NM_080680.3(COL11A2):c.1382G>A (p.Gly461Asp) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(2) (Last evaluated: May 13, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000725559.3

Allele description [Variation Report for NM_080680.3(COL11A2):c.1382G>A (p.Gly461Asp)]

NM_080680.3(COL11A2):c.1382G>A (p.Gly461Asp)

Gene:
COL11A2:collagen type XI alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.32
Genomic location:
Preferred name:
NM_080680.3(COL11A2):c.1382G>A (p.Gly461Asp)
HGVS:
  • NC_000006.12:g.33179783C>T
  • NG_011589.1:g.17686G>A
  • NM_080679.2:c.1061G>A
  • NM_080680.3:c.1382G>AMANE SELECT
  • NM_080681.3:c.1124G>A
  • NP_542410.2:p.Gly354Asp
  • NP_542411.2:p.Gly461Asp
  • NP_542411.2:p.Gly461Asp
  • NP_542412.2:p.Gly375Asp
  • NC_000006.11:g.33147560C>T
  • NM_080680.2:c.1382G>A
Protein change:
G354D
Links:
dbSNP: rs141140798
NCBI 1000 Genomes Browser:
rs141140798
Molecular consequence:
  • NM_080679.2:c.1061G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080680.3:c.1382G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_080681.3:c.1124G>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
SCV000337783EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Sep 7, 2017)
germlineclinical testing

Citation Link,

SCV000535709GeneDxcriteria provided, single submitter
Uncertain significance
(May 13, 2021)
germlineclinical testing

Citation Link,

SCV001601928Invitaecriteria provided, single submitter
Likely benign
(Oct 29, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000337783.4

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

From GeneDx, SCV000535709.4

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

Description

Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Reported in ClinVar with conflicting interpretations (ClinVar Variant ID# 284958; Landrum et al., 2016)

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

From Invitae, SCV001601928.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 18, 2021

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