NM_001844.5(COL2A1):c.1962C>T (p.Gly654=) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Pathogenic(1);Uncertain significance(1) (Last evaluated: Apr 21, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000177457.4

Allele description [Variation Report for NM_001844.5(COL2A1):c.1962C>T (p.Gly654=)]

NM_001844.5(COL2A1):c.1962C>T (p.Gly654=)

Gene:
COL2A1:collagen type II alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.11
Genomic location:
Preferred name:
NM_001844.5(COL2A1):c.1962C>T (p.Gly654=)
HGVS:
  • NC_000012.12:g.47983716G>A
  • NG_008072.1:g.25787C>T
  • NM_001844.5:c.1962C>TMANE SELECT
  • NM_033150.3:c.1755C>T
  • NP_001835.3:p.Gly654=
  • NP_149162.2:p.Gly585=
  • NC_000012.11:g.48377499G>A
  • NM_001844.4:c.1962C>T
Links:
dbSNP: rs794727533
NCBI 1000 Genomes Browser:
rs794727533
Molecular consequence:
  • NM_001844.5:c.1962C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_033150.3:c.1755C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000229316EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Jan 5, 2015)
germlineclinical testing

Citation Link,

SCV000322314GeneDxcriteria provided, single submitter
Pathogenic
(Apr 21, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000229316.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000322314.6

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

Description

The c.1962 C>T variant in the COL2A1 gene has been reported previously in seven individuals from a family with Stickler syndrome (Richards et al., 2007). The c.1962 C>T variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Functional studies indicate that c.1962 C>T creates an alternative donor splice site within exon 30, leading to a 35 base pair deletion that shifts the reading frame and results in premature termination of the message (Richards et al., 2007). We interpret c.1962 C>T as a pathogenic variant.

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

Last Updated: Feb 27, 2021

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