NM_206933.4(USH2A):c.5698T>C (p.Cys1900Arg) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Feb 2, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000756893.2

Allele description [Variation Report for NM_206933.4(USH2A):c.5698T>C (p.Cys1900Arg)]

NM_206933.4(USH2A):c.5698T>C (p.Cys1900Arg)

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.5698T>C (p.Cys1900Arg)
HGVS:
  • NC_000001.11:g.216073175A>G
  • NG_009497.1:g.355222T>C
  • NG_009497.2:g.355274T>C
  • NM_206933.4:c.5698T>CMANE SELECT
  • NP_996816.3:p.Cys1900Arg
  • NC_000001.10:g.216246517A>G
  • NM_206933.2:c.5698T>C
Protein change:
C1900R
Links:
dbSNP: rs201026468
NCBI 1000 Genomes Browser:
rs201026468
Molecular consequence:
  • NM_206933.4:c.5698T>C - 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
SCV000884861ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratoriescriteria provided, single submitter
Uncertain significance
(Feb 2, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884861.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.Cys1900Arg variant has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. A different variant at the same codon (p.Cys1900Gly) was reported in a heterozygous patient with retinitis pigmentosa (Haer-Wigman 2017). The p.Cys1900Arg is absent from general population databases such as 1000 Genomes, NHLBI GO Exome Sequencing Project (ESP), and the Genome Aggregation Database (gnomAD). The cysteine at position 1900 is moderately conserved considering 12 species (Alamut v2.10) and computational analyses of the effects of the p.Cys1900Arg variant on protein structure and function provide conflicting results (SIFT: tolerated, MutationTaster: disease causing, PolyPhen-2: probably damaging). Altogether, there is not enough evidence to classify the p.Cys1900Arg variant with certainty.

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

Last Updated: Nov 27, 2021

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