assertion criteria provided	Benign (Sep 16, 2020)	germline	clinical testing
SCV001750417	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 1, 2021)	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

SCV001257059

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV001462272

Natera, Inc.

no assertion criteria provided

Benign
(Sep 16, 2020)

germline

clinical testing

SCV001750417

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 1, 2021)

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

Citations

PubMed

Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations.

Garcia-Garcia G, Aparisi MJ, Jaijo T, Rodrigo R, Leon AM, Avila-Fernandez A, Blanco-Kelly F, Bernal S, Navarro R, Diaz-Llopis M, Baiget M, Ayuso C, Millan JM, Aller E.

Orphanet J Rare Dis. 2011 Oct 17;6:65. doi: 10.1186/1750-1172-6-65.

PubMed [citation]

PMID:: 22004887
PMCID:: PMC3207874

Spectrum of mutations in USH2A in British patients with Usher syndrome type II.

Leroy BP, Aragon-Martin JA, Weston MD, Bessant DA, Willis C, Webster AR, Bird AC, Kimberling WJ, Payne AM, Bhattacharya SS.

Exp Eye Res. 2001 May;72(5):503-9.

PubMed [citation]

PMID:: 11311042

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001257059.1

#	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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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., SCV001462272.1

#	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, SCV001750417.1

#	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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