NM_000393.4(COL5A2):c.2968G>A (p.Gly990Arg) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Feb 24, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000483758.1

Allele description

NM_000393.4(COL5A2):c.2968G>A (p.Gly990Arg)

Gene:
COL5A2:collagen type V alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q32.2
Genomic location:
Preferred name:
NM_000393.4(COL5A2):c.2968G>A (p.Gly990Arg)
HGVS:
  • NC_000002.12:g.189050640C>T
  • NG_011799.2:g.134240G>A
  • NM_000393.4:c.2968G>A
  • NP_000384.2:p.Gly990Arg
  • NC_000002.11:g.189915366C>T
  • NM_000393.3:c.2968G>A
Protein change:
G990R
Links:
dbSNP: rs1040238147
NCBI 1000 Genomes Browser:
rs1040238147
Molecular consequence:
  • NM_000393.4:c.2968G>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
SCV000573632GeneDxcriteria provided, single submitter
Likely pathogenic
(Feb 24, 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, SCV000573632.3

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

Description

The G990R variant in the COL5A2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The G990R variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The G990R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a Glycine residue of a Gly-X-Y repeat within the triple-helical region, at position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret G990R as a strong candidate for a pathogenic variant; however, the possibility that it may be a rare benign variant cannot be completely excluded.

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

Last Updated: Jan 12, 2019

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