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

Clinical significance:Uncertain significance (Last evaluated: Nov 2, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000281273.5

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:
2

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000711006Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Uncertain significance
(Nov 2, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided62not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000711006.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided6not providednot providedclinical testing PubMed (1)

Description

Variant classified as Uncertain Significance - Favor Benign. The p.Gly461Asp var iant in COL11A2 has been previously reported by our laboratory in 2 families wit h hearing loss; however, it did not segregate with hearing loss in one of the fa milies. This variant has been identified in several populations including in 29/ 34412 Latino chromosomes and 87/126550 of European chromosomes by the Genome Ag gregation Consortium (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs14114079 8). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tool s and conservation analyses do not provide strong support for or against an impa ct to the protein. In summary, while the clinical significance of the p.Gly461As p variant is uncertain, the population frequency and non-segregation data sugges t that it is more likely to be benign. ACMG/AMP criteria applied: BS4, BS1_Suppo rting.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided6not provided2not provided

Last Updated: Aug 18, 2021

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