NM_206933.4(USH2A):c.12284G>A (p.Gly4095Asp) AND Usher syndrome type 2A

Germline classification:: Likely pathogenic (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:: RCV001271125.6

Allele description [Variation Report for NM_206933.4(USH2A):c.12284G>A (p.Gly4095Asp)]

NM_206933.4(USH2A):c.12284G>A (p.Gly4095Asp)

Gene:

USH2A:usherin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_206933.4(USH2A):c.12284G>A (p.Gly4095Asp)

HGVS:

NC_000001.11:g.215680159C>T
NG_009497.2:g.748290G>A
NM_206933.4:c.12284G>AMANE SELECT
NP_996816.2:p.Gly4095Asp
NP_996816.3:p.Gly4095Asp
NC_000001.10:g.215853501C>T
NG_009497.1:g.748238G>A
NM_206933.2:c.12284G>A
NM_206933.3:c.12284G>A

Protein change:

G4095D

Links:

dbSNP: rs759898765

NCBI 1000 Genomes Browser:

rs759898765

Molecular consequence:

NM_206933.4:c.12284G>A - 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

Recent activity

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4-alpha-glucanotransferase [Corynebacterium aurimucosum ATCC 700975]
4-alpha-glucanotransferase [Corynebacterium aurimucosum ATCC 700975]
gi|227454657|gnl|cebbi|cauri_1817|g 33410.1|

Protein
4-Alpha-glucanotransferase [Cupriavidus necator H16]
4-Alpha-glucanotransferase [Cupriavidus necator H16]
gi|113530001|emb|CAJ96348.1|

Protein
4-alpha-glucanotransferase [Bifidobacterium animalis subsp. lactis]
4-alpha-glucanotransferase [Bifidobacterium animalis subsp. lactis]
gi|2079585418|gnl|PRJNA752179|K1717 0|gb|QYU55782.1|

Protein
LOC103976721 [Musa acuminata AAA Group]
LOC103976721 [Musa acuminata AAA Group]
Gene ID:103976721

Gene
TC_RS01805 [Chlamydia muridarum str. Nigg]
TC_RS01805 [Chlamydia muridarum str. Nigg]
Gene ID:1245715

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001451976	Natera, Inc.	no assertion criteria provided	Likely pathogenic (Sep 16, 2020)	germline	clinical testing
SCV002060039	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Nov 16, 2021)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25333064, 32675063, 27460420, 32531858 Citation Link,
SCV004182022	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (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

SCV001451976

Natera, Inc.

no assertion criteria provided

Likely pathogenic
(Sep 16, 2020)

germline

clinical testing

SCV002060039

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Nov 16, 2021)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV004182022

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(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	unknown	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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome.

Krawitz PM, Schiska D, Krüger U, Appelt S, Heinrich V, Parkhomchuk D, Timmermann B, Millan JM, Robinson PN, Mundlos S, Hecht J, Gross M.

Mol Genet Genomic Med. 2014 Sep;2(5):393-401. doi: 10.1002/mgg3.92. Epub 2014 Jun 15.

PubMed [citation]

PMID:: 25333064
PMCID:: PMC4190874

USH2A variants in Chinese patients with Usher syndrome type II and non-syndromic retinitis pigmentosa.

Zhu T, Chen DF, Wang L, Wu S, Wei X, Li H, Jin ZB, Sui R.

Br J Ophthalmol. 2021 May;105(5):694-703. doi: 10.1136/bjophthalmol-2019-315786. Epub 2020 Jul 16.

PubMed [citation]

PMID:: 32675063

See all PubMed Citations (5)

Details of each submission

From Natera, Inc., SCV001451976.1

#	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 Myriad Genetics, Inc., SCV002060039.2

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

Description

NM_206933.2(USH2A):c.12284G>A(G4095D) is a missense variant classified as likely pathogenic in the context of USH2A-related disorders. G4095D has been observed in cases with relevant disease (PMID: 32675063, 25333064, 27460420, 32531858). Functional assessments of this variant are not available in the literature. G4095D has been observed in population frequency databases (gnomAD: AFR 0.01%). In summary, NM_206933.2(USH2A):c.12284G>A(G4095D) is a missense variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV004182022.1

#	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: Oct 13, 2024

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