NM_004369.4(COL6A3):c.6193G>A (p.Gly2065Ser) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Sep 7, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000050245.9

Allele description

NM_004369.4(COL6A3):c.6193G>A (p.Gly2065Ser)

Gene:
COL6A3:collagen type VI alpha 3 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q37.3
Genomic location:
Preferred name:
NM_004369.4(COL6A3):c.6193G>A (p.Gly2065Ser)
HGVS:
  • NC_000002.12:g.237361138C>T
  • NG_008676.1:g.58070G>A
  • NM_004369.3:c.6193G>A
  • NM_004369.4:c.6193G>AMANE SELECT
  • NM_057166.5:c.4372G>A
  • NM_057167.3:c.5575G>A
  • NM_057167.4:c.5575G>A
  • NP_004360.2:p.Gly2065Ser
  • NP_004360.2:p.Gly2065Ser
  • NP_476507.3:p.Gly1458Ser
  • NP_476508.2:p.Gly1859Ser
  • NP_476508.2:p.Gly1859Ser
  • LRG_473t1:c.6193G>A
  • LRG_473:g.58070G>A
  • LRG_473p1:p.Gly2065Ser
  • NC_000002.11:g.238269781C>T
  • NM_057164.3:c.5692G>A
  • NM_057165.3:c.5593G>A
  • NM_057166.3:c.5590G>A
  • NM_057166.4:c.4372G>A
Protein change:
G1458S
Links:
dbSNP: rs397515332
NCBI 1000 Genomes Browser:
rs397515332
Molecular consequence:
  • NM_004369.3:c.6193G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004369.4:c.6193G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_057166.5:c.4372G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_057167.3:c.5575G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_057167.4:c.5575G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
3

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000331198EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Likely pathogenic
(May 3, 2016)
germlineclinical testing

Citation Link,

SCV000620625GeneDxcriteria provided, single submitter
Likely pathogenic
(Sep 7, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown3not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000331198.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided3not providednot providednot provided

From GeneDx, SCV000620625.2

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

Description

The G2065S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G2065S variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This 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 within the Gly-X-Y motif in the triple helical (TH) domain of collagen VI, a region that is well-conserved across species. Additionally, a different missense variant at the same position (G2065D) has been reported in an individual with Ullrich congenital muscular dystrophy (Pace et al., 2008). In silico analysis predicts this variant is probably damaging to the protein structure/function.

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

Last Updated: Nov 20, 2021

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