NM_001844.5(COL2A1):c.2101C>T (p.Arg701Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Apr 12, 2021)

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:
RCV000522045.5

Allele description [Variation Report for NM_001844.5(COL2A1):c.2101C>T (p.Arg701Ter)]

NM_001844.5(COL2A1):c.2101C>T (p.Arg701Ter)

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.2101C>T (p.Arg701Ter)
HGVS:
  • NC_000012.12:g.47982940G>A
  • NG_008072.1:g.26563C>T
  • NM_001844.5:c.2101C>TMANE SELECT
  • NM_033150.3:c.1894C>T
  • NP_001835.3:p.Arg701Ter
  • NP_149162.2:p.Arg632Ter
  • NC_000012.11:g.48376723G>A
  • NM_001844.4:c.2101C>T
Protein change:
R632*
Links:
dbSNP: rs1555166555
NCBI 1000 Genomes Browser:
rs1555166555
Molecular consequence:
  • NM_001844.5:c.2101C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_033150.3:c.1894C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000617521GeneDxcriteria provided, single submitter
Pathogenic
(Apr 12, 2021)
germlineclinical testing

Citation Link,

SCV001410672Invitaecriteria provided, single submitter
Pathogenic
(Apr 21, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

High efficiency of mutation detection in type 1 stickler syndrome using a two-stage approach: vitreoretinal assessment coupled with exon sequencing for screening COL2A1.

Richards AJ, Laidlaw M, Whittaker J, Treacy B, Rai H, Bearcroft P, Baguley DM, Poulson A, Ang A, Scott JD, Snead MP.

Hum Mutat. 2006 Jul;27(7):696-704. Erratum in: Hum Mutat. 2006 Nov;27(11):1156.

PubMed [citation]
PMID:
16752401

Stickler syndrome and the vitreous phenotype: mutations in COL2A1 and COL11A1.

Richards AJ, McNinch A, Martin H, Oakhill K, Rai H, Waller S, Treacy B, Whittaker J, Meredith S, Poulson A, Snead MP.

Hum Mutat. 2010 Jun;31(6):E1461-71. doi: 10.1002/humu.21257.

PubMed [citation]
PMID:
20513134
See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000617521.3

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

Description

Not observed in large population cohorts (Lek et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 20179744, 16752401, 18276201, 20513134)

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

From Invitae, SCV001410672.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Arg701*) in the COL2A1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with autosomal dominant Stickler syndrome (PMID: 16752401, 20513134, 18276201). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 449397). Loss-of-function variants in COL2A1 are known to be pathogenic (PMID: 20179744). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 27, 2021

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