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NM_001844.5(COL2A1):c.3138del (p.Gly1047fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Aug 20, 2021)
Last evaluated:
May 27, 2020
Accession:
VCV000017365.5
Variation ID:
17365
Description:
1bp deletion
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NM_001844.5(COL2A1):c.3138del (p.Gly1047fs)

Allele ID
32404
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47977627 (GRCh38) GRCh38 UCSC
12: 48371410 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48371410del
NC_000012.12:g.47977627del
NG_008072.1:g.31876del
... more HGVS
Protein change
G978fs, G1047fs
Other names
P846*
Canonical SPDI
NC_000012.12:47977626:A:
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA281745
OMIM: 120140.0015
dbSNP: rs121912873
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts May 27, 2020 RCV000725373.5
Pathogenic 1 no assertion criteria provided Jul 1, 1993 RCV000018909.30
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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
(Oct 28, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Eurofins NTD, LLC
Accession: SCV000336451.4
Submitted: (Sep 19, 2018)
Publications:
PubMed (1)
PubMed: 8406454
Other databases
http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL2A1
Number of individuals with the variant: 1
Zygosity: 1 Single Heterozygote
Sex: mixed
Pathogenic
(May 27, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV001803780.1
Submitted: (Aug 20, 2021)
Comment:
Not observed in large population cohorts (Lek et al., 2016); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene … (more)
Pathogenic
(May 16, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: unknown
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885224.1
Submitted: (Oct 10, 2018)
Comment:
The COL2A1 c.3138delT; p.Gly1047fs variant (rs121912873) has been described in individuals with Stickler syndrome (Hoornaert 2010, Richards 2010). It is reported as pathogenic in ClinVar … (more)
Pathogenic
(Jul 01, 1993)
no assertion criteria provided
Method: literature only
STICKLER SYNDROME, TYPE I
Affected status: not provided
Allele origin: germline
OMIM
Accession: SCV000039193.2
Submitted: (Dec 30, 2010)
Publications:
PubMed (1)
PubMed: 8406454
Comment on evidence:
In a family with Stickler syndrome (STL1; 108300) in members of 4 successive generations, Ritvaniemi et al. (1993) found a deletion of a T in … (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
A fourth example suggests that premature termination codons in the COL2A1 gene are a common cause of the Stickler syndrome: analysis of the COL2A1 gene by denaturing gradient gel electrophoresis. Ritvaniemi P Genomics 1993 PMID: 8406454
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL2A1 - - - -

Text-mined citations for rs121912873...

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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 Dec 12, 2021