NM_000089.3(COL1A2):c.1350+11A>T AND Osteogenesis imperfecta

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Apr 27, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000029591.2

Allele description [Variation Report for NM_000089.3(COL1A2):c.1350+11A>T]

NM_000089.3(COL1A2):c.1350+11A>T

Gene:
COL1A2:collagen type I alpha 2 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.3
Genomic location:
Preferred name:
NM_000089.3(COL1A2):c.1350+11A>T
HGVS:
  • NC_000007.14:g.94411165A>T
  • NG_007405.1:g.21605A>T
  • NM_000089.3:c.1350+11A>T
  • LRG_2t1:c.1350+11A>T
  • LRG_2:g.21605A>T
  • NC_000007.13:g.94040477A>T
Links:
dbSNP: rs193922160
NCBI 1000 Genomes Browser:
rs193922160
Molecular consequence:
  • NM_000089.3:c.1350+11A>T - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Osteogenesis imperfecta (OI)
Synonyms:
Brittle bone disease
Identifiers:
MONDO: MONDO:0019019; MeSH: D010013; MedGen: C0029434; OMIM: PS166200

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000052243Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
uncertain
(Aug 18, 2011)
germlinecuration, clinical testing

Citation Link,

SCV001322821Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Likely benign
(Apr 27, 2017)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedcuration
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

A novel DHPLC-based procedure for the analysis of COL1A1 and COL1A2 mutations in osteogenesis imperfecta.

Fuccio A, Iorio M, Amato F, Elce A, Ingino R, Filocamo M, Castaldo G, Salvatore F, Tomaiuolo R.

J Mol Diagn. 2011 Nov;13(6):648-56. doi: 10.1016/j.jmoldx.2011.06.006. Epub 2011 Aug 30.

PubMed [citation]
PMID:
21884818
PMCID:
PMC3194059

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052243.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
2not providednot providednot providednot providedclinical testingnot provided

Description

Converted during submission to Uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providedBloodassert pathogenicitynot providednot providednot providednot provided
2germlineunknownnot providedBloodassert pathogenicitynot providednot providednot provided See 2

Co-occurrences

#ZygosityAllelesNumber of Observations
2SingleHeterozygoteCOL1A1:c.299-20C>G, COL1A1:c.4249-12G>A, COL1A1:c.3223A>G, COL1A1:c.2560-18C>G, COL1A1:c.2897A>G, COL1A2:c.937-3C>T, COL1A2:c.936+14C>T, COL1A2:c.246T>C, COL1A2:c.1645C>G, COL1A2:c.87T>C1

From Illumina Clinical Services Laboratory,Illumina, SCV001322821.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

Last Updated: Jun 14, 2021

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