NM_000495.4(COL4A5):c.4687C>T (p.Arg1563Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jan 25, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000435037.1

Allele description [Variation Report for NM_000495.4(COL4A5):c.4687C>T (p.Arg1563Ter)]

NM_000495.4(COL4A5):c.4687C>T (p.Arg1563Ter)

Gene:
COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq22.3
Genomic location:
Preferred name:
NM_000495.4(COL4A5):c.4687C>T (p.Arg1563Ter)
HGVS:
  • NC_000023.11:g.108692924C>T
  • NG_011977.1:g.258001C>T
  • NM_000495.4:c.4687C>T
  • NM_033380.2:c.4705C>T
  • NP_000486.1:p.Arg1563Ter
  • NP_203699.1:p.Arg1569Ter
  • NC_000023.10:g.107936154C>T
  • NM_000495.3:c.4687C>T
  • NM_033380.1:c.4705C>T
Nucleotide change:
4889C>T
Protein change:
R1563*
Links:
dbSNP: rs104886286
NCBI 1000 Genomes Browser:
rs104886286
Molecular consequence:
  • NM_000495.4:c.4687C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000520870GeneDxcriteria provided, single submitter
Pathogenic
(Jan 25, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000520870.3

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

Description

The R1569X nonsense variant in the COL4A5 gene has been reported previously in association with Alport syndrome, including an apparently de novo occurrence (Zhou et al., 1993; Knebelmann et al., 1996). This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R1569X variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Additionally, functional studies have shown that R1569X prevents the expression of a3, a4, and a5 collagen chains (Kobayashi et al., 2008). Therefore, we consider this variant to be pathogenic.

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

Last Updated: Sep 8, 2018