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NM_001844.5(COL2A1):c.625C>T (p.Arg209Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Sep 29, 2021)
Last evaluated:
Feb 15, 2020
Accession:
VCV000017360.4
Variation ID:
17360
Description:
single nucleotide variant
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NM_001844.5(COL2A1):c.625C>T (p.Arg209Ter)

Allele ID
32399
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47995904 (GRCh38) GRCh38 UCSC
12: 48389687 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48389687G>A
NC_000012.12:g.47995904G>A
NG_008072.1:g.13599C>T
... more HGVS
Protein change
R140*, R209*
Other names
R9*
Canonical SPDI
NC_000012.12:47995903:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA281742
OMIM: 120140.0010
dbSNP: rs121912869
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Feb 15, 2020 RCV000579130.3
Pathogenic 1 no assertion criteria provided Jan 1, 1993 RCV000018904.28
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL2A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1212 1223

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(Feb 15, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001585159.1
Submitted: (Jan 07, 2021)
Publications:
PubMed (2)
PubMed: 843460420179744
Comment:
This sequence change creates a premature translational stop signal (p.Arg209*) in the COL2A1 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(May 20, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000680706.3
Submitted: (Sep 29, 2021)
Comment:
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; Not … (more)
Pathogenic
(Jan 01, 1993)
no assertion criteria provided
Method: literature only
STICKLER SYNDROME, TYPE I
Affected status: not provided
Allele origin: germline
OMIM
Accession: SCV000039188.2
Submitted: (Dec 30, 2010)
Publications:
PubMed (2)
PubMed: 84346042803268
Comment on evidence:
In a family with Stickler syndrome (STL1; 108300), Ahmad et al. (1993) found a single-base mutation that converted codon 9 of the COL2A1 gene. (The … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Stickler syndrome caused by COL2A1 mutations: genotype-phenotype correlation in a series of 100 patients. Hoornaert KP European journal of human genetics : EJHG 2010 PMID: 20179744
A second mutation in the type II procollagen gene (COL2AI) causing stickler syndrome (arthro-ophthalmopathy) is also a premature termination codon. Ahmad NN American journal of human genetics 1993 PMID: 8434604
Structure of cDNA clones coding for human type II procollagen. The alpha 1(II) chain is more similar to the alpha 1(I) chain than two other alpha chains of fibrillar collagens. Baldwin CT The Biochemical journal 1989 PMID: 2803268

Text-mined citations for rs121912869...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021