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NM_001844.5(COL2A1):c.1649G>T (p.Arg550Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Jan 29, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000258213.6
Variation ID:
258213
Description:
single nucleotide variant
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NM_001844.5(COL2A1):c.1649G>T (p.Arg550Leu)

Allele ID
254552
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 47985759 (GRCh38) GRCh38 UCSC
12: 48379542 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48379542C>A
NC_000012.12:g.47985759C>A
NM_001844.5:c.1649G>T MANE Select NP_001835.3:p.Arg550Leu missense
... more HGVS
Protein change
R550L, R481L
Other names
-
Canonical SPDI
NC_000012.12:47985758:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00090
1000 Genomes Project 0.00060
Trans-Omics for Precision Medicine (TOPMed) 0.00065
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Links
ClinGen: CA6535432
dbSNP: rs186233557
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 4 criteria provided, multiple submitters, no conflicts Oct 4, 2018 RCV000254258.6
Benign 2 criteria provided, multiple submitters, no conflicts Dec 31, 2019 RCV000894899.3
Benign 1 criteria provided, single submitter May 28, 2019 RCV000988827.1
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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
1101 1112

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000308070.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Jan 22, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000533455.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Sep 29, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000335713.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
Stickler syndrome type 1
Allele origin: unknown
Mendelics
Accession: SCV001138712.1
Submitted: (Oct 22, 2019)
Evidence details
Benign
(Aug 05, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143206.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (1)
Likely benign
(Oct 04, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001159223.1
Submitted: (Aug 05, 2019)
Evidence details
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001038914.2
Submitted: (Jan 29, 2020)
Evidence details

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
Exome analysis of connective tissue dysplasia: death and rebirth of clinical genetics? Wilson GN American journal of medical genetics. Part A 2014 PMID: 24664531
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL2A1 - - - -

Text-mined citations for rs186233557...

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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 Jun 23, 2021