NM_206933.4(USH2A):c.5581G>A (p.Gly1861Ser) AND not provided

Clinical significance:Pathogenic (Last evaluated: Oct 8, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001214945.2

Allele description [Variation Report for NM_206933.4(USH2A):c.5581G>A (p.Gly1861Ser)]

NM_206933.4(USH2A):c.5581G>A (p.Gly1861Ser)

Genes:
USH2A-AS2:USH2A antisense RNA 2 [Gene - HGNC]
USH2A:usherin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_206933.4(USH2A):c.5581G>A (p.Gly1861Ser)
Other names:
NM_206933.2(USH2A):c.5581G>A(p.Gly1861Ser); NM_206933.2(USH2A):c.5581G>A
HGVS:
  • NC_000001.11:g.216073292C>T
  • NG_009497.1:g.355105G>A
  • NG_009497.2:g.355157G>A
  • NM_206933.4:c.5581G>AMANE SELECT
  • NP_996816.3:p.Gly1861Ser
  • NC_000001.10:g.216246634C>T
  • NM_206933.2:c.5581G>A
  • O75445:p.Gly1861Ser
  • c.5581G>A
Protein change:
G1861S
Links:
UniProtKB: O75445#VAR_072008; dbSNP: rs375668376
NCBI 1000 Genomes Browser:
rs375668376
Molecular consequence:
  • NM_206933.4:c.5581G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001386654Invitaecriteria provided, single submitter
Pathogenic
(Oct 8, 2020)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Targeted exome sequencing identified novel USH2A mutations in Usher syndrome families.

Huang XF, Xiang P, Chen J, Xing DJ, Huang N, Min Q, Gu F, Tong Y, Pang CP, Qu J, Jin ZB.

PLoS One. 2013 May 30;8(5):e63832. doi: 10.1371/journal.pone.0063832. Print 2013.

PubMed [citation]
PMID:
23737954
PMCID:
PMC3667821

Whole-exome sequencing identifies USH2A mutations in a pseudo-dominant Usher syndrome family.

Zheng SL, Zhang HL, Lin ZL, Kang QY.

Int J Mol Med. 2015 Oct;36(4):1035-41. doi: 10.3892/ijmm.2015.2322. Epub 2015 Aug 24.

PubMed [citation]
PMID:
26310143
PMCID:
PMC4564089
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001386654.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change replaces glycine with serine at codon 1861 of the USH2A protein (p.Gly1861Ser). The glycine residue is highly conserved and there is a small physicochemical difference between glycine and serine. This variant is present in population databases (rs375668376, ExAC 0.01%). This variant has been observed in individual(s) with Usher syndrome (PMID: 23737954, 26310143, 26338283, 25356976, 29625443). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 48535). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C5. The serine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. For these reasons, this variant has been classified as Pathogenic. 5

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 30, 2021

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